101
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Navone L, Vogl T, Luangthongkam P, Blinco JA, Luna-Flores C, Chen X, von Hellens J, Speight R. Synergistic optimisation of expression, folding, and secretion improves E. coli AppA phytase production in Pichia pastoris. Microb Cell Fact 2021; 20:8. [PMID: 33494776 PMCID: PMC7836175 DOI: 10.1186/s12934-020-01499-7] [Citation(s) in RCA: 6] [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: 07/21/2020] [Accepted: 12/18/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Pichia pastoris (Komagataella phaffii) is an important platform for heterologous protein production due to its growth to high cell density and outstanding secretory capabilities. Recent developments in synthetic biology have extended the toolbox for genetic engineering of P. pastoris to improve production strains. Yet, overloading the folding and secretion capacity of the cell by over-expression of recombinant proteins is still an issue and rational design of strains is critical to achieve cost-effective industrial manufacture. Several enzymes are commercially produced in P. pastoris, with phytases being one of the biggest on the global market. Phytases are ubiquitously used as a dietary supplement for swine and poultry to increase digestibility of phytic acid, the main form of phosphorous storage in grains. RESULTS Potential bottlenecks for expression of E. coli AppA phytase in P. pastoris were explored by applying bidirectional promoters (BDPs) to express AppA together with folding chaperones, disulfide bond isomerases, trafficking proteins and a cytosolic redox metabolism protein. Additionally, transcriptional studies were used to provide insights into the expression profile of BDPs. A flavoprotein encoded by ERV2 that has not been characterised in P. pastoris was used to improve the expression of the phytase, indicating its role as an alternative pathway to ERO1. Subsequent AppA production increased by 2.90-fold compared to the expression from the state of the AOX1 promoter. DISCUSSION The microbial production of important industrial enzymes in recombinant systems can be improved by applying newly available molecular tools. Overall, the work presented here on the optimisation of phytase production in P. pastoris contributes to the improved understanding of recombinant protein folding and secretion in this important yeast microbial production host.
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Affiliation(s)
- Laura Navone
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD, Australia.
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia.
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Pawarisa Luangthongkam
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jo-Anne Blinco
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD, Australia
| | - Carlos Luna-Flores
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD, Australia
- Bioproton Pty Ltd, Acacia Ridge, QLD, Australia
| | | | | | - Robert Speight
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia
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102
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Paes BG, Steindorff AS, Formighieri EF, Pereira IS, Almeida JRM. Physiological characterization and transcriptome analysis of Pichia pastoris reveals its response to lignocellulose-derived inhibitors. AMB Express 2021; 11:2. [PMID: 33389238 PMCID: PMC7779389 DOI: 10.1186/s13568-020-01170-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022] Open
Abstract
The negative effects of lignocellulose-derived inhibitors such as acetic acid and furaldehydes on microbial metabolism constitute a significant drawback to the usage of biomass feedstocks for the production of fuels and chemicals. The yeast Pichia pastoris has shown a great biotechnological potential for producing heterologous proteins and renewable chemicals. Despite its relevance, the performance of P. pastoris in presence of lignocellulose-derived inhibitors remains unclear. In this work, our results show for the first time the dose-dependent response of P. pastoris to acetic acid, furaldehydes (HMF and furfural), and sugarcane biomass hydrolysate, both at physiological and transcriptional levels. The yeast was able to grow in synthetic media with up to 6 g.L-1 acetic acid, 1.75 g.L-1 furaldehydes or hydrolysate diluted to 10% (v/v). However, its metabolism was completely hindered in presence of hydrolysate diluted to 30% (v/v). Additionally, the yeast was capable to co-consume acetic acid and glucose. At the transcriptional level, P. pastoris response to lignocellulose-derived inhibitors relays on the up-regulation of genes related to transmembrane transport, oxidoreductase activities, RNA processing, and the repression of pathways related to biosynthetic processes and central carbon metabolism. These results demonstrate a polygenetic response that involves detoxification activities, and maintenance of energy and cellular homeostasis. In this context, ALD4, OYE3, QOR2, NTL100, YCT1, and PPR1 were identified as target genes to improve P. pastoris tolerance. Altogether, this work provides valuable insights into the P. pastoris stress tolerance, which can be useful to expand its use in different bioprocesses.
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Affiliation(s)
- Barbara G Paes
- Laboratory of Genetics and Biotechnology, Embrapa Agroenergia, Parque Estação Biológica, PqEB - W3 Norte Final s/no, Brasília, DF, 70.770-901, Brazil
- Graduate Program of Molecular Biology, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, Brazil
| | - Andrei Stecca Steindorff
- Laboratory of Genetics and Biotechnology, Embrapa Agroenergia, Parque Estação Biológica, PqEB - W3 Norte Final s/no, Brasília, DF, 70.770-901, Brazil
| | - Eduardo F Formighieri
- Laboratory of Genetics and Biotechnology, Embrapa Agroenergia, Parque Estação Biológica, PqEB - W3 Norte Final s/no, Brasília, DF, 70.770-901, Brazil
| | - Ildinete Silva Pereira
- Laboratory of Genetics and Biotechnology, Embrapa Agroenergia, Parque Estação Biológica, PqEB - W3 Norte Final s/no, Brasília, DF, 70.770-901, Brazil
- Graduate Program of Molecular Biology, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, Brazil
| | - João Ricardo M Almeida
- Laboratory of Genetics and Biotechnology, Embrapa Agroenergia, Parque Estação Biológica, PqEB - W3 Norte Final s/no, Brasília, DF, 70.770-901, Brazil.
- Graduate Program of Microbial Biology, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, Brazil.
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103
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Ardila-Leal LD, Poutou-Piñales RA, Morales-Álvarez ED, Rivera-Hoyos CM, Pedroza-Rodríguez AM, Quevedo-Hidalgo BE, Pérez-Flórez A. Methanol addition after glucose depletion improves rPOXA 1B production under the pGap in P. pastoris X33: breaking the habit. SN APPLIED SCIENCES 2021. [DOI: 10.1007/s42452-020-04093-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
AbstractThe purpose of this study was to demonstrate that methanol addition after glucose depletion has a positive effect on improving rPOXA 1B production under the control of pGap in P. pastoris. Four different culture media (A, B, C and D) were used to culture P. pastoris X33/pGapZαA-LaccPost-Stop (clone 1), containing a previously optimized POXA 1B synthetic gene coding for P. ostreatus laccase, which after glucose depletion was supplemented or not with methanol. Enzyme activity in culture media without methanol (A, B, C and D) was influenced by media components, presenting activity of 1254.30 ± 182.44, 1373.70 ± 182.44, 1343.50 ± 40.30 and 8771.61 ± 218.79 U L−1, respectively. In contrast, the same culture media (A, B, C and D) with methanol addition 24 h after glucose depletion attained activity of 4280.43 ± 148.82, 3339.02 ± 64.36, 3569.39 ± 68.38 and 14,868.06 ± 461.58 U L−1 at 192 h, respectively, representing an increase of approximately 3.9-, 2.4-, 3.3- and 1.6-fold compared with culture media without methanol. Methanol supplementation had a greater impact on volumetric enzyme activity in comparison with biomass production. We demonstrated what was theoretically and biochemically expected: recombinant protein production under pGap control by methanol supplementation after glucose depletion was successful, as a feasible laboratory production strategy of sequential carbon source addition, breaking the habit of utilizing pGap with glucose.
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104
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Liu T, Liu B, Zhou H, Zhang J. Knockout of the DAS gene increases S-adenosylmethionine production in Komagataella phaffii. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2020.1837012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Taiyu Liu
- Shanghai Engineering Research Center for Food Rapid Detection, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Baolin Liu
- Shanghai Engineering Research Center for Food Rapid Detection, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Hualan Zhou
- Shanghai Engineering Research Center for Food Rapid Detection, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Jianguo Zhang
- Shanghai Engineering Research Center for Food Rapid Detection, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
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105
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Wang D, Chen M, Zeng X, Li W, Liang S, Lin Y. Improving the catalytic performance of Pichia pastoris whole-cell biocatalysts by fermentation process. RSC Adv 2021; 11:36329-36339. [PMID: 35492776 PMCID: PMC9043429 DOI: 10.1039/d1ra06253k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/03/2021] [Indexed: 11/21/2022] Open
Abstract
Whole-cell biocatalysts have a wide range of applications in many fields. However, the transport of substrates is tricky when applying whole-cell biocatalysts for industrial production. In this research, P. pastoris whole-cell biocatalysts were constructed for rebaudioside A synthesis. Sucrose synthase was expressed intracellularly while UDP-glycosyltransferase was displayed on the cell wall surface simultaneously. As an alternative method, a fermentation process is applied to relieve the substrate transport-limitation of P. pastoris whole-cell biocatalysts. This fermentation process was much simpler, more energy-saving, and greener than additional operating after collecting cells to improve the catalytic ability of whole-cell biocatalysts. Compared with the general fermentation process, the protein production capacity of cells did not decrease. Meanwhile, the activity of whole-cell biocatalysts was increased to 262%, which indicates that the permeability and space resistance were improved to relieve the transport-limitations. Furthermore, the induction time was reduced from 60 h to 36 h. The fermentation process offered significant advantages over traditional permeabilizing reagent treatment and ultrasonication treatment based on the high efficiency and simplicity. Fermentation process was applied to relieve the substrate transport-limitation of P. pastoris whole-cell biocatalysts, which was much simpler, more energy-saving and greener than c traditional permeabilizing reagent and ultrasonication treatment.![]()
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Affiliation(s)
- Denggang Wang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Panyu, Guangzhou 510006, People's Republic of China
| | - Meiqi Chen
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Panyu, Guangzhou 510006, People's Republic of China
| | - Xin Zeng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Panyu, Guangzhou 510006, People's Republic of China
| | - Wenjie Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Panyu, Guangzhou 510006, People's Republic of China
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Panyu, Guangzhou 510006, People's Republic of China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Panyu, Guangzhou 510006, People's Republic of China
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106
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Zhang Y, Nielsen J, Liu Z. Yeast based biorefineries for oleochemical production. Curr Opin Biotechnol 2020; 67:26-34. [PMID: 33360103 DOI: 10.1016/j.copbio.2020.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/04/2020] [Accepted: 11/22/2020] [Indexed: 12/17/2022]
Abstract
Biosynthesis of oleochemicals enables sustainable production of natural and unnatural alternatives from renewable feedstocks. Yeast cell factories have been extensively studied and engineered to produce a variety of oleochemicals, focusing on both central carbon metabolism and lipid metabolism. Here, we review recent progress towards oleochemical synthesis in yeast based biorefineries, as well as utilization of alternative renewable feedstocks, such as xylose and l-arabinose. We also review recent studies of C1 compound utilization or co-utilization and discuss how these studies can lead to third generation yeast based biorefineries for oleochemical production.
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Affiliation(s)
- Yiming Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jens Nielsen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; BioInnovation Institute, Ole Maaløes Vej 3, DK2200 Copenhagen N, Denmark.
| | - Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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107
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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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108
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Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
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109
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Filkin SY, Chertova NV, Vavilova EA, Zatsepin SS, Eldarov MA, Sadykhov EG, Fedorov AN, Lipkin AV. Optimization of the Production Method for Recombinant Chymosin in the Methylotrophic Yeast Komagataella phaffii. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820060058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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110
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Abarghooi Kahaki F, Monzavi S, Bamehr H, Bandani E, Payandeh Z, Jahangiri A, Khalili S. Expression and Purification of Membrane Proteins in Different Hosts. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-10009-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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111
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Radoman B, Grünwald-Gruber C, Schmelzer B, Zavec D, Gasser B, Altmann F, Mattanovich D. The Degree and Length of O-Glycosylation of Recombinant Proteins Produced in Pichia pastoris Depends on the Nature of the Protein and the Process Type. Biotechnol J 2020; 16:e2000266. [PMID: 32975831 DOI: 10.1002/biot.202000266] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/09/2020] [Indexed: 12/16/2022]
Abstract
The methylotrophic yeast Pichia pastoris is known as an efficient host for the production of heterologous proteins. While N-linked protein glycosylation is well characterized in P. pastoris there is less knowledge of the patterns of O-glycosylation. O-glycans produced by P. pastoris consist of short linear mannose chains, which in the case of recombinant biopharmaceuticals can trigger an immune response in humans. This study aims to reveal the influence of different cultivation strategies on O-mannosylation profiles in P. pastoris. Sixteen different model proteins, produced by different P. pastoris strains, are analyzed for their O-glycosylation profile. Based on the obtained data, human serum albumin (HSA) is chosen to be produced in fast and slow growth fed batch fermentations by using common promoters, PGAP and PAOX1 . After purification and protein digestion, glycopeptides are analyzed by LC/ESI-MS. In the samples expressed with PGAP it is found that the degree of glycosylation is slightly higher when a slow growth rate is used, regardless of the efficiency of the producing strain. The highest glycosylation intensity is observed in HSA produced with PAOX1 . The results indicate that the O-glycosylation level is markedly higher when the protein is produced in a methanol-based expression system.
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Affiliation(s)
- Bojana Radoman
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Clemens Grünwald-Gruber
- Department of Chemistry, BOKU-University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Bernhard Schmelzer
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Domen Zavec
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Brigitte Gasser
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Friedrich Altmann
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria.,Department of Chemistry, BOKU-University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, 1190, Austria
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112
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Karaoğlan M, Erden-Karaoğlan F. Effect of codon optimization and promoter choice on recombinant endo-polygalacturonase production in Pichia pastoris. Enzyme Microb Technol 2020; 139:109589. [DOI: 10.1016/j.enzmictec.2020.109589] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/12/2020] [Accepted: 04/29/2020] [Indexed: 01/17/2023]
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113
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Demir İ, Çalık P. Hybrid-architectured double-promoter expression systems enhance and upregulate-deregulated gene expressions in Pichia pastoris in methanol-free media. Appl Microbiol Biotechnol 2020; 104:8381-8397. [DOI: 10.1007/s00253-020-10796-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/29/2020] [Accepted: 07/21/2020] [Indexed: 12/13/2022]
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114
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Zhou HY, Zhou JB, Yi XN, Wang YM, Xue YP, Chen DS, Cheng XP, Li M, Wang HY, Chen KQ, Liu ZQ, Zheng YG. Heterologous expression and biochemical characterization of a thermostable endo-β-1,4-glucanase from Colletotrichum orchidophilum. Bioprocess Biosyst Eng 2020; 44:67-79. [PMID: 32772153 DOI: 10.1007/s00449-020-02420-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/29/2020] [Indexed: 01/23/2023]
Abstract
To develop new cellulases for efficient utilization of the lignocellulose, an endoglucanase (CoCel5A) gene from Colletotrichum orchidophilum was synthesized and a recombinant Pichia pastoris GS115/pPIC9K/cocel5A was constructed for secretory expression of CoCel5A. After purification, the protein CoCel5A was biochemically characterized. The endoglucanase CoCel5A exhibited the optimal activity at 55-75 °C and high thermostability (about 85% residual activity) at the temperature of 55 °C after incubation for 3 h. The highest activity of CoCel5A was detected when 100 mM citric acid buffer (pH 4.0-5.0) was used and excellent pH stability (up to 95% residual activity) was observed after incubation in 100 mM citric acid buffer (pH 3.0-6.0) at 4 °C for 24 h. Carboxymethyl cellulose sodium salt (n = approx. 500) (CMC) and β-D-glucan were the best substrates for CoCel5A among the tested substrates. The kinetic parameters Vmax, Km, and Kcat/Km values against CMC were 290.70 U/mg, 2.65 mg/mL, and 75.67 mL/mg/s, respectively; and 228.31 U/mg, 2.06 mg/mL, and 76.45 mL/mg/s against β-D-glucan, respectively, suggesting that CoCel5A has high affinity and catalytic efficiency. These properties supported the potential application of CoCel5A in biotechnological and environmental fields.
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Affiliation(s)
- Hai-Yan Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local, Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Jian-Bao Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local, Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Xiao-Nan Yi
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local, Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yan-Mei Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local, Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local, Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - De-Shui Chen
- Zhejiang Huakang Pharmaceutical Co., LTD, 18 Huagong Road, Huabu Town, Kaihua, 324302, People's Republic of China
| | - Xin-Ping Cheng
- Zhejiang Huakang Pharmaceutical Co., LTD, 18 Huagong Road, Huabu Town, Kaihua, 324302, People's Republic of China
| | - Mian Li
- Zhejiang Huakang Pharmaceutical Co., LTD, 18 Huagong Road, Huabu Town, Kaihua, 324302, People's Republic of China
| | - Hong-Yan Wang
- Zhejiang Huakang Pharmaceutical Co., LTD, 18 Huagong Road, Huabu Town, Kaihua, 324302, People's Republic of China
| | - Kai-Qian Chen
- Zhejiang Huakang Pharmaceutical Co., LTD, 18 Huagong Road, Huabu Town, Kaihua, 324302, People's Republic of China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China.
- The National and Local, Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local, Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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115
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Nieto-Taype MA, Garcia-Ortega X, Albiol J, Montesinos-Seguí JL, Valero F. Continuous Cultivation as a Tool Toward the Rational Bioprocess Development With Pichia Pastoris Cell Factory. Front Bioeng Biotechnol 2020; 8:632. [PMID: 32671036 PMCID: PMC7330098 DOI: 10.3389/fbioe.2020.00632] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 05/22/2020] [Indexed: 12/15/2022] Open
Abstract
The methylotrophic yeast Pichia pastoris (Komagataella phaffii) is currently considered one of the most promising hosts for recombinant protein production (RPP) and metabolites due to the availability of several tools to efficiently regulate the recombinant expression, its ability to perform eukaryotic post-translational modifications and to secrete the product in the extracellular media. The challenge of improving the bioprocess efficiency can be faced from two main approaches: the strain engineering, which includes enhancements in the recombinant expression regulation as well as overcoming potential cell capacity bottlenecks; and the bioprocess engineering, focused on the development of rational-based efficient operational strategies. Understanding the effect of strain and operational improvements in bioprocess efficiency requires to attain a robust knowledge about the metabolic and physiological changes triggered into the cells. For this purpose, a number of studies have revealed chemostat cultures to provide a robust tool for accurate, reliable, and reproducible bioprocess characterization. It should involve the determination of key specific rates, productivities, and yields for different C and N sources, as well as optimizing media formulation and operating conditions. Furthermore, studies along the different levels of systems biology are usually performed also in chemostat cultures. Transcriptomic, proteomic and metabolic flux analysis, using different techniques like differential target gene expression, protein description and 13C-based metabolic flux analysis, are widely described as valued examples in the literature. In this scenario, the main advantage of a continuous operation relies on the quality of the homogeneous samples obtained under steady-state conditions, where both the metabolic and physiological status of the cells remain unaltered in an all-encompassing picture of the cell environment. This contribution aims to provide the state of the art of the different approaches that allow the design of rational strain and bioprocess engineering improvements in Pichia pastoris toward optimizing bioprocesses based on the results obtained in chemostat cultures. Interestingly, continuous cultivation is also currently emerging as an alternative operational mode in industrial biotechnology for implementing continuous process operations.
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Affiliation(s)
- Miguel Angel Nieto-Taype
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Xavier Garcia-Ortega
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Joan Albiol
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - José Luis Montesinos-Seguí
- 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
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116
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Engineered dynamic distribution of malonyl-CoA flux for improving polyketide biosynthesis in Komagataella phaffii. J Biotechnol 2020; 320:80-85. [PMID: 32574793 DOI: 10.1016/j.jbiotec.2020.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/27/2020] [Accepted: 06/16/2020] [Indexed: 12/29/2022]
Abstract
Malonyl-CoA is a basic but limited precursor for the biosynthesis of various bioactive compounds and life-supporting fatty acids in cells. This study develops a biosynthetic system to dynamically redirect malonyl-CoA flux and improve production of malonyl-CoA derived polyketide (6-MSA) in Komagataella phaffii. A synthetic regulatory protein fusing a yeast activator Prm1 with a bacterial repressor FapR was proved to work with a hybrid promoter (-7)fapO-cPAOX1 and activate gene expression. Expression mode by the Prm1-FapR/(-7)fapO-cPAOX1 device was not affected by intracellular malonyl-CoA levels. Further, 9 promoter variants of PGAP with insertion of fapO at various sites were tested with the Prm1-FapR. It generated a biosensor of Prm1-FapR/PGAP-(+2)fapO with regulation behavior of malonyl-CoA-low-level repression/high-level derepression. Both devices were subsequently integrated into a single cell, for which fatty acid synthesis module was driven by Prm1-FapR/PGAP-(+2)fapO but 6-MSA synthesis module was expressed by Prm1-FapR/(-7)fapO-cPAOX1. The integrated system allowed continuous polyketide synthesis but malonyl-CoA-high-level "on"/low-level "off" fatty acid synthesis. This design finally increased 6-MSA production capacity by 260 %, proving the positive effects of dynamic malonyl-CoA distribution to the target compounds. It provides a new strategy for synthesis of malonyl-CoA derived compounds in eukaryotic chassis hosts.
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117
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Zhang L, Liu WQ, Li J. Establishing a Eukaryotic Pichia pastoris Cell-Free Protein Synthesis System. Front Bioeng Biotechnol 2020; 8:536. [PMID: 32626695 PMCID: PMC7314905 DOI: 10.3389/fbioe.2020.00536] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/04/2020] [Indexed: 12/13/2022] Open
Abstract
In recent years, cell-free protein synthesis (CFPS) systems have been used to synthesize proteins, prototype genetic elements, manufacture chemicals, and diagnose diseases. These exciting, novel applications lead to a new wave of interest in the development of new CFPS systems that are derived from prokaryotic and eukaryotic organisms. The eukaryotic Pichia pastoris is emerging as a robust chassis host for recombinant protein production. To expand the current CFPS repertoire, we report here the development and optimization of a eukaryotic CFPS system, which is derived from a protease-deficient strain P. pastoris SMD1163. By developing a simple crude extract preparation protocol and optimizing CFPS reaction conditions, we were able to achieve superfolder green fluorescent protein (sfGFP) yields of 50.16 ± 7.49 μg/ml in 5 h batch reactions. Our newly developed P. pastoris CFPS system fits to the range of the productivity achieved by other eukaryotic CFPS platforms, normally ranging from several to tens of micrograms protein per milliliter in batch mode reactions. Looking forward, we believe that our P. pastoris CFPS system will not only expand the CFPS toolbox for synthetic biology applications, but also provide a novel platform for cost-effective, high-yielding production of complex proteins that need post-translational modification and functionalization.
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Affiliation(s)
| | | | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
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118
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Evaluation of Product Distribution in Chemostat and Batch Fermentation in Lactic Acid-Producing Komagataella phaffii Strains Utilizing Glycerol as Substrate. Microorganisms 2020; 8:microorganisms8050781. [PMID: 32455925 PMCID: PMC7285341 DOI: 10.3390/microorganisms8050781] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 01/03/2023] Open
Abstract
Lactic acid is the monomeric unit of polylactide (PLA), a bioplastic widely used in the packaging, automotive, food, and pharmaceutical industries. Previously, the yeast Komagataella phaffii was genetically modified for the production of lactate from glycerol. For this, the bovine L-lactate dehydrogenase- (LDH)-encoding gene was inserted and the gene encoding the pyruvate decarboxylase (PDC) was disrupted, resulting in the GLp strain. This showed a yield of 67% L-lactic acid and 20% arabitol as a by-product in batches with oxygen limitation. Following up on these results, the present work endeavored to perform a detailed study of the metabolism of this yeast, as well as perturbing arabitol synthesis in an attempt to increase lactic acid titers. The GLp strain was cultivated in a glycerol-limited chemostat at different dilution rates, confirming that the production of both lactic acid and arabitol is dependent on the specific growth rate (and consequently on the concentration of the limiting carbon source) as well as on the oxygen level. Moreover, disruption of the gene encoding arabitol dehydrogenase (ArDH) was carried out, resulting in an increase of 20% in lactic acid and a 50% reduction in arabitol. This study clarifies the underlying metabolic reasons for arabitol formation in K. phaffii and points to ways for improving production of lactic acid using K. phaffii as a biocatalyst.
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119
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Liu X, Jiang Z, Ma S, Yan Q, Chen Z, Liu H. High-level production and characterization of a novel β-1,3-1,4-glucanase from Aspergillus awamori and its potential application in the brewing industry. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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120
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Ardila-Leal LD, Alvarado-Ramírez MF, Gutiérrez-Rojas IS, Poutou-Piñales RA, Quevedo-Hidalgo B, Pérez-Flórez A, Pedroza-Rodríguez AM. Low-cost media statistical design for laccase rPOXA 1B production in P. pastoris. Heliyon 2020; 6:e03852. [PMID: 32368658 PMCID: PMC7184261 DOI: 10.1016/j.heliyon.2020.e03852] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/09/2020] [Accepted: 04/21/2020] [Indexed: 01/09/2023] Open
Abstract
Laccases (E.C. 1.10.3.2) are multicopper oxidases of great importance in the industry due to their non-specificity and high oxidative potential. Laccases are useful to bleach synthetic dyes, oxidize phenolic compounds and degrade pesticides, among others. Hence, the objective of this work was to optimize low cost culture media for recombinant (rPOXA 1B) laccase production from Pleurotus ostreatus in Pichia pastoris. To this end, low cost nitrogen sources were studied, such as malt extract, isolated soy protein and milk serum. Following, two central composite designs (CCD) were performed. In CCD-1 different concentrations of glucose USP (0–13.35 gL-1), protein isolated soy protein (5–25 gL-1), malt extract (3.5–17.5 gL-1) and (NH4)2SO4 (1.3–6.5 gL-1) were evaluated. In CCD-2 only different concentrations of glucose USP (7.9–22 gL-1) and isolated soy protein (15.9–44.9 gL-1) were evaluated. CCD-2 results led to a One Factor Experimental design (OFED) to evaluate higher isolated soy protein (20–80 gL-1) concentrations. In all designs, (CCD-1, CCD-2 and OFED) CuSO4 (0.16 gL-1) and chloramphenicol (0.1 gL-1) concentrations remained unchanged. For the OFED after sequential statistical optimization, an enzyme activity of 12,877.3 ± 481.2 UL−1 at 168 h was observed. rPOXA 1B activity increased 30.54 % in comparison with CCD-2 results. Final composition of optimized media was: 20 gL-1 glucose USP, 50 gL-1 isolated soy protein 90 % (w/w), 11.74 gL-1 malt extract, and 4.91 gL-1 (NH4)2SO4. With this culture media, it was possible to reduce culture media costs by 89.84 % in comparison with improved culture media previously described by our group.
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Affiliation(s)
- Leidy D Ardila-Leal
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana (PUJ), Bogotá, D.C., Colombia
| | - María F Alvarado-Ramírez
- Laboratorio de Biotecnología Aplicada, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana (PUJ), Bogotá, D.C., Colombia
| | - Ivonne S Gutiérrez-Rojas
- Laboratorio de Biotecnología Aplicada, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana (PUJ), Bogotá, D.C., Colombia
| | - Raúl A Poutou-Piñales
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana (PUJ), Bogotá, D.C., Colombia
| | - Balkys Quevedo-Hidalgo
- Laboratorio de Biotecnología Aplicada, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana (PUJ), Bogotá, D.C., Colombia
| | - Alejandro Pérez-Flórez
- Grupo de Fitoquímica de la PUJ (GIFUJ), Departamento de Química, Facultad de Ciencias, Pontificia Universidad Javeriana (PUJ), Bogotá, D.C., Colombia
| | - Aura M Pedroza-Rodríguez
- Laboratorio de Microbiología Ambiental y de Suelos, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana (PUJ), Bogotá, D.C., Colombia
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121
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Rahmat E, Kang Y. Yeast metabolic engineering for the production of pharmaceutically important secondary metabolites. Appl Microbiol Biotechnol 2020; 104:4659-4674. [DOI: 10.1007/s00253-020-10587-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 01/30/2020] [Accepted: 03/24/2020] [Indexed: 11/29/2022]
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122
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Siripong W, Angela C, Tanapongpipat S, Runguphan W. Metabolic engineering of Pichia pastoris for production of isopentanol (3-Methyl-1-butanol). Enzyme Microb Technol 2020; 138:109557. [PMID: 32527534 DOI: 10.1016/j.enzmictec.2020.109557] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/24/2020] [Accepted: 03/26/2020] [Indexed: 12/21/2022]
Abstract
In recent years, the increasingly serious and clear effects of climate change have increased interest in renewable fuels and platform chemicals. Microbial platforms that can produce these compounds in an economically efficient way have emerged as an attractive alternative to the traditional production approaches. Here, we engineered the industrially-relevant yeast Pichia pastoris to produce the platform chemical 3-methyl-1-butanol (3M1B, isopentanol) directly from the renewable carbon source glucose. Specifically, we overexpressed the endogenous valine and leucine biosynthetic pathways to increase the production of the key pathway intermediate, 2-ketoisocaproate (2-KIC). Overexpression of the artificial keto-acid degradation pathway converted 2-KIC into 3M1B. Down-regulation of the side-product ethanol production using the CRISPR/Cas9 system led to a strain that is able to produce 3M1B at a titer of 191.0 ± 9.6 mg/L, the highest titer reported to date in a non-conventional yeast. We envision that our yeast system will pave the way for an efficient production system for this important class of platform compounds.
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Affiliation(s)
- Wiparat Siripong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Clara Angela
- Indonesia International Institute for Life-Sciences, Jl. Pulomas Barat Kav. 88, Kayu Putih, Pulo Gadung, Jakarta Timur, 13210, Indonesia
| | - Sutipa Tanapongpipat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Weerawat Runguphan
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand.
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123
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Markina NM, Kotlobay AA, Tsarkova AS. Heterologous Metabolic Pathways: Strategies for Optimal Expression in Eukaryotic Hosts. Acta Naturae 2020; 12:28-39. [PMID: 32742725 PMCID: PMC7385092 DOI: 10.32607/actanaturae.10966] [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: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 11/20/2022] Open
Abstract
Heterologous pathways are linked series of biochemical reactions occurring in a host organism after the introduction of foreign genes. Incorporation of metabolic pathways into host organisms is a major strategy used to increase the production of valuable secondary metabolites. Unfortunately, simple introduction of the pathway genes into the heterologous host in most cases does not result in successful heterologous expression. Extensive modification of heterologous genes and the corresponding enzymes on many different levels is required to achieve high target metabolite production rates. This review summarizes the essential techniques used to create heterologous biochemical pathways, with a focus on the key challenges arising in the process and the major strategies for overcoming them.
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Affiliation(s)
- N. M. Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Planta LLC, Moscow, 121205 Russia
| | - A. A. Kotlobay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. S. Tsarkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
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124
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Vogl T, Fischer JE, Hyden P, Wasmayer R, Sturmberger L, Glieder A. Orthologous promoters from related methylotrophic yeasts surpass expression of endogenous promoters of Pichia pastoris. AMB Express 2020; 10:38. [PMID: 32100120 PMCID: PMC7042429 DOI: 10.1186/s13568-020-00972-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 02/11/2020] [Indexed: 11/18/2022] Open
Abstract
Methylotrophic yeasts such as Komagataella phaffii (syn. Pichia pastoris, Pp), Hansenula polymorpha (Hp), Candida boidinii (Cb) and Pichia methanolica (Pm) are widely used protein production platforms. Typically, strong, tightly regulated promoters of genes coding for their methanol utilization (MUT) pathways are used to drive heterologous gene expression. Despite highly similar open reading frames in the MUT pathways of the four yeasts, the regulation of the respective promoters varies strongly between species. While most endogenous Pp MUT promoters remain tightly repressed after depletion of a repressing carbon, Hp, Cb and Pm MUT promoters are derepressed to up to 70% of methanol induced levels, enabling methanol free production processes in their respective host background. Here, we have tested a series of orthologous promoters from Hp, Cb and Pm in Pp. Unexpectedly, when induced with methanol, the promoter of the HpMOX gene reached very similar expression levels as the strong methanol, inducible, and most frequently used promoter of the Pp alcohol oxidase 1 gene (PPpAOX1). The HpFMD promoter even surpassed PPpAOX1 up to three-fold, when induced with methanol, and reached under methanol-free/derepressed conditions similar expression as the methanol induced PPpAOX1. These results demonstrate that orthologous promoters from related yeast species can give access to otherwise unobtainable regulatory profiles and may even considerably surpass endogenous promoters in P. pastoris.
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125
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Chu LL, Montecillo JAV, Bae H. Recent Advances in the Metabolic Engineering of Yeasts for Ginsenoside Biosynthesis. Front Bioeng Biotechnol 2020; 8:139. [PMID: 32158753 PMCID: PMC7052115 DOI: 10.3389/fbioe.2020.00139] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/11/2020] [Indexed: 01/03/2023] Open
Abstract
Ginsenosides are a group of glycosylated triterpenes isolated from Panax species. Ginsenosides are promising candidates for the prevention and treatment of cancer as well as food additives. However, owing to a lack of efficient approaches for ginsenoside production from plants and chemical synthesis, ginsenosides may not yet have reached their full potential as medicinal resources. In recent years, an alternative approach for ginsenoside production has been developed using the model yeast Saccharomyces cerevisiae and non-conventional yeasts such as Yarrowia lipolytica and Pichia pastoris. In this review, various metabolic engineering strategies, including heterologous gene expression, balancing, and increasing metabolic flux, and enzyme engineering, have been described as recent advanced engineering techniques for improving ginsenoside production. Furthermore, the usefulness of a systems approach and fermentation strategy has been presented. Finally, the present challenges and future research direction for industrial cell factories have been discussed.
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Affiliation(s)
- Luan Luong Chu
- Department of Biotechnology, Yeungnam University, Gyeongsan-si, South Korea
| | | | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan-si, South Korea
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126
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Ren Y, Liu Q, Liu H, Zhou X, Zhang Y, Cai M. Engineering substrate and energy metabolism for living cell production of cytidine-5'-diphosphocholine. Biotechnol Bioeng 2020; 117:1426-1435. [PMID: 31997310 DOI: 10.1002/bit.27291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/26/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Cytidine-5'-diphosphocholine (CDP-choline) is a widely used neuroprotective drug for multiple indications. In industry, CDP-choline is synthesized by a two-step cell culture/permeabilized cell biotransformation method because substrates often do not enter cells in an efficient manner. This study develops a novel one-step living cell fermentation method for CDP-choline production. For this purpose, the feasibility of Pichia pastoris as a chassis was demonstrated by substrate feeding and CDP-choline production. Overexpression of choline phosphate cytidylyltransferase and choline kinase enhanced the choline transformation pathway and improved the biosynthesis of CDP-choline. Furthermore, co-overexpression of ScHnm1, which is a heterologous choline transporter, highly improved the utilization of choline substrates, despite its easy degradation in cells. This strategy increased CDP-choline titer by 55-folds comparing with the wild-type (WT). Overexpression of cytidine-5'-monophosphate (CMP) kinase and CDP kinase in the CMP transformation pathway showed no positive effects. An increase in the ATP production by citrate stimulation or metabolic pathway modification further improved CDP-choline biosynthesis by 120%. Finally, the orthogonal optimization of key substrates and pH was carried out, and the resulting CDP-choline titer (6.0 g/L) at optimum conditions increased 88 times the original titer in the WT. This study provides a new paradigm for CDP-choline bioproduction by living cells.
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Affiliation(s)
- Yanna Ren
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Qi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Haifeng Liu
- China Resources Angde Biotech Pharmaceutical Co, Ltd, Liaocheng, China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,China Resources Angde Biotech Pharmaceutical Co, Ltd, Liaocheng, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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127
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Thak EJ, Yoo SJ, Moon HY, Kang HA. Yeast synthetic biology for designed cell factories producing secretory recombinant proteins. FEMS Yeast Res 2020; 20:5721243. [DOI: 10.1093/femsyr/foaa009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/30/2020] [Indexed: 12/17/2022] Open
Abstract
ABSTRACT
Yeasts are prominent hosts for the production of recombinant proteins from industrial enzymes to therapeutic proteins. Particularly, the similarity of protein secretion pathways between these unicellular eukaryotic microorganisms and higher eukaryotic organisms has made them a preferential host to produce secretory recombinant proteins. However, there are several bottlenecks, in terms of quality and quantity, restricting their use as secretory recombinant protein production hosts. In this mini-review, we discuss recent developments in synthetic biology approaches to constructing yeast cell factories endowed with enhanced capacities of protein folding and secretion as well as designed targeted post-translational modification process functions. We focus on the new genetic tools for optimizing secretory protein expression, such as codon-optimized synthetic genes, combinatory synthetic signal peptides and copy number-controllable integration systems, and the advanced cellular engineering strategies, including endoplasmic reticulum and protein trafficking pathway engineering, synthetic glycosylation, and cell wall engineering, for improving the quality and yield of secretory recombinant proteins.
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Affiliation(s)
- Eun Jung Thak
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Su Jin Yoo
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hye Yun Moon
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hyun Ah Kang
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
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128
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Zhang M. Recent developments of methyl-labeling strategies in Pichia pastoris for NMR spectroscopy. Protein Expr Purif 2020; 166:105521. [DOI: 10.1016/j.pep.2019.105521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 11/26/2022]
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129
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Gassler T, Sauer M, Gasser B, Egermeier M, Troyer C, Causon T, Hann S, Mattanovich D, Steiger MG. The industrial yeast Pichia pastoris is converted from a heterotroph into an autotroph capable of growth on CO 2. Nat Biotechnol 2020; 38:210-216. [PMID: 31844294 PMCID: PMC7008030 DOI: 10.1038/s41587-019-0363-0] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 11/15/2019] [Indexed: 12/20/2022]
Abstract
The methylotrophic yeast Pichia pastoris is widely used in the manufacture of industrial enzymes and pharmaceuticals. Like most biotechnological production hosts, P. pastoris is heterotrophic and grows on organic feedstocks that have competing uses in the production of food and animal feed. In a step toward more sustainable industrial processes, we describe the conversion of P. pastoris into an autotroph that grows on CO2. By addition of eight heterologous genes and deletion of three native genes, we engineer the peroxisomal methanol-assimilation pathway of P. pastoris into a CO2-fixation pathway resembling the Calvin-Benson-Bassham cycle, the predominant natural CO2-fixation pathway. The resulting strain can grow continuously with CO2 as a sole carbon source at a µmax of 0.008 h-1. The specific growth rate was further improved to 0.018 h-1 by adaptive laboratory evolution. This engineered P. pastoris strain may promote sustainability by sequestering the greenhouse gas CO2, and by avoiding consumption of an organic feedstock with alternative uses in food production.
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Affiliation(s)
- Thomas Gassler
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
| | - Michael Sauer
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
- CD-Laboratory for Biotechnology of Glycerol, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
| | - Michael Egermeier
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Christina Troyer
- Institute of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Tim Causon
- Institute of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Stephan Hann
- Institute of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria.
| | - Matthias G Steiger
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
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130
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Ma C, Tan ZL, Lin Y, Han S, Xing X, Zhang C. Gel microdroplet–based high-throughput screening for directed evolution of xylanase-producing Pichia pastoris. J Biosci Bioeng 2019; 128:662-668. [DOI: 10.1016/j.jbiosc.2019.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 05/11/2019] [Accepted: 05/13/2019] [Indexed: 01/24/2023]
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131
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Specific growth rate governs AOX1 gene expression, affecting the production kinetics of Pichia pastoris (Komagataella phaffii) P AOX1-driven recombinant producer strains with different target gene dosage. Microb Cell Fact 2019; 18:187. [PMID: 31675969 PMCID: PMC6824138 DOI: 10.1186/s12934-019-1240-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/23/2019] [Indexed: 12/02/2022] Open
Abstract
Background The PAOX1-based expression system is the most widely used for producing recombinant proteins in the methylotrophic yeast Pichia pastoris (Komagataella phaffii). Despite relevant recent advances in regulation of the methanol utilization (MUT) pathway have been made, the role of specific growth rate (µ) in AOX1 regulation remains unknown, and therefore, its impact on protein production kinetics is still unclear. Results The influence of heterologous gene dosage, and both, operational mode and strategy, on culture physiological state was studied by cultivating the two PAOX1-driven Candida rugosa lipase 1 (Crl1) producer clones. Specifically, a clone integrating a single expression cassette of CRL1 was compared with one containing three cassettes over broad dilution rate and µ ranges in both chemostat and fed-batch cultivations. Chemostat cultivations allowed to establish the impact of µ on the MUT-related MIT1 pool which leads to a bell-shaped relationship between µ and PAOX1-driven gene expression, influencing directly Crl1 production kinetics. Also, chemostat and fed-batch cultivations exposed the favorable effects of increasing the CRL1 gene dosage (up to 2.4 fold in qp) on Crl1 production with no significant detrimental effects on physiological capabilities. Conclusions PAOX1-driven gene expression and Crl1 production kinetics in P. pastoris were successfully correlated with µ. In fact, µ governs MUT-related MIT1 amount that triggers PAOX1-driven gene expression—heterologous genes included—, thus directly influencing the production kinetics of recombinant protein.
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Nieto-Taype MA, Garrigós-Martínez J, Sánchez-Farrando M, Valero F, Garcia-Ortega X, Montesinos-Seguí JL. Rationale-based selection of optimal operating strategies and gene dosage impact on recombinant protein production in Komagataella phaffii (Pichia pastoris). Microb Biotechnol 2019; 13:315-327. [PMID: 31657146 PMCID: PMC7017824 DOI: 10.1111/1751-7915.13498] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 12/26/2022] Open
Abstract
Its features as a microbial and eukaryotic organism have turned Komagataella phaffii (Pichia pastoris) into an emerging cell factory for recombinant protein production (RPP). As a key step of the bioprocess development, this work aimed to demonstrate the importance of tailor designing the cultivation strategy according to the production kinetics of the cell factory. For this purpose, K. phaffii clones constitutively expressing (PGAP) Candida rugosa lipase 1 (Crl1) with different gene dosage were used as models in continuous and fed‐batch cultures. Production parameters were much greater with a multicopy clone (MCC) than with the single‐copy clone (SCC). Regarding production kinetics, the specific product generation rate (qP) increased linearly with increasing specific growth rate (µ) in SCC; by contrast, qP exhibited saturation in MCC. A transcriptional analysis in chemostat cultures suggested the presence of eventual post‐transcriptional bottlenecks in MCC. After the strain characterization, in order to fulfil overall development of the bioprocess, the performance of both clones was also evaluated in fed‐batch mode. Strikingly, different optimal strategies were determined for both models due to the different production kinetic patterns observed as a trade‐off for product titre, yields and productivity. The combined effect of gene dosage and adequate µ enables rational process development with a view to optimize K. phaffii RPP bioprocesses.
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Affiliation(s)
- Miguel Angel Nieto-Taype
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Javier Garrigós-Martínez
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Marc Sánchez-Farrando
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Xavier Garcia-Ortega
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - José Luis Montesinos-Seguí
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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Torres P, Saa PA, Albiol J, Ferrer P, Agosin E. Contextualized genome-scale model unveils high-order metabolic effects of the specific growth rate and oxygenation level in recombinant Pichia pastoris. Metab Eng Commun 2019; 9:e00103. [PMID: 31720218 PMCID: PMC6838487 DOI: 10.1016/j.mec.2019.e00103] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 11/26/2022] Open
Abstract
Pichia pastoris is recognized as a biotechnological workhorse for recombinant protein expression. The metabolic performance of this microorganism depends on genetic makeup and culture conditions, amongst which the specific growth rate and oxygenation level are critical. Despite their importance, only their individual effects have been assessed so far, and thus their combined effects and metabolic consequences still remain to be elucidated. In this work, we present a comprehensive framework for revealing high-order (i.e., individual and combined) metabolic effects of the above parameters in glucose-limited continuous cultures of P. pastoris, using thaumatin production as a case study. Specifically, we employed a rational experimental design to calculate statistically significant metabolic effects from multiple chemostat data, which were later contextualized using a refined and highly predictive genome-scale metabolic model of this yeast under the simulated conditions. Our results revealed a negative effect of the oxygenation on the specific product formation rate (thaumatin), and a positive effect on the biomass yield. Notably, we identified a novel positive combined effect of both the specific growth rate and oxygenation level on the specific product formation rate. Finally, model predictions indicated an opposite relationship between the oxygenation level and the growth-associated maintenance energy (GAME) requirement, suggesting a linear GAME decrease of 0.56 mmol ATP/gDCW per each 1% increase in oxygenation level, which translated into a 44% higher metabolic cost under low oxygenation compared to high oxygenation. Overall, this work provides a systematic framework for mapping high-order metabolic effects of different culture parameters on the performance of a microbial cell factory. Particularly in this case, it provided valuable insights about optimal operational conditions for protein production in P. pastoris.
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Affiliation(s)
- Paulina Torres
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna, 4860, Santiago, Chile
| | - Pedro A Saa
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna, 4860, Santiago, Chile
| | - Joan Albiol
- Department of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
| | - Pau Ferrer
- Department of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
| | - Eduardo Agosin
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna, 4860, Santiago, Chile
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Sun X, Liu H, Wang P, Wang L, Ni W, Yang Q, Wang H, Tang H, Zhao G, Zheng Z. Construction of a novel MK-4 biosynthetic pathway in Pichia pastoris through heterologous expression of HsUBIAD1. Microb Cell Fact 2019; 18:169. [PMID: 31601211 PMCID: PMC6786277 DOI: 10.1186/s12934-019-1215-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023] Open
Abstract
Background With a variety of physiological and pharmacological functions, menaquinone is an essential prenylated product that can be endogenously converted from phylloquinone (VK1) or menadione (VK3) via the expression of Homo sapiens UBIAD1 (HsUBIAD1). The methylotrophic yeast, Pichia pastoris, is an attractive expression system that has been successfully applied to the efficient expression of heterologous proteins. However, the menaquinone biosynthetic pathway has not been discovered in P. pastoris. Results Firstly, we constructed a novel synthetic pathway in P. pastoris for the production of menaquinone-4 (MK-4) via heterologous expression of HsUBIAD1. Then, the glyceraldehyde-3-phosphate dehydrogenase constitutive promoter (PGAP) appeared to be mostsuitable for the expression of HsUBIAD1 for various reasons. By optimizing the expression conditions of HsUBIAD1, its yield increased by 4.37 times after incubation at pH 7.0 and 24 °C for 36 h, when compared with that under the initial conditions. We found HsUBIAD1 expressed in recombinant GGU-23 has the ability to catalyze the biosynthesis of MK-4 when using VK1 and VK3 as the isopentenyl acceptor. In addition, we constructed a ribosomal DNA (rDNA)-mediated multi-copy expression vector for the fusion expression of SaGGPPS and PpIDI, and the recombinant GGU-GrIG afforded higher MK-4 production, so that it was selected as the high-yield strain. Finally, the yield of MK-4 was maximized at 0.24 mg/g DCW by improving the GGPP supply when VK3 was the isopentenyl acceptor. Conclusions In this study, we constructed a novel synthetic pathway in P. pastoris for the biosynthesis of the high value-added prenylated product MK-4 through heterologous expression of HsUBIAD1 and strengthened accumulation of GGPP. This approach could be further developed and accomplished for the biosynthesis of other prenylated products, which has great significance for theoretical research and industrial application.
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Affiliation(s)
- Xiaowen Sun
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.,University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Hui Liu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China
| | - Peng Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China
| | - Li Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China
| | - Wenfeng Ni
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.,University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Qiang Yang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.,University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Han Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.,University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Hengfang Tang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.,University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Genhai Zhao
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.
| | - Zhiming Zheng
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.
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135
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Statistically Designed Medium Reveals Interactions between Metabolism and Genetic Information Processing for Production of Stable Human Serum Albumin in Pichia pastoris. Biomolecules 2019; 9:biom9100568. [PMID: 31590267 PMCID: PMC6843683 DOI: 10.3390/biom9100568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/27/2019] [Accepted: 10/02/2019] [Indexed: 12/17/2022] Open
Abstract
Human serum albumin (HSA), sourced from human serum, has been an important therapeutic protein for several decades. Pichia pastoris is strongly considered as an expression platform, but proteolytic degradation of recombinant HSA in the culture filtrate remains a major bottleneck for use of this system. In this study, we have reported the development of a medium that minimized proteolytic degradation across different copy number constructs. A synthetic codon-optimized copy of HSA was cloned downstream of α-factor secretory signal sequence and expressed in P. pastoris under the control of Alcohol oxidase 1 promoter. A two-copy expression cassette was also prepared. Culture conditions and medium components were identified and optimized using statistical tools to develop a medium that supported stable production of HSA. Comparative analysis of transcriptome data obtained by cultivation on optimized and unoptimized medium indicated upregulation of genes involved in methanol metabolism, alternate nitrogen assimilation, and DNA transcription, whereas enzymes of translation and secretion were downregulated. Several new genes were identified that could serve as possible targets for strain engineering of this yeast.
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136
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Liu Q, Shi X, Song L, Liu H, Zhou X, Wang Q, Zhang Y, Cai M. CRISPR-Cas9-mediated genomic multiloci integration in Pichia pastoris. Microb Cell Fact 2019; 18:144. [PMID: 31434578 PMCID: PMC6704636 DOI: 10.1186/s12934-019-1194-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/14/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pichia pastoris (syn. Komagataella phaffii) is a widely used generally recognized as safe host for heterologous expression of proteins in both industry and academia. Recently, it has been shown to be a potentially good chassis host for the production of high-value pharmaceuticals and chemicals. Nevertheless, limited availability of selective markers and low efficiency of homologous recombination make this process difficult and time-consuming, particularly in the case of multistep biosynthetic pathways. Therefore, it is crucial to develop an efficient and marker-free multiloci gene knock-in method in P. pastoris. RESULTS A non-homologous-end-joining defective strain (Δku70) was first constructed using the CRISPR-Cas9 based gene deficiency approach. It was then used as a parent strain for multiloci gene integration. Ten guide RNA (gRNA) targets were designed within 100 bp upstream of the promoters or downstream of terminator, and then tested using an eGFP reporter and confirmed as suitable single-locus integration sites. Three high-efficiency gRNA targets (PAOX1UP-g2, PTEF1UP-g1, and PFLD1UP-g1) were selected for double- and triple-locus co-integration. The integration efficiency ranged from 57.7 to 70% and 12.5 to 32.1% for double-locus and triple-locus integration, respectively. In addition, biosynthetic pathways of 6-methylsalicylic acid and 3-methylcatechol were successfully assembled using the developed method by one-step integration of functional genes. The desired products were obtained, which further established the effectiveness and applicability of the developed CRISPR-Cas9-mediated gene co-integration method in P. pastoris. CONCLUSIONS A CRISPR-Cas9-mediated multiloci gene integration method was developed with efficient gRNA targets in P. pastoris. Using this method, multiple gene cassettes can be simultaneously integrated into the genome without employing selective markers. The multiloci integration strategy is beneficial for pathway assembly of complicated pharmaceuticals and chemicals expressed in P. pastoris.
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Affiliation(s)
- Qi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Xiaona Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Lili Song
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Haifeng Liu
- Chinare Resources Angde Biotech Pharmaceutical Co., Ltd., 78 E-jiao Street, Liaocheng, China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
- Chinare Resources Angde Biotech Pharmaceutical Co., Ltd., 78 E-jiao Street, Liaocheng, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
- Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai, 200237 China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
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137
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Zhu T, Sun H, Wang M, Li Y. Pichia pastoris
as a Versatile Cell Factory for the Production of Industrial Enzymes and Chemicals: Current Status and Future Perspectives. Biotechnol J 2019; 14:e1800694. [DOI: 10.1002/biot.201800694] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 04/19/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Taicheng Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing 100101 P. R. China
| | - Hongbing Sun
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin 300308 China
| | - Meiyu Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing 100101 P. R. China
- University of Chinese Academy of SciencesBeijing 100190 China
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing 100101 P. R. China
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin 300308 China
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138
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Tian Y, Li Y, Zhao F, Meng C. Engineered Pichia pastoris production of fusaruside, a selective immunomodulator. BMC Biotechnol 2019; 19:37. [PMID: 31208387 PMCID: PMC6580515 DOI: 10.1186/s12896-019-0532-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/10/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUD Fusaruside is an immunomodulatory fungal sphingolipid which has medical potentials for treating colitis and liver injury, but its poor natural abundance limits its further study. RESULTS In this study, we described a synthetic biology approach for fusaruside production by engineered Pichia pastoris that was based on polycistronic expression. Two fusaruside biosynthesis genes (Δ3(E)-sd and Δ10(E)-sd), were introduced into P. pastoris to obtain fusaruside producing strain FUS2. To further enhance the yield of fusaruside, three relevant biosynthetic genes (Δ3(E)-sd, Δ10(E)-sd and gcs) were subsequently introduced into P. pastoris to obtain FUS3. All of the biosynthetic genes were successfully co-expressed in FUS2 and FUS3. Compared to that produced by FUS2, fusaruside achieved from FUS3 were slightly increased. In addition, the culture conditions including pH, temperature and methanol concentration were optimized to improve the fusaruside production level. CONCLUSIONS Here a novel P. pastoris fusaruside production system was developed by introducing the biosynthetic genes linked by 2A peptide gene sequences into a polycistronic expression construct, laying a foundation for further development and application of fusaruside.
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Affiliation(s)
- Yuan Tian
- College of Life Science, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271016, Shandong, China.
| | - Yanling Li
- College of Life Science, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271016, Shandong, China
| | - Fengchun Zhao
- Department of Microbiology, College of Life Science, Key Laboratory for Agriculture Microbiology, Shandong Agricultural University, Taian, 271018, China
| | - Chao Meng
- College of Life Science, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271016, Shandong, China
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139
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Gu Y, Gao J, Cao M, Dong C, Lian J, Huang L, Cai J, Xu Z. Construction of a series of episomal plasmids and their application in the development of an efficient CRISPR/Cas9 system in Pichia pastoris. World J Microbiol Biotechnol 2019; 35:79. [PMID: 31134410 DOI: 10.1007/s11274-019-2654-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/10/2019] [Indexed: 01/07/2023]
Abstract
The methylotrophic yeast Pichia pastoris is widely used in recombinant expression of eukaryotic proteins owing to the ability of post-translational modification, tightly regulated promoters, and high cell density fermentation. However, episomal plasmids for heterologous gene expression and the CRISPR/Cas9 system for genome editing have not been well developed in P. pastoris. In the present study, a panel of episomal plasmids containing various autonomously replicating sequences (ARSs) were constructed and their performance in transformation efficiency, copy numbers, and propagation stability were systematically compared. Among the five ARSs with different origins, panARS isolated from Kluyveromyces lactis was determined to have the best performance and used to develop an efficient CRISPR/Cas9 based genome editing system. Compared with a previously reported system using the endogenous and most commonly used ARS (PARS1), the CRISPR/Cas9 genome editing efficiency was increased for more than tenfold. Owing to the higher plasmid stability with panARS, efficient CRISPR/Cas9-mediated genome editing with a type III promoter (i.e. SER promoter) to drive the expression of the single guide RNA (sgRNA) was achieved for the first time. The constructed episomal plasmids and developed CRISPR/Cas9 system will be important synthetic biology tools for both fundamental studies and industrial applications of P. pastoris.
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Affiliation(s)
- Yang Gu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jucan Gao
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Mingfeng Cao
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Chang Dong
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
| | - Lei Huang
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jin Cai
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
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Liu Y, Bai C, Liu Q, Xu Q, Qian Z, Peng Q, Yu J, Xu M, Zhou X, Zhang Y, Cai M. Engineered ethanol-driven biosynthetic system for improving production of acetyl-CoA derived drugs in Crabtree-negative yeast. Metab Eng 2019; 54:275-284. [PMID: 31077813 DOI: 10.1016/j.ymben.2019.05.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 04/26/2019] [Accepted: 05/02/2019] [Indexed: 01/17/2023]
Abstract
Many natural drugs use acetyl-CoA as the key biosynthetic precursor. While in eukaryotic chassis host like yeast, efficient biosynthesis of these drugs is often hampered by insufficient acetyl-CoA supply because of its compartmentalized metabolism. Reported acetyl-CoA engineering commonly modifies central carbon metabolism to pull and push acetyl-CoA into cytosol from sugars or redirects biosynthetic pathways in organelles, involving complicated metabolic engineering strategies. We constructed a new biosynthetic system based on a Crabtree-negative yeast, which grew exceptionally on ethanol and assimilated ethanol directly in cytosol to acetyl-CoA (3 steps). A glucose-repressed and ethanol-induced transcriptional signal amplification device (ESAD) with 20-fold signal increase was constructed by rewiring native transcriptional regulation circuits. This made ethanol the sole and fast-growing substrate, acetyl-CoA precursor, and strong biosynthetic pathway inducer simultaneously. The ESAD was used for biosynthesis of a commercial hypolipidemic drug intermediate, monacolin J. A strain producing dihydromonacolin L was firstly constructed and systematically engineered. We further developed a coculture system equipped with this upstream strain and a downstream strain with dihydromonacolin L-to-monacolin J module controlled by a synthetic constitutive transcriptional signal amplification device (CSAD). It produced a high monacolin J titre of 2.2 g/L on ethanol in bioreactor. Engineering glucose-supported and ethanol-repressed fatty acids biosynthesis in the upstream strain contributed more acetyl-CoA for monacolin J and improved its titre to 3.2 g/L, far surpassing other reported productions in yeasts. This study provides a new paradigm for facilitating the high-yield production of acetyl-CoA derived pharmaceuticals and value-added molecules.
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Affiliation(s)
- Yiqi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Chenxiao Bai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qin Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zhilan Qian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiangqiang Peng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jiahui Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Mingqiang Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai 200237, China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
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The Multiplanetary Future of Plant Synthetic Biology. Genes (Basel) 2018; 9:genes9070348. [PMID: 29996548 PMCID: PMC6071031 DOI: 10.3390/genes9070348] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 11/24/2022] Open
Abstract
The interest in human space journeys to distant planets and moons has been re-ignited in recent times and there are ongoing plans for sending the first manned missions to Mars in the near future. In addition to generating oxygen, fixing carbon, and recycling waste and water, plants could play a critical role in producing food and biomass feedstock for the microbial manufacture of materials, chemicals, and medicines in long-term interplanetary outposts. However, because life on Earth evolved under the conditions of the terrestrial biosphere, plants will not perform optimally in different planetary habitats. The construction or transportation of plant growth facilities and the availability of resources, such as sunlight and liquid water, may also be limiting factors, and would thus impose additional challenges to efficient farming in an extraterrestrial destination. Using the framework of the forthcoming human missions to Mars, here we discuss a series of bioengineering endeavors that will enable us to take full advantage of plants in the context of a Martian greenhouse. We also propose a roadmap for research on adapting life to Mars and outline our opinion that synthetic biology efforts towards this goal will contribute to solving some of the main agricultural and industrial challenges here on Earth.
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