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Zhou H, Zhang W, Qian J. Hypersecretory production of glucose oxidase in Pichia pastoris through combinatorial engineering of protein properties, synthesis, and secretion. Biotechnol Bioeng 2024; 121:735-748. [PMID: 38037762 DOI: 10.1002/bit.28600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 12/02/2023]
Abstract
Glucose oxidase (EC 1.1.3.4, GOD) is a widely used industrial enzyme. To construct a GOD-hyperproducing Pichia pastoris strain, combinatorial strategies have been applied to improve GOD activity, synthesis, and secretion. First, wild-type GOD was subjected to saturation mutagenesis to obtain an improved variant, MGOD1 (V20W/T30S), with 1.7-fold higher kcat /KM . Subsequently, efficient signal peptides were screened, and the copy number of MGOD1 was optimized to generate a high-producing strain, 8GM1, containing eight copies of AOX1 promoter-GAS1 signal peptide-MGOD1 expression cassette. Finally, the vesicle trafficking of 8GM1 was engineered to obtain the hyperproducing strain G1EeSe co-expressing the trafficking components EES and SEC. 22, and the EES gene (PAS_chr3_0685) was found to facilitate both protein secretion and production for the first time. Using these strategies, GOD secretion was enhanced 65.2-fold. In the 5-L bioreactor, conventional fed-batch fermentation without any process optimization resulted in up to 7223.0 U/mL extracellular GOD activity (3.3-fold higher than the highest level reported to date), with almost only GOD in the fermentation supernatant at a protein concentration of 30.7 g/L. Therefore, a GOD hyperproducing strain for industrial applications was developed, and this successful case can provide a valuable reference for the construction of high-producing strains for other industrial enzymes.
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Affiliation(s)
- Huzhi Zhou
- School of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Wenyu Zhang
- School of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jiangchao Qian
- School of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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2
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Zhang C, Chen H, Zhu Y, Zhang Y, Li X, Wang F. Saccharomyces cerevisiae cell surface display technology: Strategies for improvement and applications. Front Bioeng Biotechnol 2022; 10:1056804. [PMID: 36568309 PMCID: PMC9767963 DOI: 10.3389/fbioe.2022.1056804] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Microbial cell surface display technology provides a powerful platform for engineering proteins/peptides with enhanced properties. Compared to the classical intracellular and extracellular expression (secretion) systems, this technology avoids enzyme purification, substrate transport processes, and is an effective solution to enzyme instability. Saccharomyces cerevisiae is well suited to cell surface display as a common cell factory for the production of various fuels and chemicals, with the advantages of large cell size, being a Generally Regarded As Safe (GRAS) organism, and post-translational processing of secreted proteins. In this review, we describe various strategies for constructing modified S. cerevisiae using cell surface display technology and outline various applications of this technology in industrial processes, such as biofuels and chemical products, environmental pollution treatment, and immunization processes. The approaches for enhancing the efficiency of cell surface display are also discussed.
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Affiliation(s)
- Chenmeng Zhang
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Hongyu Chen
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Yiping Zhu
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Yu Zhang
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Xun Li
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Fei Wang
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China,*Correspondence: Fei Wang,
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Li J, Zeng Y, Wang WB, Wan QQ, Liu CG, den Haan R, van Zyl WH, Zhao XQ. Increasing extracellular cellulase activity of the recombinant Saccharomyces cerevisiae by engineering cell wall-related proteins for improved consolidated processing of carbon neutral lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2022; 365:128132. [PMID: 36252752 DOI: 10.1016/j.biortech.2022.128132] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Sustainable bioproduction usingcarbon neutral feedstocks, especially lignocellulosic biomass, has attracted increasing attention due to concern over climate change and carbon reduction. Consolidated bioprocessing (CBP) of lignocellulosic biomass using recombinantyeast of Saccharomyces cerevisiaeis a promising strategy forlignocellulosic biorefinery. However, the economic viability is restricted by low enzyme secretion levels.For more efficient CBP, MIG1spsc01isolated from the industrial yeast which encodes the glucose repression regulator derivative was overexpressed. Increased extracellular cellobiohydrolase (CBH) activity was observed with unexpectedly decreased cell wall integrity. Further studies revealed that disruption ofCWP2, YGP1, andUTH1,which are functionally related toMIG1spsc01, also enhanced CBH secretion. Subsequently, improved cellulase production was achieved by simultaneous disruption ofYGP1and overexpression ofSED5, which remarkably increased extracellular CBH activity of 2.2-fold over the control strain. These results provide a novel strategy to improve the CBP yeast for bioconversion of carbon neutral biomass.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu Zeng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei-Bin Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qing-Qing Wan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville 7530, South Africa
| | - Willem H van Zyl
- Department of Microbiology, University of Stellenbosch, Stellenbosch 7600, South Africa
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Zahrl RJ, Prielhofer R, Ata Ö, Baumann K, Mattanovich D, Gasser B. Pushing and pulling proteins into the yeast secretory pathway enhances recombinant protein secretion. Metab Eng 2022; 74:36-48. [PMID: 36057427 DOI: 10.1016/j.ymben.2022.08.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022]
Abstract
Yeasts and especially Pichia pastoris (syn Komagataella spp.) are popular microbial expression systems for the production of recombinant proteins. One of the key advantages of yeast host systems is their ability to secrete the recombinant protein into the culture media. However, secretion of some recombinant proteins is less efficient. These proteins include antibody fragments such as Fabs or scFvs. We have recently identified translocation of nascent Fab fragments from the cytosol into the endoplasmic reticulum (ER) as one major bottleneck. Conceptually, this bottleneck requires engineering to increase the flux of recombinant proteins at the translocation step by pushing on the cytosolic side and pulling on the ER side. This engineering strategy is well-known in the field of metabolic engineering. To apply the push-and-pull strategy to recombinant protein secretion, we chose to modulate the cytosolic and ER Hsp70 cycles, which have a key impact on the translocation process. After identifying the relevant candidate factors of the Hsp70 cycles, we combined the push-and-pull factors in a single strain and achieved synergistic effects for antibody fragment secretion. With this concept we were able to successfully engineer strains and improve protein secretion up to 5-fold for different model protein classes. Overall, titers of more than 1.3 g/L Fab and scFv were reached in bioreactor cultivations.
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Affiliation(s)
- Richard J Zahrl
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Roland Prielhofer
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Özge Ata
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Kristin Baumann
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Diethard Mattanovich
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Brigitte Gasser
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria.
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5
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Chetty BJ, Inokuma K, Hasunuma T, van Zyl WH, den Haan R. Improvement of cell-tethered cellulase activity in recombinant strains of Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2022; 106:6347-6361. [PMID: 35951080 DOI: 10.1007/s00253-022-12114-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/30/2022]
Abstract
Consolidated bioprocessing (CBP) remains an attractive option for the production of commodity products from pretreated lignocellulose if a process-suitable organism can be engineered. The yeast Saccharomyces cerevisiae requires engineered cellulolytic activity to enable its use in CBP production of second-generation (2G) bioethanol. A promising strategy for heterologous cellulase production in yeast entails displaying enzymes on the cell surface by means of glycosylphosphatidylinositol (GPI) anchors. While strains producing a core set of cell-adhered cellulases that enabled crystalline cellulose hydrolysis have been created, secreted levels of enzyme were insufficient for complete cellulose hydrolysis. In fact, all reported recombinant yeast CBP candidates must overcome the drawback of generally low secretion titers. Rational strain engineering can be applied to enhance the secretion phenotype. This study aimed to improve the amount of cell-adhered cellulase activities of recombinant S. cerevisiae strains expressing a core set of four cellulases, through overexpression of genes that were previously shown to enhance cellulase secretion. Results showed significant increases in cellulolytic activity for all cell-adhered cellulase enzyme types. Cell-adhered cellobiohydrolase activity was improved by up to 101%, β-glucosidase activity by up to 99%, and endoglucanase activity by up to 231%. Improved hydrolysis of crystalline cellulose of up to 186% and improved ethanol yields from this substrate of 40-50% in different strain backgrounds were also observed. In addition, improvement in resistance to fermentation stressors was noted in some strains. These strains represent a step towards more efficient organisms for use in 2G biofuel production. KEY POINTS: • Cell-surface-adhered cellulase activity was improved in strains engineered for CBP. • Levels of improvement of activity were strain and enzyme dependent. • Crystalline cellulose conversion to ethanol could be improved up to 50%.
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Affiliation(s)
- Bronwyn Jean Chetty
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Kentaro Inokuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | | | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa.
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6
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Cho JS, Oh HJ, Jang YE, Kim HJ, Kim A, Song JA, Lee EJ, Lee J. Synthetic pro-peptide design to enhance the secretion of heterologous proteins by Saccharomyces cerevisiae. Microbiologyopen 2022; 11:e1300. [PMID: 35765186 PMCID: PMC9178654 DOI: 10.1002/mbo3.1300] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 12/02/2022] Open
Abstract
Heterologous protein production in Saccharomyces cerevisiae is a useful and effective strategy with many advantages, including the secretion of proteins that require posttranslational processing. However, heterologous proteins in S. cerevisiae are often secreted at comparatively low levels. To improve the production of the heterologous protein, human granulocyte colony‐stimulating factor (hG‐CSF) in S. cerevisiae, a secretion‐enhancing peptide cassette including an hIL‐1β‐derived propeptide, was added and used as a secretion enhancer to alleviate specific bottlenecks in the yeast secretory pathway. The effects of three key parameters—N‐glycosylation, net negative charge balance, and glycine‐rich flexible linker—were investigated in batch cultures of S. cerevisiae. Using a three‐stage design involving screening, selection, and optimization, the production and secretion of hG‐CSF by S. cerevisiae were significantly increased. The amount of extracellular mature hG‐CSF produced by the optimized propeptide after the final stage increased by 190% compared to that of the original propeptide. Although hG‐CSF was used as the model protein in the current study, this strategy applies to the enhanced production of other heterologous proteins, using S. cerevisiae as the host.
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Affiliation(s)
- Ji Sung Cho
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, Korea
| | - Hye Ji Oh
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, Korea
| | - Young Eun Jang
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, Korea
| | - Hyun Jin Kim
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, Korea
| | - Areum Kim
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, Korea
| | - Jong-Am Song
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, Korea
| | - Eun Jung Lee
- Department of Chemical Engineering, School of Applied Chemical Engineering, Kyungpook National University, Daegu, Korea
| | - Jeewon Lee
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, Korea
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7
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den Haan R, Rose SH, Cripwell RA, Trollope KM, Myburgh MW, Viljoen-Bloom M, van Zyl WH. Heterologous production of cellulose- and starch-degrading hydrolases to expand Saccharomyces cerevisiae substrate utilization: Lessons learnt. Biotechnol Adv 2021; 53:107859. [PMID: 34678441 DOI: 10.1016/j.biotechadv.2021.107859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/28/2022]
Abstract
Selected strains of Saccharomyces cerevisiae are used for commercial bioethanol production from cellulose and starch, but the high cost of exogenous enzymes for substrate hydrolysis remains a challenge. This can be addressed through consolidated bioprocessing (CBP) where S. cerevisiae strains are engineered to express recombinant glycoside hydrolases during fermentation. Looking back at numerous strategies undertaken over the past four decades to improve recombinant protein production in S. cerevisiae, it is evident that various steps in the protein production "pipeline" can be manipulated depending on the protein of interest and its anticipated application. In this review, we briefly introduce some of the strategies and highlight lessons learned with regards to improved transcription, translation, post-translational modification and protein secretion of heterologous hydrolases. We examine how host strain selection and modification, as well as enzyme compatibility, are crucial determinants for overall success. Finally, we discuss how lessons from heterologous hydrolase expression can inform modern synthetic biology and genome editing tools to provide process-ready yeast strains in future. However, it is clear that the successful expression of any particular enzyme is still unpredictable and requires a trial-and-error approach.
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Affiliation(s)
- Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Shaunita H Rose
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Rosemary A Cripwell
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Kim M Trollope
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Marthinus W Myburgh
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | | | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa.
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Farh MEA, Abdellaoui N, Seo JA. pH Changes Have a Profound Effect on Gene Expression, Hydrolytic Enzyme Production, and Dimorphism in Saccharomycopsis fibuligera. Front Microbiol 2021; 12:672661. [PMID: 34248880 PMCID: PMC8265565 DOI: 10.3389/fmicb.2021.672661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/25/2021] [Indexed: 11/21/2022] Open
Abstract
Saccharomycopsis fibuligera is an amylolytic yeast that plays an important role within nuruk (a traditional Korean fermentation starter) used for the production of makgeolli (Korean rice wine), which is characterized by high acidity. However, the effect of pH change (neutral to acidic) on the yeast cell to hyphal transition and carbohydrate-hydrolyzing enzyme activities for S. fibuligera has not been investigated yet. In this study, S. fibuligera strains were cultured under the different pH conditions, and the effect on the enzyme production and gene expression were investigated. An acidic pH induced a hyphal transition from yeast cell of S. fibuligera KPH12 and the hybrid strain KJJ81. In addition, both strains showed a gradual decrease in the ability to degrade starch and cellulose as the pH went down. Furthermore, a transcriptome analysis demonstrated that the pH decline caused global expression changes in genes, which were classified into five clusters. Among the differentially expressed genes (DEGs) under acidic pH, the downregulated genes were involved in protein synthesis, carbon metabolism, and RIM101 and cAMP-PKA signaling transduction pathways for the yeast-hyphal transition. A decrease in pH induced a dimorphic lifestyle switch from yeast cell formation to hyphal growth in S. fibuligera and caused a decrease in carbohydrate hydrolyzing enzyme production, as well as marked changes in the expression of genes related to enzyme production and pH adaptation. This study will help to elucidate the mechanism of adaptation of S. fibuligera to acidification that occur during the fermentation process of makgeolli using nuruk.
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Affiliation(s)
| | - Najib Abdellaoui
- School of Systems Biomedical Science, Soongsil University, Seoul, South Korea
| | - Jeong-Ah Seo
- School of Systems Biomedical Science, Soongsil University, Seoul, South Korea
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Korpys-Woźniak P, Celińska E. Global transcriptome profiling reveals genes responding to overproduction of a small secretory, a high cysteine- and a high glycosylation-bearing protein in Yarrowia lipolytica. ACTA ACUST UNITED AC 2021; 31:e00646. [PMID: 34189064 PMCID: PMC8220174 DOI: 10.1016/j.btre.2021.e00646] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022]
Abstract
Secretion of a protein results in > 10-fold higher titer compared to its retention. Overproduction of rs-Prots induces oxidative stress and detoxification response. Excessive vacuolar protein degradation limits rs-Prot production in Y. lipolytica. Non-classical export protein NCE102 is upregulated upon rs-Prot overloading. Downregulation of cyclin CLN1 marks growth arrest in G1 under rs-Prot synthesis.
Investigation of the yeast cell’s response to recombinant secretory protein (rs-Prot) overproduction is relevant for both basic and applied research. Imbalance, overloading or stress within this process impacts the whole cell. In the present study, by using steady-state cultures and transcriptomics, we investigated the cellular response of Yarrowia lipolytica challenged with high-level expression of genes encoding proteins with significantly different biochemical characteristics: a small protein retained within the cell i) or secreted ii), a medium size secretory protein with a high number of disulfide bonds iii), or glycosylation sites iv). Extensive analysis of omics data, supported by careful manual curation, led to some anticipated observations on oxidative and unfolded protein stress (CTT1, PXMP2/4, HAC1), glycosylation (ALGs, KTRs, MNTs, MNNs), folding and translocation (SSAs, SSEs) but also generated new exciting knowledge on non-conventional protein secretion (NCE102), transcriptional regulators (FLO11, MHY1, D01353 g, RSFA, E23925g or MAF1), vacuolar proteolysis targets in Y. lipolytica (ATGs, VPSs, HSE1, PRB1, PRC1, PEP4) or growth arrest (CLN1) upon rs-Prots overproduction.
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Lamour J, Wan C, Zhang M, Zhao X, Den Haan R. Overexpression of endogenous stress-tolerance related genes in Saccharomyces cerevisiae improved strain robustness and production of heterologous cellobiohydrolase. FEMS Yeast Res 2020; 19:5479884. [PMID: 31073597 DOI: 10.1093/femsyr/foz035] [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: 02/19/2019] [Accepted: 04/25/2019] [Indexed: 12/11/2022] Open
Abstract
To enable Saccharomyces cerevisiae to produce renewable fuels from lignocellulose in a consolidated bioprocess, a heterologous cellulase system must be engineered into this yeast. In addition, inherently low secretion titers and sensitivity to adverse environmental conditions must be overcome. Here, two native S. cerevisiae genes related to yeast stress tolerance, YHB1 and SET5, were overexpressed under transcriptional control of the constitutive PGK1 promoter and their effects on heterologous secretion of Talaromyces emersonii cel7A cellobiohydrolase was investigated. Transformants showed increased secreted enzyme activity that ranged from 22% to 55% higher compared to the parental strains and this did not lead to deleterious growth effects. The recombinant strains overexpressing either YHB1 or SET5 also demonstrated multi-tolerant characteristics desirable in bioethanol production, i.e. improved tolerance to osmotic and heat stress. Quantitative reverse transcriptase PCR analysis in these strains showed decreased transcription of secretion pathway genes. However, decreased unfolded protein response was also observed, suggesting novel mechanisms for enhancing enzyme production through stress modulation. Overexpression of YHB1 in an unrelated diploid strain also enhanced stress tolerance and improved ethanol productivity in medium containing acetic acid. To our knowledge, this is the first demonstration that improved heterologous secretion and environmental stress tolerance could be engineered into yeast simultaneously.
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Affiliation(s)
- Jarryd Lamour
- Department of Biotechnology, University of the Western Cape, Bellville 7530, South Africa
| | - Chun Wan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingming Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinqing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Riaan Den Haan
- Department of Biotechnology, University of the Western Cape, Bellville 7530, South Africa
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11
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Exploiting strain diversity and rational engineering strategies to enhance recombinant cellulase secretion by Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2020; 104:5163-5184. [PMID: 32337628 DOI: 10.1007/s00253-020-10602-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic material into bioethanol has progressed in the past decades; however, several challenges still exist which impede the industrial application of this technology. Identifying the challenges that exist in all unit operations is crucial and needs to be optimised, but only the barriers related to the secretion of recombinant cellulolytic enzymes in Saccharomyces cerevisiae will be addressed in this review. Fundamental principles surrounding CBP as a biomass conversion platform have been established through the successful expression of core cellulolytic enzymes, namely β-glucosidases, endoglucanases, and exoglucanases (cellobiohydrolases) in S. cerevisiae. This review will briefly address the challenges involved in the construction of an efficient cellulolytic yeast, with particular focus on the secretion efficiency of cellulases from this host. Additionally, strategies for studying enhanced cellulolytic enzyme secretion, which include both rational and reverse engineering approaches, will be discussed. One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development. Furthermore, with the advancement in next-generation sequencing, studies that utilise this method of exploiting intra-strain diversity for industrially relevant traits will be reviewed. Finally, future prospects are discussed for the creation of ideal CBP strains with high enzyme production levels.Key Points• Several challenges are involved in the construction of efficient cellulolytic yeast, in particular, the secretion efficiency of cellulases from the hosts.• Strategies for enhancing cellulolytic enzyme secretion, a core requirement for CBP host microorganism development, include both rational and reverse engineering approaches.• One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development.
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12
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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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13
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Cedras G, Kroukamp H, Van Zyl WH, Den Haan R. The
in vivo
detection and measurement of the unfolded protein response in recombinant cellulase producing
Saccharomyces cerevisiae
strains. Biotechnol Appl Biochem 2020; 67:82-94. [DOI: 10.1002/bab.1819] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/16/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Gillian Cedras
- Department of BiotechnologyUniversity of the Western Cape Bellville South Africa
| | - Heinrich Kroukamp
- Department of Molecular SciencesMacquarie University North Ryde NSW Australia
| | | | - Riaan Den Haan
- Department of BiotechnologyUniversity of the Western Cape Bellville South Africa
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14
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Improved cellulase production in recombinant Saccharomyces cerevisiae by disrupting the cell wall protein-encoding gene CWP2. J Biosci Bioeng 2019; 129:165-171. [PMID: 31537451 DOI: 10.1016/j.jbiosc.2019.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/23/2019] [Accepted: 08/23/2019] [Indexed: 12/27/2022]
Abstract
Budding yeast Saccharomyces cerevisiae has been widely used for heterologous protein production. However, low protein production titer and secretion levels continue to challenge its practical applications. The yeast cell wall plays important roles in yeast cell growth and environmental responses. Nevertheless, the effects of yeast cell wall proteins on heterologous protein production and secretion remain unclear. CWP2 encodes a mannoprotein that is the major component of the yeast cell wall. So far, studies on its function have been very limited. Here we show that CWP2 disruption improved extracellular cellobiohydrolase activity by 85.9%. A calcofluor white hypersensitivity assay revealed increased sensitivity of the mutant compared to the parental strain, indicating impaired cell wall integrity. However, no changes were observed in normal cell growth or growth stressed by tunicamycin and dithiothreitol, suggesting that the unfolded protein response pathway was not affected by the gene disruption. Comparative transcriptome analysis revealed changes in multiple genes involved in cell wall structure, biosynthesis, and cell wall integrity induced by CWP2 disruption, suggesting a pivotal role of Cwp2p in yeast cell wall organization. Notably, CWP2 disruption also led to elevated transcription of a large number of genes involved in ribosome biogenesis, which indicated that CWP2 is not only in yeast cell wall biosynthesis, but also in protein translation. This work reveals novel insights into the functions of CWP2 and also presents a new strategy to increase heterologous protein production in yeast strains by manipulating cell wall-related proteins.
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15
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Davison SA, den Haan R, van Zyl WH. Identification of superior cellulase secretion phenotypes in haploids derived from natural Saccharomyces cerevisiae isolates. FEMS Yeast Res 2019; 19:5154912. [PMID: 30388213 DOI: 10.1093/femsyr/foy117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/31/2018] [Indexed: 01/11/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is considered an important host for consolidated bioprocessing and the production of high titres of recombinant cellulases is required for efficient hydrolysis of lignocellulosic substrates to fermentable sugars. Since recombinant protein secretion profiles vary highly among different strain backgrounds, careful selection of robust strains with optimal secretion profiles is of crucial importance. Here, we construct and screen sets of haploid derivatives, derived from natural strain isolates YI13, FINI and YI59, for improved general cellulase secretion. This report details a novel approach that combines secretion profiles of strains and phenotypic responses to stresses known to influence the secretion pathway for the development of a phenotypic screen to isolate strains with improved secretory capacities. A clear distinction was observed between the YI13 haploid derivatives and industrial and laboratory counterparts, Ethanol Red and S288c, respectively. By using sub-lethal concentrations of the secretion stressor tunicamycin and cell wall stressor Congo Red, YI13 haploid derivative strains demonstrated tolerance profiles related to their heterologous secretion profiles. Our results demonstrated that a new screening technique combined with a targeted mating approach could produce a pool of novel strains capable of high cellulase secretion.
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Affiliation(s)
- Steffi A Davison
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa
| | - Willem Heber van Zyl
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
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16
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Linders PT, Horst CVD, Beest MT, van den Bogaart G. Stx5-Mediated ER-Golgi Transport in Mammals and Yeast. Cells 2019; 8:cells8080780. [PMID: 31357511 PMCID: PMC6721632 DOI: 10.3390/cells8080780] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 01/12/2023] Open
Abstract
The soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) syntaxin 5 (Stx5) in mammals and its ortholog Sed5p in Saccharomyces cerevisiae mediate anterograde and retrograde endoplasmic reticulum (ER)-Golgi trafficking. Stx5 and Sed5p are structurally highly conserved and are both regulated by interactions with other ER-Golgi SNARE proteins, the Sec1/Munc18-like protein Scfd1/Sly1p and the membrane tethering complexes COG, p115, and GM130. Despite these similarities, yeast Sed5p and mammalian Stx5 are differently recruited to COPII-coated vesicles, and Stx5 interacts with the microtubular cytoskeleton, whereas Sed5p does not. In this review, we argue that these different Stx5 interactions contribute to structural differences in ER-Golgi transport between mammalian and yeast cells. Insight into the function of Stx5 is important given its essential role in the secretory pathway of eukaryotic cells and its involvement in infections and neurodegenerative diseases.
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Affiliation(s)
- Peter Ta Linders
- Tumor Immunology Lab, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Chiel van der Horst
- Tumor Immunology Lab, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Martin Ter Beest
- Tumor Immunology Lab, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Geert van den Bogaart
- Tumor Immunology Lab, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands.
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
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17
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Favaro L, Jansen T, van Zyl WH. Exploring industrial and naturalSaccharomyces cerevisiaestrains for the bio-based economy from biomass: the case of bioethanol. Crit Rev Biotechnol 2019; 39:800-816. [DOI: 10.1080/07388551.2019.1619157] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lorenzo Favaro
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy
| | - Trudy Jansen
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
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18
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Adnan M, Islam W, Zhang J, Zheng W, Lu GD. Diverse Role of SNARE Protein Sec22 in Vesicle Trafficking, Membrane Fusion, and Autophagy. Cells 2019; 8:E337. [PMID: 30974782 PMCID: PMC6523435 DOI: 10.3390/cells8040337] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/02/2019] [Accepted: 04/05/2019] [Indexed: 01/09/2023] Open
Abstract
Protein synthesis begins at free ribosomes or ribosomes attached with the endoplasmic reticulum (ER). Newly synthesized proteins are transported to the plasma membrane for secretion through conventional or unconventional pathways. In conventional protein secretion, proteins are transported from the ER lumen to Golgi lumen and through various other compartments to be secreted at the plasma membrane, while unconventional protein secretion bypasses the Golgi apparatus. Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) proteins are involved in cargo vesicle trafficking and membrane fusion. The ER localized vesicle associated SNARE (v-SNARE) protein Sec22 plays a major role during anterograde and retrograde transport by promoting efficient membrane fusion and assisting in the assembly of higher order complexes by homodimer formation. Sec22 is not only confined to ER-Golgi intermediate compartments (ERGIC) but also facilitates formation of contact sites between ER and plasma membranes. Sec22 mutation is responsible for the development of atherosclerosis and symptoms in the brain in Alzheimer's disease and aging in humans. In the fruit fly Drosophila melanogaster, Sec22 is essential for photoreceptor morphogenesis, the wingless signaling pathway, and normal ER, Golgi, and endosome morphology. In the plant Arabidopsis thaliana, it is involved in development, and in the nematode Caenorhabditis elegans, it is in involved in the RNA interference (RNAi) pathway. In filamentous fungi, it affects cell wall integrity, growth, reproduction, pathogenicity, regulation of reactive oxygen species (ROS), expression of extracellular enzymes, and transcriptional regulation of many development related genes. This review provides a detailed account of Sec22 function, summarizes its domain structure, discusses its genetic redundancy with Ykt6, discusses what is known about its localization to discrete membranes, its contributions in conventional and unconventional autophagy, and a variety of other roles across different cellular systems ranging from higher to lower eukaryotes, and highlights some of the surprises that have originated from research on Sec22.
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Affiliation(s)
- Muhammad Adnan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, and Key Laboratory of Bio-pesticides and Chemical Biology Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Waqar Islam
- College of Geographical Sciences, Fujian Normal University, Fuzhou 350007, Fujian, China.
| | - Jing Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, and Key Laboratory of Bio-pesticides and Chemical Biology Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, and Key Laboratory of Bio-pesticides and Chemical Biology Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Guo-Dong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, and Key Laboratory of Bio-pesticides and Chemical Biology Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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19
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Wei H, Wang W, Alper HS, Xu Q, Knoshaug EP, Van Wychen S, Lin CY, Luo Y, Decker SR, Himmel ME, Zhang M. Ameliorating the Metabolic Burden of the Co-expression of Secreted Fungal Cellulases in a High Lipid-Accumulating Yarrowia lipolytica Strain by Medium C/N Ratio and a Chemical Chaperone. Front Microbiol 2019; 9:3276. [PMID: 30687267 PMCID: PMC6333634 DOI: 10.3389/fmicb.2018.03276] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022] Open
Abstract
Yarrowia lipolytica, known to accumulate lipids intracellularly, lacks the cellulolytic enzymes needed to break down solid biomass directly. This study aimed to evaluate the potential metabolic burden of expressing core cellulolytic enzymes in an engineered high lipid-accumulating strain of Y. lipolytica. Three fungal cellulases, Talaromyces emersonii-Trichoderma reesei chimeric cellobiohydrolase I (chimeric-CBH I), T. reesei cellobiohydrolase II (CBH II), and T. reesei endoglucanase II (EG II) were expressed using three constitutive strong promoters as a single integrative expression block in a recently engineered lipid hyper-accumulating strain of Y. lipolytica (HA1). In yeast extract-peptone-dextrose (YPD) medium, the resulting cellulase co-expressing transformant YL165-1 had the chimeric-CBH I, CBH II, and EG II secretion titers being 26, 17, and 132 mg L-1, respectively. Cellulase co-expression in YL165-1 in culture media with a moderate C/N ratio of ∼4.5 unexpectedly resulted in a nearly two-fold reduction in cellular lipid accumulation compared to the parental control strain, a sign of cellular metabolic drain. Such metabolic drain was ameliorated when grown in media with a high C/N ratio of 59 having a higher glucose utilization rate that led to approximately twofold more cell mass and threefold more lipid production per liter culture compared to parental control strain, suggesting cross-talk between cellulase and lipid production, both of which involve the endoplasmic reticulum (ER). Most importantly, we found that the chemical chaperone, trimethylamine N-oxide dihydride increased glucose utilization, cell mass and total lipid titer in the transformants, suggesting further amelioration of the metabolic drain. This is the first study examining lipid production in cellulase-expressing Y. lipolytica strains under various C/N ratio media and with a chemical chaperone highlighting the metabolic complexity for developing robust, cellulolytic and lipogenic yeast strains.
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Affiliation(s)
- Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Hal S Alper
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Eric P Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Stefanie Van Wychen
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States.,National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Chien-Yuan Lin
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Yonghua Luo
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Stephen R Decker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States.,National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
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20
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Zahrl RJ, Gasser B, Mattanovich D, Ferrer P. Detection and Elimination of Cellular Bottlenecks in Protein-Producing Yeasts. Methods Mol Biol 2019; 1923:75-95. [PMID: 30737735 DOI: 10.1007/978-1-4939-9024-5_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Yeasts are efficient cell factories and are commonly used for the production of recombinant proteins for biopharmaceutical and industrial purposes. For such products high levels of correctly folded proteins are needed, which sometimes requires improvement and engineering of the expression system. The article summarizes major breakthroughs that led to the efficient use of yeasts as production platforms and reviews bottlenecks occurring during protein production. Special focus is given to the metabolic impact of protein production. Furthermore, strategies that were shown to enhance secretion of recombinant proteins in different yeast species are presented.
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Affiliation(s)
- Richard J Zahrl
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Brigitte Gasser
- Christian Doppler-Laboratory for Growth-Decoupled Protein Production in Yeast, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) and Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) and Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Pau Ferrer
- Luxembourg Institute of Science and Technology, Belvaux, Luxembourg. .,Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain.
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21
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Liu Y, Mo WJ, Shi TF, Wang MZ, Zhou JG, Yu Y, Yew WS, Lu H. Mutational Mtc6p attenuates autophagy and improves secretory expression of heterologous proteins in Kluyveromyces marxianus. Microb Cell Fact 2018; 17:144. [PMID: 30217195 PMCID: PMC6138896 DOI: 10.1186/s12934-018-0993-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/08/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The yeast Kluyveromyces marxianus is an emerging cell factory for heterologous protein biosynthesis and its use holds tremendous advantages for multiple applications. However, which genes influence the productivity of desired proteins in K. marxianus has so far been investigated by very few studies. RESULTS In this study, we constructed a K. marxianus recombinant (FIM1/Est1E), which expressed the heterologous ruminal feruloyl esterase Est1E as reporter. UV-60Co-γ irradiation mutagenesis was performed on this recombinant, and one mutant (be termed as T1) was screened and reported, in which the productivity of heterologous Est1E was increased by at least tenfold compared to the parental FIM1/Est1E recombinant. Transcriptional perturbance was profiled and presented that the intracellular vesicle trafficking was enhanced while autophagy be weakened in the T1 mutant. Moreover, whole-genome sequencing combined with CRISPR/Cas9 mediated gene-editing identified a novel functional protein Mtc6p, which was prematurely terminated at Tyr251 by deletion of a single cytosine at 755 loci of its ORF in the T1 mutant. We found that deleting C755 of MTC6 in FIM1 led to 4.86-fold increase in the production of Est1E compared to FIM1, while the autophagy level decreased by 47%; on the contrary, when reinstating C755 of MTC6 in the T1 mutant, the production of Est1E decreased by 66% compared to T1, while the autophagy level increased by 124%. Additionally, in the recombinant with attenuated autophagy (i.e., FIM1 mtc6C755Δ and T1) or interdicted autophagy (i.e., FIM1 atg1Δ and T1 atg1Δ), the productivity of three other heterologous proteins was also increased, specifically the heterologous mannase Man330, the β-1,4-endoxylanase XynCDBFV or the conventional EGFP. CONCLUSIONS Our results demonstrated that Mtc6p was involved in regulating autophagy; attenuating or interdicting autophagy would dramatically improve the yields of desired proteins in K. marxianus, and this modulation could be achieved by focusing on the premature mutation of Mtc6p target.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, People's Republic of China
| | - Wen-Juan Mo
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, People's Republic of China
| | - Tian-Fang Shi
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, People's Republic of China
| | - Meng-Zhu Wang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, People's Republic of China
| | - Jun-Gang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, People's Republic of China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, People's Republic of China
| | - Wen-Shan Yew
- NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore, 117456, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China. .,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, People's Republic of China.
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Pichler H, Emmerstorfer-Augustin A. Modification of membrane lipid compositions in single-celled organisms – From basics to applications. Methods 2018; 147:50-65. [DOI: 10.1016/j.ymeth.2018.06.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/18/2018] [Accepted: 06/16/2018] [Indexed: 12/12/2022] Open
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23
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Wu Y, Sun X, Xue X, Luo H, Yao B, Xie X, Su X. Overexpressing key component genes of the secretion pathway for enhanced secretion of an Aspergillus niger glucose oxidase in Trichoderma reesei. Enzyme Microb Technol 2017; 106:83-87. [DOI: 10.1016/j.enzmictec.2017.07.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/13/2017] [Accepted: 07/14/2017] [Indexed: 11/29/2022]
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24
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Lee CR, Sung BH, Lim KM, Kim MJ, Sohn MJ, Bae JH, Sohn JH. Co-fermentation using Recombinant Saccharomyces cerevisiae Yeast Strains Hyper-secreting Different Cellulases for the Production of Cellulosic Bioethanol. Sci Rep 2017; 7:4428. [PMID: 28667330 PMCID: PMC5493647 DOI: 10.1038/s41598-017-04815-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/19/2017] [Indexed: 01/02/2023] Open
Abstract
To realize the economical production of ethanol and other bio-based chemicals from lignocellulosic biomass by consolidated bioprocessing (CBP), various cellulases from different sources were tested to improve the level of cellulase secretion in the yeast Saccharomyces cerevisiae by screening an optimal translational fusion partner (TFP) as both a secretion signal and fusion partner. Among them, four indispensable cellulases for cellulose hydrolysis, including Chaetomium thermophilum cellobiohydrolase (CtCBH1), Chrysosporium lucknowense cellobiohydrolase (ClCBH2), Trichoderma reesei endoglucanase (TrEGL2), and Saccharomycopsis fibuligera β-glucosidase (SfBGL1), were identified to be highly secreted in active form in yeast. Despite variability in the enzyme levels produced, each recombinant yeast could secrete approximately 0.6–2.0 g/L of cellulases into the fermentation broth. The synergistic effect of the mixed culture of the four strains expressing the essential cellulases with the insoluble substrate Avicel and several types of cellulosic biomass was demonstrated to be effective. Co-fermentation of these yeast strains produced approximately 14 g/L ethanol from the pre-treated rice straw containing 35 g/L glucan with 3-fold higher productivity than that of wild type yeast using a reduced amount of commercial cellulases. This process will contribute to the cost-effective production of bioenergy such as bioethanol and biochemicals from cellulosic biomass.
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Affiliation(s)
- Cho-Ryong Lee
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Bong Hyun Sung
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Kwang-Mook Lim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Mi-Jin Kim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Min Jeong Sohn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jung-Hoon Bae
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jung-Hoon Sohn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea. .,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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25
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Wang G, Huang M, Nielsen J. Exploring the potential of Saccharomyces cerevisiae for biopharmaceutical protein production. Curr Opin Biotechnol 2017; 48:77-84. [PMID: 28410475 DOI: 10.1016/j.copbio.2017.03.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 02/19/2017] [Accepted: 03/15/2017] [Indexed: 02/06/2023]
Abstract
Production of recombinant proteins by yeast plays a vital role in the biopharmaceutical industry. It is therefore desirable to develop yeast platform strains for over-production of various biopharmaceutical proteins, but this requires fundamental knowledge of the cellular machinery, especially the protein secretory pathway. Integrated analyses of multi-omics datasets can provide comprehensive understanding of cellular function, and can enable systems biology-driven and mathematical model-guided strain engineering. Rational engineering and introduction of trackable genetic modifications using synthetic biology tools, coupled with high-throughput screening are, however, also efficient approaches to relieve bottlenecks hindering high-level protein production. Here we review advances in systems biology and metabolic engineering of yeast for improving recombinant protein production.
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Affiliation(s)
- Guokun Wang
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296 Gothenburg, Sweden
| | - Mingtao Huang
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2970 Hørsholm, Denmark.
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Choo JH, Hong CP, Lim JY, Seo JA, Kim YS, Lee DW, Park SG, Lee GW, Carroll E, Lee YW, Kang HA. Whole-genome de novo sequencing, combined with RNA-Seq analysis, reveals unique genome and physiological features of the amylolytic yeast Saccharomycopsis fibuligera and its interspecies hybrid. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:246. [PMID: 27872659 PMCID: PMC5106798 DOI: 10.1186/s13068-016-0653-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/22/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Genomic studies on fungal species with hydrolytic activity have gained increased attention due to their great biotechnological potential for biomass-based biofuel production. The amylolytic yeast Saccharomycopsis fibuligera has served as a good source of enzymes and genes involved in saccharification. Despite its long history of use in food fermentation and bioethanol production, very little is known about the basic physiology and genomic features of S. fibuligera. RESULTS We performed whole-genome (WG) de novo sequencing and complete assembly of S. fibuligera KJJ81 and KPH12, two isolates from wheat-based Nuruk in Korea. Intriguingly, the KJJ81 genome (~38 Mb) was revealed as a hybrid between the KPH12 genome (~18 Mb) and another unidentified genome sharing 88.1% nucleotide identity with the KPH12 genome. The seven chromosome pairs of KJJ81 subgenomes exhibit highly conserved synteny, indicating a very recent hybridization event. The phylogeny inferred from WG comparisons showed an early divergence of S. fibuligera before the separation of the CTG and Saccharomycetaceae clades in the subphylum Saccharomycotina. Reconstructed carbon and sulfur metabolic pathways, coupled with RNA-Seq analysis, suggested a marginal Crabtree effect under high glucose and activation of sulfur metabolism toward methionine biosynthesis under sulfur limitation in this yeast. Notably, the lack of sulfate assimilation genes in the S. fibuligera genome reflects a unique phenotype for Saccharomycopsis clades as natural sulfur auxotrophs. Extended gene families, including novel genes involved in saccharification and proteolysis, were identified. Moreover, comparative genome analysis of S. fibuligera ATCC 36309, an isolate from chalky rye bread in Germany, revealed that an interchromosomal translocation occurred in the KPH12 genome before the generation of the KJJ81 hybrid genome. CONCLUSIONS The completely sequenced S. fibuligera genome with high-quality annotation and RNA-Seq analysis establishes an important foundation for functional inference of S. fibuligera in the degradation of fermentation mash. The gene inventory facilitates the discovery of new genes applicable to the production of novel valuable enzymes and chemicals. Moreover, as the first gapless genome assembly in the genus Saccharomycopsis including members with desirable traits for bioconversion, the unique genomic features of S. fibuligera and its hybrid will provide in-depth insights into fungal genome dynamics as evolutionary adaptation.
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Affiliation(s)
- Jin Ho Choo
- Department of Life Science, Chung-Ang University, Seoul, 06974 South Korea
| | - Chang Pyo Hong
- Theragen Bio Institute, TheragenEtex, Suwon, 16229 South Korea
| | - Jae Yun Lim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 South Korea
| | - Jeong-Ah Seo
- School of Systems Biomedical Science, Soongsil University, Seoul, 06978 South Korea
| | - Young-Suk Kim
- Department of Food Science and Engineering, Ewha Womans University, Seoul, 03760 South Korea
| | - Dong Wook Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974 South Korea
| | - Sin-Gi Park
- Theragen Bio Institute, TheragenEtex, Suwon, 16229 South Korea
| | - Gir Won Lee
- Theragen Bio Institute, TheragenEtex, Suwon, 16229 South Korea
| | - Emily Carroll
- School of Systems Biomedical Science, Soongsil University, Seoul, 06978 South Korea
| | - Yin-Won Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 South Korea
| | - Hyun Ah Kang
- Department of Life Science, Chung-Ang University, Seoul, 06974 South Korea
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