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O’Riordan N, Jurić V, O’Neill SK, Roche AP, Young PW. A Yeast Modular Cloning (MoClo) Toolkit Expansion for Optimization of Heterologous Protein Secretion and Surface Display in Saccharomyces cerevisiae. ACS Synth Biol 2024; 13:1246-1258. [PMID: 38483353 PMCID: PMC11036508 DOI: 10.1021/acssynbio.3c00743] [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: 12/12/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 04/20/2024]
Abstract
Saccharomyces cerevisiae is an attractive host for the expression of secreted proteins in a biotechnology context. Unfortunately, many heterologous proteins fail to enter, or efficiently progress through, the secretory pathway, resulting in poor yields. Similarly, yeast surface display has become a widely used technique in protein engineering but achieving sufficient levels of surface expression of recombinant proteins is often challenging. Signal peptides (SPs) and translational fusion partners (TFPs) can be used to direct heterologous proteins through the yeast secretory pathway, however, selection of the optimal secretion promoting sequence is largely a process of trial and error. The yeast modular cloning (MoClo) toolkit utilizes type IIS restriction enzymes to facilitate an efficient assembly of expression vectors from standardized parts. We have expanded this toolkit to enable the efficient incorporation of a panel of 16 well-characterized SPs and TFPs and five surface display anchor proteins into S. cerevisiae expression cassettes. The secretion promoting signals are validated by using five different proteins of interest. Comparison of intracellular and secreted protein levels reveals the optimal secretion promoting sequence for each individual protein. Large, protein of interest-specific variations in secretion efficiency are observed. SP sequences are also used with the five surface display anchors, and the combination of SP and anchor protein proves critical for efficient surface display. These observations highlight the value of the described panel of MoClo compatible parts to allow facile screening of SPs and TFPs and anchor proteins for optimal secretion and/or surface display of a given protein of interest in S. cerevisiae.
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Affiliation(s)
- Nicola
M. O’Riordan
- School
of Biochemistry and Cell Biology, University
College Cork, Cork T12 YN60, Ireland
| | - Vanja Jurić
- School
of Biochemistry and Cell Biology, University
College Cork, Cork T12 YN60, Ireland
- AMBER
Centre, Environmental Research Institute, University College Cork, Cork T23 XE10, Ireland
| | - Sarah K. O’Neill
- School
of Biochemistry and Cell Biology, University
College Cork, Cork T12 YN60, Ireland
| | - Aoife P. Roche
- School
of Biochemistry and Cell Biology, University
College Cork, Cork T12 YN60, Ireland
| | - Paul W. Young
- School
of Biochemistry and Cell Biology, University
College Cork, Cork T12 YN60, Ireland
- AMBER
Centre, Environmental Research Institute, University College Cork, Cork T23 XE10, Ireland
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2
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Minnaar LS, Kruger F, Fortuin J, Hoffmeester LJ, den Haan R. Engineering Saccharomyces cerevisiae for application in integrated bioprocessing biorefineries. Curr Opin Biotechnol 2024; 85:103030. [PMID: 38091873 DOI: 10.1016/j.copbio.2023.103030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 02/09/2024]
Abstract
After decades of research and development, no organism - natural or engineered - has been described that can produce commodity products through direct microbial conversion to meet industry demands in terms of rates and yields. Variation in lignocellulosic biomass (LCB) feedstocks, the lack of a widely applicable pretreatment method, and the limited economic value of energy products further complicates second-generation biofuel production. Nevertheless, the emergence of advanced genomic editing tools and a more comprehensive understanding of yeast metabolic systems offer promising avenues for the creation of yeast strains tailored to LCB biorefineries. Here, we discuss recent advances toward developing yeast strains that could convert different LCB fractions into a series of economically viable commodity products in a biorefinery.
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Affiliation(s)
- Letitia S Minnaar
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Francois Kruger
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Jordan Fortuin
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Lazzlo J Hoffmeester
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa.
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3
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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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4
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Zhao M, Ma J, Zhang L, Qi H. Engineering strategies for enhanced heterologous protein production by Saccharomyces cerevisiae. Microb Cell Fact 2024; 23:32. [PMID: 38247006 PMCID: PMC10801990 DOI: 10.1186/s12934-024-02299-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Microbial proteins are promising substitutes for animal- and plant-based proteins. S. cerevisiae, a generally recognized as safe (GRAS) microorganism, has been frequently employed to generate heterologous proteins. However, constructing a universal yeast chassis for efficient protein production is still a challenge due to the varying properties of different proteins. With progress in synthetic biology, a multitude of molecular biology tools and metabolic engineering strategies have been employed to alleviate these issues. This review first analyses the advantages of protein production by S. cerevisiae. The most recent advances in improving heterologous protein yield are summarized and discussed in terms of protein hyperexpression systems, protein secretion engineering, glycosylation pathway engineering and systems metabolic engineering. Furthermore, the prospects for efficient and sustainable heterologous protein production by S. cerevisiae are also provided.
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Affiliation(s)
- Meirong Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China
| | - Jianfan Ma
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China
| | - Lei Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China
| | - Haishan Qi
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China.
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5
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Aza P, Camarero S. Fungal Laccases: Fundamentals, Engineering and Classification Update. Biomolecules 2023; 13:1716. [PMID: 38136587 PMCID: PMC10741624 DOI: 10.3390/biom13121716] [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: 10/27/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Multicopper oxidases (MCOs) share a common catalytic mechanism of activation by oxygen and cupredoxin-like folding, along with some common structural determinants. Laccases constitute the largest group of MCOs, with fungal laccases having the greatest biotechnological applicability due to their superior ability to oxidize a wide range of aromatic compounds and lignin, which is enhanced in the presence of redox mediators. The adaptation of these versatile enzymes to specific application processes can be achieved through the directed evolution of the recombinant enzymes. On the other hand, their substrate versatility and the low sequence homology among laccases make their exact classification difficult. Many of the ever-increasing amounts of MCO entries from fungal genomes are automatically (and often wrongly) annotated as laccases. In a recent comparative genomic study of 52 basidiomycete fungi, MCO classification was revised based on their phylogeny. The enzymes clustered according to common structural motifs and theoretical activities, revealing three novel groups of laccase-like enzymes. This review provides an overview of the structure, catalytic activity, and oxidative mechanism of fungal laccases and how their biotechnological potential as biocatalysts in industry can be greatly enhanced by protein engineering. Finally, recent information on newly identified MCOs with laccase-like activity is included.
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Affiliation(s)
| | - Susana Camarero
- Margarita Salas Center for Biological Research, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain;
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Durmusoglu D, Al'Abri I, Li Z, Islam Williams T, Collins LB, Martínez JL, Crook N. Improving therapeutic protein secretion in the probiotic yeast Saccharomyces boulardii using a multifactorial engineering approach. Microb Cell Fact 2023; 22:109. [PMID: 37287064 PMCID: PMC10245609 DOI: 10.1186/s12934-023-02117-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/20/2023] [Indexed: 06/09/2023] Open
Abstract
The probiotic yeast Saccharomyces boulardii (Sb) is a promising chassis to deliver therapeutic proteins to the gut due to Sb's innate therapeutic properties, resistance to phage and antibiotics, and high protein secretion capacity. To maintain therapeutic efficacy in the context of challenges such as washout, low rates of diffusion, weak target binding, and/or high rates of proteolysis, it is desirable to engineer Sb strains with enhanced levels of protein secretion. In this work, we explored genetic modifications in both cis- (i.e. to the expression cassette of the secreted protein) and trans- (i.e. to the Sb genome) that enhance Sb's ability to secrete proteins, taking a Clostridioides difficile Toxin A neutralizing peptide (NPA) as our model therapeutic. First, by modulating the copy number of the NPA expression cassette, we found NPA concentrations in the supernatant could be varied by sixfold (76-458 mg/L) in microbioreactor fermentations. In the context of high NPA copy number, we found a previously-developed collection of native and synthetic secretion signals could further tune NPA secretion between 121 and 463 mg/L. Then, guided by prior knowledge of S. cerevisiae's secretion mechanisms, we generated a library of homozygous single gene deletion strains, the most productive of which achieved 2297 mg/L secretory production of NPA. We then expanded on this library by performing combinatorial gene deletions, supplemented by proteomics experiments. We ultimately constructed a quadruple protease-deficient Sb strain that produces 5045 mg/L secretory NPA, an improvement of > tenfold over wild-type Sb. Overall, this work systematically explores a broad collection of engineering strategies to improve protein secretion in Sb and highlights the ability of proteomics to highlight under-explored mediators of this process. In doing so, we created a set of probiotic strains that are capable of delivering a wide range of protein titers and therefore furthers the ability of Sb to deliver therapeutics to the gut and other settings to which it is adapted.
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Affiliation(s)
- Deniz Durmusoglu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Ibrahim Al'Abri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Zidan Li
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Taufika Islam Williams
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC, USA
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Leonard B Collins
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC, USA
| | - José L Martínez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
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7
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Karaoğlan M. Alternative secretory signal sequences for recombinant protein production in Pichia pastoris. Enzyme Microb Technol 2023; 168:110256. [PMID: 37196384 DOI: 10.1016/j.enzmictec.2023.110256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
Extracellular protein production is primarily preferred to facilitate the downstream processes in recombinant protein production. Secretion of recombinant proteins is mediated by the processing of signal peptides in their N-terminal portion by the secretory mechanism of host expression systems. These molecular elements involved in secretion are functionally interchangeable between different species and secretion sequence screening is one of the widely used approaches to improve extracellular protein production. In this study, α-mating and protein internal repeats (PIR) secretion sequences isolated from different yeasts (Kluyveromyces lactis, Kluyveromyces marxianus and Hansenula polymorpha) were tested in Pichia pastoris for the production of two different proteins (α-amylase and xylanase) and compared with the well-known secretory signals, S. cerevisiae α-mating factor (Sc-MF) and P. pastoris protein internal repeats PIR (PpPIR). The results obtained showed the potential of signal sequences tested. Among the tested peptides, the highest yields were achieved with H. polymorpha protein internal repeats (HpPIR) and K. lactis α-mating factor (Kl-MF) for xylanase and K. marxianus protein internal repeats (KmPIR) and K. lactis α-mating factor (Kl-MF) for amylase. In further studies, these sequences can be evaluated as alternatives in the production of different proteins in P. pastoris and in the production of recombinant proteins in different expression systems.
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Affiliation(s)
- Mert Karaoğlan
- Department of Food Engineering, Erzincan Binali Yıldırım University, Erzincan, Türkiye.
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8
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Jin Y, Yang N, Teng D, Hao Y, Mao R, Wang J. Molecular Modification of Kex2 P1' Site Enhances Expression and Druggability of Fungal Defensin. Antibiotics (Basel) 2023; 12:antibiotics12040786. [PMID: 37107149 PMCID: PMC10135057 DOI: 10.3390/antibiotics12040786] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Pichia pastoris is the widely used expression system for producing recombinant secretory proteins. It is known that Kex2 protease plays a vital role in the process of protein secretion, in which the P1' site affects its cleavage efficiency. To enhance the expression level of fungal defensin-derived peptide NZ2114, this work attempts to optimize the P1' site of Kex2 by replacing it with 20 amino acids in turn. The results showed that when the amino acid of the P1' site was changed to Phe (F), the yield of target peptide significantly increased from 2.39 g/L to 4.81 g/L. Additionally, the novel peptide F-NZ2114 (short for FNZ) showed strong antimicrobial activity against Gram-positive (G+) bacteria, especially for Staphylococcus aureus and Streptococcus agalactiae (MIC: 4-8 μg/mL). The FNZ was very stable and retained high activity in various conditions; in addition, a low cytotoxicity and no hemolysis were observed even at a high concentration of 128 μg/mL, and a longer postantibiotic effect was reached. The above results indicate that this engineering strategy provided a feasible optimization scheme for enhancing the expression level and druggability of this antimicrobial peptide from fungal defensin and other similar targets by this updated recombinant yeast.
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Affiliation(s)
- Yanjie Jin
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Na Yang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Da Teng
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Ya Hao
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Ruoyu Mao
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Jianhua Wang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
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Xue S, Liu X, Pan Y, Xiao C, Feng Y, Zheng L, Zhao M, Huang M. Comprehensive Analysis of Signal Peptides in Saccharomyces cerevisiae Reveals Features for Efficient Secretion. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2203433. [PMID: 36478443 PMCID: PMC9839866 DOI: 10.1002/advs.202203433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/10/2022] [Indexed: 05/30/2023]
Abstract
Signal peptides (SPs) are N-terminus sequences on the nascent polypeptide for protein export or localization delivery, which are essential for maintaining cell function. SPs are also employed as a key element for industrial production of secreted recombinant proteins. Yet, detailed information and rules about SPs and their cellular interactions are still not well understood. Here, systematic bioinformatics analysis and secretion capacity measurement of genome-wide SPs from the model organism Saccharomyces cerevisiae is performed. Several key features of SPs, including region properties, consensus motifs, evolutionary relationships, codon bias, e.g., are successfully revealed. Diverse cell metabolism can be trigged by using different SPs for heterologous protein secretion. Influences on SPs with different properties by chaperones can cause different secretory efficiencies. Protein secretion by the SP NCW2 in SEC72 deletion strain is 10 times than the control. These findings provide insights into the properties and functions of SPs and contribute to both fundamental research and industrial application.
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Affiliation(s)
- Songlyu Xue
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Xiufang Liu
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Yuyang Pan
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Chufan Xiao
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Yunzi Feng
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Lin Zheng
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Mouming Zhao
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Mingtao Huang
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
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Expression of a Salt-Tolerant Pseudolysin in Yeast for Efficient Protein Hydrolysis under High-Salt Conditions. Biomolecules 2022; 13:biom13010083. [PMID: 36671468 PMCID: PMC9855795 DOI: 10.3390/biom13010083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/30/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
Protease biocatalysis in a high-salt environment is very attractive for applications in the detergent industry, the production of diagnostic kits, and traditional food fermentation. However, high-salt conditions can reduce protease activity or even inactivate enzymes. Herein, in order to explore new protease sources, we expressed a salt-tolerant pseudolysin of Pseudomonas aeruginosa SWJSS3 isolated from deep-sea mud in Saccharomyces cerevisiae. After optimizing the concentration of ion cofactors in yeast peptone dextrose (YPD) medium, the proteolytic activity in the supernatant was 2.41 times more than that in the control group when supplemented with 5 mM CaCl2 and 0.4 mM ZnCl2. The extracellular proteolytic activity of pseudolysin reached 258.95 U/mL with optimized expression cassettes. In addition, the S. cerevisiae expression system increased the salt tolerance of pseudolysin to sodium chloride (NaCl)and sodium dodecyl sulfate (SDS) and the recombinant pseudolysin retained 15.19% activity when stored in 3 M NaCl for 7 days. The recombinant pseudolysin was able to efficiently degrade the β-conglycinin from low-denatured soy protein isolates and glycinin from high-denatured soy protein isolates under high temperatures (60 °C) and high-salt (3 M NaCl) conditions. Our study provides a salt-tolerant recombinant protease with promising applications in protein hydrolysis under high-salt conditions.
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Rodríguez-Escribano D, Pliego-Magán R, de Salas F, Aza P, Gentili P, Ihalainen P, Levée T, Meyer V, Petit-Conil M, Tapin-Lingua S, Lecourt M, Camarero S. Tailor-made alkaliphilic and thermostable fungal laccases for industrial wood processing. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:149. [PMID: 36581887 PMCID: PMC9798632 DOI: 10.1186/s13068-022-02247-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND During the kraft process to obtain cellulosic pulp from wood, most of the lignin is removed by high-temperature alkaline cooking, released in the black liquors and usually incinerated for energy. However, kraft lignins are a valuable source of phenolic compounds that can be valorized in new bio-based products. The aim of this work is to develop laccases capable of working under the extreme conditions of high temperature and pH, typical of the industrial conversion of wood into kraft pulp and fibreboard, in order to provide extremophilic biocatalysts for depolymerising kraft lignin, and enzyme-assisted technologies for kraft pulp and fibreboard production. RESULTS Through systematic enzyme engineering, combining enzyme-directed evolution and rational design, we changed the optimal pH of the laccase for oxidation of lignin phenols from acidic to basic, enhanced the catalytic activity at alkaline pH and increased the thermal tolerance of the enzyme by accumulating up to eight mutations in the protein sequence. The extremophilic laccase variants show maximum activity at 70 °C and oxidize kraft lignin at pH 10. Their integration into industrial-type processes saves energy and chemicals. As a pre-bleaching stage, the enzymes promote kraft pulp bleachability and significantly reduce the need for chlorine dioxide compared to the industrial sequence. Their application in wood chips during fibreboard production, facilitates the defibering stage, with less energy required. CONCLUSIONS A set of new alkaliphilic and thermophilic fungal laccases has been developed to operate under the extreme conditions of high temperature and pH typical of industrial wood conversion processes. For the first time basidiomycete laccases of high-redox potential show activity on lignin-derived phenols and polymeric lignin at pH 10. Considering the extreme conditions of current industrial processes for kraft pulp and fibreboard production, the new tailor-made laccases constitute a step forward towards turning kraft pulp mills into biorefineries. Their use as biocatalysts in the wood conversion sector is expected to support the development of more environmentally sound and efficient processes, and more sustainable products.
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Affiliation(s)
| | - Rocío Pliego-Magán
- Centro de Investigaciones Biológicas Margarita Salas, CSIC. Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Felipe de Salas
- Centro de Investigaciones Biológicas Margarita Salas, CSIC. Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Pablo Aza
- Centro de Investigaciones Biológicas Margarita Salas, CSIC. Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Patrizia Gentili
- Sapienza Università Di Roma, Piazzale Aldo Moro, 5, 00185 Rome, RM Italy
| | | | - Thomas Levée
- MetGen Oy, Rakentajantie 26, 20780 Kaarina, Finland
| | - Valérie Meyer
- Centre Technique du Papier (CTP), Domaine Universitaire, 38044 Grenoble Cedex 9, France
| | - Michel Petit-Conil
- Centre Technique du Papier (CTP), Domaine Universitaire, 38044 Grenoble Cedex 9, France
| | | | - Michael Lecourt
- FCBA Institut Technologique, 341 Rue de La Papeterie, 38610 Gières, France
| | - Susana Camarero
- Centro de Investigaciones Biológicas Margarita Salas, CSIC. Ramiro de Maeztu 9, 28040 Madrid, Spain
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12
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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: 0] [Impact Index Per Article: 0] [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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Feng MW, Delneri D, Millar CB, O'Keefe RT. Eisosome disruption by noncoding RNA deletion increases protein secretion in yeast. PNAS NEXUS 2022; 1:pgac241. [PMID: 36712349 PMCID: PMC9802208 DOI: 10.1093/pnasnexus/pgac241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
Noncoding RNAs (ncRNAs) regulate many aspects of gene expression. We investigated how ncRNAs affected protein secretion in yeast by large-scale screening for improved endogenous invertase secretion in ncRNA deletion strains with deletion of stable unannotated transcripts (SUTs), cryptic unstable transcripts (CUTs), tRNAs, or snRNAs. We identified three candidate ncRNAs, SUT418, SUT390, and SUT125, that improved endogenous invertase secretion when deleted. As SUTs can affect expression of nearby genes, we quantified adjacent gene transcription and found that the PIL1 gene was down-regulated in the SUT125 deletion strain. Pil1 is a core component of eisosomes, nonmobile invaginations found throughout the plasma membrane. PIL1 knockout alone, or in combination with eisosome components LSP1 or SUR7, resulted in further increased secretion of invertase. Secretion of heterologous GFP was also increased upon PIL1 deletion, but this increase was signal sequence dependent. To reveal the potential for increased biopharmaceutical production, secretion of monoclonal antibody Pexelizumab scFv peptide was increased by PIL1 deletion. Global analysis of secreted proteins revealed that approximately 20% of secreted proteins, especially serine-enriched secreted proteins, including invertase, were increased upon eisosome disruption. Eisosomes are enriched with APC transporters and sphingolipids, which are essential components for secretory vesicle formation and protein sorting. Sphingolipid and serine biosynthesis pathways were up-regulated upon PIL1 deletion. We propose that increased secretion of endogenous and heterologous proteins upon PIL1 deletion resulted from sphingolipid redistribution in the plasma membrane and up-regulated sphingolipid biosynthesis. Overall, a new pathway to improve protein secretion in yeast via eisosome disruption has been identified.
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Affiliation(s)
- Matthew Wenjie Feng
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Daniela Delneri
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK,Manchester Institute of Biotechnology, Faculty of Biology Medicine and Health, The University of Manchester, 131 Princess street, Manchester, M1 7DN, UK
| | - Catherine B Millar
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
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Ito Y, Ishigami M, Hashiba N, Nakamura Y, Terai G, Hasunuma T, Ishii J, Kondo A. Avoiding entry into intracellular protein degradation pathways by signal mutations increases protein secretion in Pichia pastoris. Microb Biotechnol 2022; 15:2364-2378. [PMID: 35656803 PMCID: PMC9437885 DOI: 10.1111/1751-7915.14061] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 03/23/2022] [Accepted: 03/31/2022] [Indexed: 12/02/2022] Open
Abstract
In our previous study, we serendipitously discovered that protein secretion in the methylotrophic yeast Pichia pastoris is enhanced by a mutation (V50A) in the mating factor alpha (MFα) prepro‐leader signal derived from Saccharomyces cerevisiae. In the present study, we investigated 20 single‐amino‐acid substitutions, including V50A, located within the MFα signal peptide, indicating that V50A and several single mutations alone provided significant increase in production of the secreted proteins. In addition to hydrophobicity index analysis, both an unfolded protein response (UPR) biosensor analysis and a microscopic observation showed a clear difference on the levels of UPR induction and mis‐sorting of secretory protein into vacuoles among the wild‐type and mutated MFα signal peptides. This work demonstrates the importance of avoiding entry of secretory proteins into the intracellular protein degradation pathways, an observation that is expected to contribute to the engineering of strains with increased production of recombinant secreted proteins.
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Affiliation(s)
- Yoichiro Ito
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Misa Ishigami
- Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe, Japan
| | - Noriko Hashiba
- Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe, Japan
| | - Yasuyuki Nakamura
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Goro Terai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tomohisa Hasunuma
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Jun Ishii
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan.,Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
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15
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Sharma J, Kumar V, Prasad R, Gaur NA. Engineering of Saccharomyces cerevisiae as a consolidated bioprocessing host to produce cellulosic ethanol: Recent advancements and current challenges. Biotechnol Adv 2022; 56:107925. [DOI: 10.1016/j.biotechadv.2022.107925] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/24/2022] [Accepted: 02/06/2022] [Indexed: 01/01/2023]
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16
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Teymennet-Ramírez KV, Martínez-Morales F, Trejo-Hernández MR. Yeast Surface Display System: Strategies for Improvement and Biotechnological Applications. Front Bioeng Biotechnol 2022; 9:794742. [PMID: 35083204 PMCID: PMC8784408 DOI: 10.3389/fbioe.2021.794742] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/20/2021] [Indexed: 12/26/2022] Open
Abstract
Yeast surface display (YSD) is a “whole-cell” platform used for the heterologous expression of proteins immobilized on the yeast’s cell surface. YSD combines the advantages eukaryotic systems offer such as post-translational modifications, correct folding and glycosylation of proteins, with ease of cell culturing and genetic manipulation, and allows of protein immobilization and recovery. Additionally, proteins displayed on the surface of yeast cells may show enhanced stability against changes in temperature, pH, organic solvents, and proteases. This platform has been used to study protein-protein interactions, antibody design and protein engineering. Other applications for YSD include library screening, whole-proteome studies, bioremediation, vaccine and antibiotics development, production of biosensors, ethanol production and biocatalysis. YSD is a promising technology that is not yet optimized for biotechnological applications. This mini review is focused on recent strategies to improve the efficiency and selection of displayed proteins. YSD is presented as a cutting-edge technology for the vectorial expression of proteins and peptides. Finally, recent biotechnological applications are summarized. The different approaches described herein could allow for a better strategy cascade for increasing protein/peptide interaction and production.
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Affiliation(s)
- Karla V Teymennet-Ramírez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mėxico
| | - Fernando Martínez-Morales
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mėxico
| | - María R Trejo-Hernández
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mėxico
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