1
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Ko H, Park YC. Mass production and characterization of an endoglucanase from Coleoptera insect (Monochamus saltuarius) in yeast Kluyveromyceslactis. Protein Expr Purif 2024; 223:106540. [PMID: 38971213 DOI: 10.1016/j.pep.2024.106540] [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: 05/06/2024] [Revised: 06/20/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
To harness the diverse industrial applications of cellulase, including its use in the food, pulp, textile, agriculture, and biofuel sectors, this study focused on the high-yield production of a bioactive insect-derived endoglucanase, Monochamus saltuarius glycoside hydrolase family 5 (MsGHF5). MsGHF5 was introduced into the genome of Kluyveromyces lactis to maintain expression stability, and mass production of the enzyme was induced using fed-batch fermentation. After 40 h of cultivation, recombinant MsGHF5 was successfully produced in the culture broth, with a yield of 29,000 U/L, upon galactose induction. The optimal conditions for the activity of purified MsGHF5 were determined to be a pH of 5 and a temperature of 35 °C, with the presence of ferrous ions enhancing the enzymatic activity by up to 1.5-fold. Notably, the activity of MsGHF5 produced in K. lactis was significantly higher than that produced in Escherichia coli, suggesting that glycosylation is crucial for the functional performance of the enzyme. This study highlights the potential use of K. lactis as a host for the production of bioactive MsGHF5, thus paving the way for its application in various industrial sectors.
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Affiliation(s)
- Hyunjun Ko
- Department of Forest Biomaterials Engineering, College of Forest and Environmental Sciences, Kangwon National University, 1 Gangwondaehak-gil, Chuncheon, 24341, Republic of Korea.
| | - Yong Chul Park
- Department of Bio-Health Technology, College of Biomedical Science, Kangwon National University, 1 Gangwondaehak-gil, Chuncheon, 24341, Republic of Korea.
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2
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Zhang Y, Fu R, Zhu C, Yuwen W, Zhang J, Duan Z, Fan D. Preparation of recombinant type I collagen (PF-I-80) and its functional characterization and biomedical applications in wound healing. Int J Biol Macromol 2024; 282:136679. [PMID: 39437939 DOI: 10.1016/j.ijbiomac.2024.136679] [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: 04/22/2024] [Revised: 10/15/2024] [Accepted: 10/16/2024] [Indexed: 10/25/2024]
Abstract
This study evaluates the potential applications of recombinant PF-I-80 protein in regenerative medicine and the treatment of inflammatory diseases, focusing on its effects on cell migration, differentiation, and anti-inflammatory properties. Various in vitro assays were conducted, including scratch assays, Transwell experiments, RT-PCR and Western Blot to analyze gene and protein expression related to differentiation and inflammation, and immunofluorescence staining to observe cellular changes. The results indicated that PF-I-80 significantly promoted cell migration, highlighting its potential in tissue repair and regeneration. It also enhanced cell differentiation, demonstrating its applicability in tissue repair, and showed significant anti-inflammatory effects by reducing the expression of pro-inflammatory cytokines. In animal models, PF-I-80 notably reduced levels of inflammatory factors IL-1β and TNF-α, shortened the inflammatory phase, and accelerated wound healing. Additionally, PF-I-80 increased FGF-2 levels, which promoted the proliferation of endothelial and fibroblast cells and enhanced collagen synthesis. These in vitro and in vivo findings position PF-I-80 as a promising biomaterial for applications in regenerative medicine and inflammatory disease treatment.
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Affiliation(s)
- Yan Zhang
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China; Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
| | - Rongzhan Fu
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China; Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
| | - Chenhui Zhu
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China; Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
| | - Weigang Yuwen
- Taibai Campus, Northwest University, Xi'an 710069, China
| | - Jiangrui Zhang
- Taibai Campus, Northwest University, Xi'an 710069, China
| | - Zhiguang Duan
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China; Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China.
| | - Daidi Fan
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China; Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China.
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3
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Xie N. Application of Protein Expression in Mycoplasma Study. SCIENTIFICA 2024; 2024:4142663. [PMID: 39435316 PMCID: PMC11493480 DOI: 10.1155/2024/4142663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 09/28/2024] [Indexed: 10/23/2024]
Abstract
Mycoplasma is a kind of pathogenic microorganism, and its survival and replication need to be parasitic inside the host cell. Therefore, studies on the metabolic pathway, protein composition, and biological characteristics of Mycoplasma require the use of protein expression techniques. In this paper, the application of protein expression in Mycoplasma research was reviewed, including commonly used protein expression systems, optimization strategy of protein expression, protein omics analysis, and protein function research, and the future development direction has been prospected.
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Affiliation(s)
- Nian Xie
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton 3168, VIC, Australia
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4
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Wang H, Wen J, Ablimit N, Deng K, Wang W, Jiang W. Degradation of Natural Undaria pinnatifida into Unsaturated Guluronic Acid Oligosaccharides by a Single Alginate Lyase. Mar Drugs 2024; 22:453. [PMID: 39452861 PMCID: PMC11509462 DOI: 10.3390/md22100453] [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: 08/26/2024] [Revised: 09/24/2024] [Accepted: 09/26/2024] [Indexed: 10/26/2024] Open
Abstract
Here, we report on a bifunctional alginate lyase (Vnalg7) expressed in Pichia pastoris, which can degrade natural Undaria pinnatifida into unsaturated guluronic acid di- and trisaccharide without pretreatment. The enzyme activity of Vnalg7 (3620.00 U/mL-culture) was 15.81-fold higher than that of the original alg (228.90 U/mL-culture), following engineering modification. The degradation rate reached 52.75%, and reducing sugar reached 30.30 mg/mL after combining Vnalg7 (200.00 U/mL-culture) and 14% (w/v) U. pinnatifida for 6 h. Analysis of the action mode indicated that Vnalg7 could degrade many substrates to produce a variety of unsaturated alginate oligosaccharides (AOSs), and the minimal substrate was tetrasaccharide. Site-directed mutagenesis showed that Glu238, Glu241, Glu312, Arg236, His307, Lys414, and Tyr418 are essential catalytic sites, while Glu334, Glu344, and Asp311 play auxiliary roles. Mechanism analysis revealed the enzymatic degradation pattern of Vnalg7, which mainly recognizes and attacks the third glycosidic linkage from the reducing end of oligosaccharide substrate. Our findings provide a novel alginate lyase tool and a sustainable and commercial production strategy for value-added biomolecules using seaweeds.
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Affiliation(s)
| | | | | | | | | | - Wei Jiang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Yuan Ming Yuan West Road No. 2, Haidian District, Beijing 100193, China; (H.W.); (J.W.); (N.A.); (K.D.); (W.W.)
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5
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Nguyen L, Schmelzer B, Wilkinson S, Mattanovich D. From natural to synthetic: Promoter engineering in yeast expression systems. Biotechnol Adv 2024; 77:108446. [PMID: 39245291 DOI: 10.1016/j.biotechadv.2024.108446] [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: 07/12/2024] [Revised: 09/04/2024] [Accepted: 09/05/2024] [Indexed: 09/10/2024]
Abstract
Synthetic promoters are particularly relevant for application not only in yeast expression systems designed for high-level heterologous protein production but also in other applications such as metabolic engineering, cell biological research, and stage-specific gene expression control. By designing synthetic promoters, researcher can create customized expression systems tailored to specific needs, whether it is maximizing protein production or precisely controlling gene expression at different stages of a process. While recognizing the limitations of endogenous promoters, they also provide important information needed to design synthetic promoters. In this review, emphasis will be placed on some key approaches to identify endogenous, and to generate synthetic promoters in yeast expression systems. It shows the connection between endogenous and synthetic promoters, highlighting how their interplay contributes to promoter development. Furthermore, this review illustrates recent developments in biotechnological advancements and discusses how this field will evolve in order to develop custom-made promoters for diverse applications. This review offers detailed information, explores the transition from endogenous to synthetic promoters, and presents valuable perspectives on the next generation of promoter design strategies.
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Affiliation(s)
- Ly Nguyen
- BOKU University, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190 Vienna, Austria
| | - Bernhard Schmelzer
- BOKU University, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190 Vienna, Austria
| | | | - Diethard Mattanovich
- BOKU University, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria.
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6
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Suri A, Hu KKY, Younas T, Dumsday G, Haritos VS. Functionalizing Yeast Lipid Droplets as Versatile Biomaterials. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308463. [PMID: 38566530 DOI: 10.1002/smll.202308463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 01/02/2024] [Indexed: 04/04/2024]
Abstract
Lipid droplets (LD) are dynamic cellular organelles of ≈1 µm diameter in yeast where a neutral lipid core is surrounded by a phospholipid monolayer and attendant proteins. Beyond the storage of lipids, opportunities for LD engineering remain underdeveloped but they show excellent potential as new biomaterials. In this research, LD from yeast Saccharomyces cerevisiae is engineered to display mCherry fluorescent protein, Halotag ligand binding protein, plasma membrane binding v-SNARE protein, and carbonic anhydrase enzyme via linkage to oleosin, an LD anchoring protein. Each protein-oleosin fusion is coded via a single gene construct. The expressed fusion proteins are specifically displayed on LD and their functions can be assessed within cells by fluorescence confocal microscopy, TEM, and as isolated materials via AFM, flow cytometry, spectrophotometry, and by enzyme activity assay. LD isolated from the cell are shown to be robust and stabilize proteins anchored into them. These engineered LD function as reporters, bind specific ligands, guide LD and their attendant proteins into union with the plasma membrane, and catalyze reactions. Here, engineered LD functions are extended well beyond traditional lipid storage toward new material applications aided by a versatile oleosin platform anchored into LD and displaying linked proteins.
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Affiliation(s)
- Ankita Suri
- Department of Chemical and Biological Engineering, Monash University, Clayton, 3800, Australia
- CSIRO Black Mountain, 2-40 Clunies Ross Street, Acton, ACT, 2601, Australia
| | - Kevin K Y Hu
- Department of Chemical and Biological Engineering, Monash University, Clayton, 3800, Australia
| | - Tayyaba Younas
- Department of Chemical and Biological Engineering, Monash University, Clayton, 3800, Australia
| | - Geoff Dumsday
- CSIRO Clayton, Research Way, Clayton, Victoria, 3168, Australia
| | - Victoria S Haritos
- Department of Chemical and Biological Engineering, Monash University, Clayton, 3800, Australia
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7
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Murali SK, Mansell TJ. Next generation probiotics: Engineering live biotherapeutics. Biotechnol Adv 2024; 72:108336. [PMID: 38432422 DOI: 10.1016/j.biotechadv.2024.108336] [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: 09/16/2023] [Revised: 02/10/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
The population dynamics of the human microbiome have been associated with inflammatory bowel disease, cancer, obesity, autoimmune diseases, and many other human disease states. An emerging paradigm in treatment is the administration of live engineered organisms, also called next-generation probiotics. However, the efficacy of these microbial therapies can be limited by the organism's overall performance in the harsh and nutrient-limited environment of the gut. In this review, we summarize the current state of the art use of bacterial and yeast strains as probiotics, highlight the recent development of genetic tools for engineering new therapeutic functions in these organisms, and report on the latest therapeutic applications of engineered probiotics, including recent clinical trials. We also discuss the supplementation of prebiotics as a method of manipulating the microbiome and improving the overall performance of engineered live biotherapeutics.
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Affiliation(s)
- Sanjeeva Kumar Murali
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA.
| | - Thomas J Mansell
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA 50011, USA.
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8
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Deng H, Gu Q, Yu X, Zhou J, Liu X. Surface-displayed phenolic acid decarboxylase for increased vinylphenolic pyranoanthocyanins in blueberry wine. Curr Res Food Sci 2024; 8:100730. [PMID: 38623272 PMCID: PMC11016931 DOI: 10.1016/j.crfs.2024.100730] [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: 12/03/2023] [Revised: 03/25/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024] Open
Abstract
During the fruit wine production, phenolic acid decarboxylase (PAD) converts free hydroxycinnamic acid into 4-vinyl derivatives that can then react spontaneously with anthocyanins, generating more stable pyranoanthocyanins that are responsible for the color stability of fruit wine. Nevertheless, the low PAD activity in yeast under the winemaking conditions has largely limited the generation of 4-vinyl derivatives. To bridge this gap, we expressed PAD from Bacillus amyloliquefaciens in Pichia pastoris and surface-displayed it on Saccharomyces cerevisiae. As a result, S. cerevisiae surface-displayed PAD (SDPAD) exhibited an enhanced thermal stability and tolerance to acidic conditions. Fermentation experiments showed that SDPAD can significantly increase the content of vinylphenolic pyranoanthocyanins and thus maintain the color stability of blueberry wine. Our study demonstrated the feasibility of surface display technology for color stability enhancement during the production of blueberry wine, providing a new and effective solution to increase the content of vinylphenolic pyranoanthocyanins in the fruit-based wines.
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Affiliation(s)
- Huaili Deng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Qiuya Gu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Xiaobin Yu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Jianli Zhou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), School of Liquor and Food Engineering, Guizhou University, Guiyang, 550025, China
| | - Xiaobo Liu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing, 210094, China
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9
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Kjeldsen T, Andersen AS, Hubálek F, Johansson E, Kreiner FF, Schluckebier G, Kurtzhals P. Molecular engineering of insulin for recombinant expression in yeast. Trends Biotechnol 2024; 42:464-478. [PMID: 37880066 DOI: 10.1016/j.tibtech.2023.09.012] [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: 08/10/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023]
Abstract
Since the first administration of insulin to a person with diabetes in 1922, scientific contributions from academia and industry have improved insulin therapy and access. The pharmaceutical need for insulin is now more than 40 tons annually, half of which is produced by recombinant secretory expression in Saccharomyces cerevisiae. We discuss how, in this yeast species, adaptation of insulin precursors by removable structural elements is pivotal for efficient secretory expression. The technologies reviewed have been implemented at industrial scale and are seminal for the supply of human insulin and insulin analogues to people with diabetes now and in the future. Engineering of a target protein with removable structural elements may provide a general approach to yield optimisation.
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10
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Zhao L, Li L, Hu M, Fang Y, Dong N, Shan A. Heterologous expression of the novel dimeric antimicrobial peptide LIG in Pichia pastoris. J Biotechnol 2024; 381:19-26. [PMID: 38181981 DOI: 10.1016/j.jbiotec.2023.12.015] [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: 08/08/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024]
Abstract
The antimicrobial peptide (AMP) LI is a fusion product of antimicrobial peptide LL37 produced by human neutrophils and Indolicidin secreted by bovine neutrophils. LI retained the antimicrobial activity of the parental peptides and showed high cell selectivity. In this study, the flexible linker Gly-Ser-Gly (G-S-G) was used to ligate LI into dimeric LIG, and constructed the Pichia pastoris (P. pastoris) expression vector pPIC9K-6×His-3×FLAG-LIG. The total protein expression of P. pastoris GS115 reached the highest level (189.6 mg/L) after 96 h induction with 3 % methanol at the initial pH value of 7.0. Finally, 5.9 mg/L of recombinant LIG (rLIG) was obtained after enterokinase digestion and purification. The rLIG had high antimicrobial activity and low hemolytic activity. Compared with monomer LI, GSG linked dimeric LIG, which had no significant change in antimicrobial activity and had good salt ions stability. In this study, the dimeric antimicrobial peptide LIG was successfully expressed, which provided a new idea for the expression of AMPs in the P. pastoris expression system, and had important significance for the application of AMPs.
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Affiliation(s)
- Lu Zhao
- Laboratory of Molecular Nutrition and Immunity, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Ling Li
- Laboratory of Molecular Nutrition and Immunity, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Mingyang Hu
- Laboratory of Molecular Nutrition and Immunity, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Yuxin Fang
- Laboratory of Molecular Nutrition and Immunity, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Na Dong
- Laboratory of Molecular Nutrition and Immunity, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China.
| | - Anshan Shan
- Laboratory of Molecular Nutrition and Immunity, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
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11
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Khlebodarova TM, Bogacheva NV, Zadorozhny AV, Bryanskaya AV, Vasilieva AR, Chesnokov DO, Pavlova EI, Peltek SE. Komagataella phaffii as a Platform for Heterologous Expression of Enzymes Used for Industry. Microorganisms 2024; 12:346. [PMID: 38399750 PMCID: PMC10892927 DOI: 10.3390/microorganisms12020346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
In the 1980s, Escherichia coli was the preferred host for heterologous protein expression owing to its capacity for rapid growth in complex media; well-studied genetics; rapid and direct transformation with foreign DNA; and easily scalable fermentation. Despite the relative ease of use of E. coli for achieving the high expression of many recombinant proteins, for some proteins, e.g., membrane proteins or proteins of eukaryotic origin, this approach can be rather ineffective. Another microorganism long-used and popular as an expression system is baker's yeast, Saccharomyces cerevisiae. In spite of a number of obvious advantages of these yeasts as host cells, there are some limitations on their use as expression systems, for example, inefficient secretion, misfolding, hyperglycosylation, and aberrant proteolytic processing of proteins. Over the past decade, nontraditional yeast species have been adapted to the role of alternative hosts for the production of recombinant proteins, e.g., Komagataella phaffii, Yarrowia lipolytica, and Schizosaccharomyces pombe. These yeast species' several physiological characteristics (that are different from those of S. cerevisiae), such as faster growth on cheap carbon sources and higher secretion capacity, make them practical alternative hosts for biotechnological purposes. Currently, the K. phaffii-based expression system is one of the most popular for the production of heterologous proteins. Along with the low secretion of endogenous proteins, K. phaffii efficiently produces and secretes heterologous proteins in high yields, thereby reducing the cost of purifying the latter. This review will discuss practical approaches and technological solutions for the efficient expression of recombinant proteins in K. phaffii, mainly based on the example of enzymes used for the feed industry.
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Affiliation(s)
- Tamara M. Khlebodarova
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Natalia V. Bogacheva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Andrey V. Zadorozhny
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alla V. Bryanskaya
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Asya R. Vasilieva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Danil O. Chesnokov
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Elena I. Pavlova
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Sergey E. Peltek
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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12
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Pipiya SO, Kudzhaev AM, Mirzoeva NZ, Mokrushina YA, Ziganshin RH, Komlev AS, Petrova PE, Smirnov IV, Gabibov AG, Shamova OV, Terekhov SS. Bioengineering the Antimicrobial Activity of Yeast by Recombinant Thanatin Production. Antibiotics (Basel) 2023; 12:1719. [PMID: 38136753 PMCID: PMC10741026 DOI: 10.3390/antibiotics12121719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The global spread of antibiotic resistance marks the end of the era of conventional antibiotics. Mankind desires new molecular tools to fight pathogenic bacteria. In this regard, the development of new antimicrobials based on antimicrobial peptides (AMPs) is again of particular interest. AMPs have various mechanisms of action on bacterial cells. Moreover, AMPs have been reported to be efficient in preclinical studies, demonstrating a low level of resistance formation. Thanatin is a small, beta-hairpin antimicrobial peptide with a bacterial-specific mode of action, predetermining its low cytotoxicity toward eukaryotic cells. This makes thanatin an exceptional candidate for new antibiotic development. Here, a microorganism was bioengineered to produce an antimicrobial agent, providing novel opportunities in antibiotic research through the directed creation of biocontrol agents. The constitutive heterologous production of recombinant thanatin (rThan) in the yeast Pichia pastoris endows the latter with antibacterial properties. Optimized expression and purification conditions enable a high production level, yielding up to 20 mg/L of rThan from the culture medium. rThan shows a wide spectrum of activity against pathogenic bacteria, similarly to its chemically synthesized analogue. The designed approach provides new avenues for AMP engineering and creating live biocontrol agents to fight antibiotic resistance.
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Affiliation(s)
- Sofiya O. Pipiya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Arsen M. Kudzhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Nisso Z. Mirzoeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Yuliana A. Mokrushina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Alexey S. Komlev
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, Saint-Petersburg 197022, Russia; (A.S.K.); (P.E.P.); (O.V.S.)
| | - Polina E. Petrova
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, Saint-Petersburg 197022, Russia; (A.S.K.); (P.E.P.); (O.V.S.)
| | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
- Department of Chemistry, Lomonosov Mscow State University, Moscow 119991, Russia
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
- Department of Chemistry, Lomonosov Mscow State University, Moscow 119991, Russia
| | - Olga V. Shamova
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, Saint-Petersburg 197022, Russia; (A.S.K.); (P.E.P.); (O.V.S.)
- Department of Biochemistry, Saint Petersburg State University, Saint-Petersburg 199034, Russia
| | - Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
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13
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Luo H, Zhou T, Cao J, Gao L, Wang S, Gui Z, Shi Y, Xie F, Yang R. Utilization of lignocellulosic biomass by glycerol organosolv pretreatment for biobutanol production integrated with bioconversion of residual glycerol into value-added products. BIORESOURCE TECHNOLOGY 2023; 387:129661. [PMID: 37573976 DOI: 10.1016/j.biortech.2023.129661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/05/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
Glycerol organosolv pretreatment (GOP) is considered an efficient method to deconstruct lignocellulose for producing fermentable sugars. Herein, the liquid fraction containing glycerol after GOP was utilized for recycled pretreatment of corn stover (CS) for four cycles. Enzymatic yield of glucose after recycled pretreatment was enhanced by 2.4-3.5 folds compared with untreated CS. Meanwhile, residual glycerol was used as carbon source for cultivation of Pichia pastoris to obtain high cell-density, and a final titer of 1.3 g/L human lysozyme was produced by P. pastoris under low temperature methanol induction strategy. Additionally, the pretreated CS was mixed with cassava as fermentable substrates for butanol production by wild-type Clostridium acetobutylicum ATCC 824. Final butanol production of 13.9 g/L was obtained from mixed substrates (25%:75% of CS/cassava) at 10% solids loading by simultaneous saccharification and fermentation. Overall, integration of residual glycerol utilization and butanol production by microbial fermentation provided an efficient strategy for biorefinery.
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Affiliation(s)
- Hongzhen Luo
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Tairan Zhou
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Jin Cao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Lei Gao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Shijie Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Zheng Gui
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Yongjiang Shi
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Fang Xie
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Rongling Yang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
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14
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Song J, Fan J, Fan C, He N, Ye X, Cao M, Yuan J. A Layered Genetic Design Enables the Yeast Galactose Regulon to Respond to Cyanamide. ACS Synth Biol 2023; 12:2783-2788. [PMID: 37603344 DOI: 10.1021/acssynbio.3c00241] [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] [Indexed: 08/22/2023]
Abstract
The commonly used expression systems in Saccharomyces cerevisiae typically rely on either constitutive or galactose-regulated promoters. The lack of inducible systems in S. cerevisiae limits the precise temporal regulation of protein function and yeast metabolism. We herein repurposed the galactose-regulated system to make it respond to cyanamide. By using a cyanamide-inducible DDI2 promoter to control Gal4 expression in CEN.PK2-1C with Δgal80, a tight and graded cyanamide-inducible GAL system with an enhanced signal output was constructed. Subsequently, we demonstrated that the cyanamide-inducible GAL system was capable of tightly regulating the pentafunctional Aro1 protein to achieve conditional shikimate pathway activity. Taken together, the cyanamide-inducible GAL system could be implemented for both fundamental research and applied biotechnology.
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Affiliation(s)
- Jingya Song
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian 361102, China
| | - Jian Fan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian 361102, China
| | - Cong Fan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian 361102, China
| | - Nike He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian 361102, China
| | - Xixi Ye
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian 361102, China
| | - Mingfeng Cao
- College of Chemistry and Chemical Engineering, Xiamen University, Fujian 361005, China
| | - Jifeng Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian 361102, China
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15
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Ahn J, Yu JE, Kim H, Sung J, Han G, Sohn MH, Seong BL. AB 5-Type Toxin as a Pentameric Scaffold in Recombinant Vaccines against the Japanese Encephalitis Virus. Toxins (Basel) 2023; 15:425. [PMID: 37505694 PMCID: PMC10467048 DOI: 10.3390/toxins15070425] [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: 06/03/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/29/2023] Open
Abstract
Japanese encephalitis virus (JEV) is an enveloped icosahedral capsid virus with a prime neutralizing epitope present in E protein domain III (EDIII). E dimers are rearranged into a five-fold symmetry of icosahedrons. Cholera toxin B (CTB) and heat-labile enterotoxin B (LTB) of AB5-type toxin was used as the structural scaffold for emulating the pentameric axis of EDIII. We produced homo-pentameric EDIII through the genetic fusion of LTB or CTB in E. coli without recourse to additional refolding steps. Harnessing an RNA-mediated chaperone further enhanced the soluble expression and pentameric assembly of the chimeric antigen. The pentameric assembly was validated by size exclusion chromatography (SEC), non-reduced gel analysis, and a GM1 binding assay. CTB/LTB-EDIII chimeric antigen triggered high neutralizing antibodies against the JEV Nakayama strain after immunization in mice. Altogether, our proof-of-principle study creating a JEV-protective antigen via fusion with an AB5-type toxin as both a pentameric scaffold and a built-in adjuvant posits the bacterially produced recombinant chimeric antigen as a cost-effective alternative to conventional inactivated vaccines against JEV.
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Affiliation(s)
- Jina Ahn
- The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea
| | - Ji Eun Yu
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03708, Republic of Korea (H.K.)
| | - Hanna Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03708, Republic of Korea (H.K.)
| | - Jemin Sung
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03708, Republic of Korea (H.K.)
| | - Gyoonhee Han
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03708, Republic of Korea (H.K.)
- Department of Integrated OMICS for Biomedical Science, WCU Program of Graduate School, Yonsei University, Seoul 03722, Republic of Korea
| | - Myung Hyun Sohn
- Department of Pediatrics, College of Medicine, Yonsei University, Seoul 03722, Republic of Korea
| | - Baik-Lin Seong
- Department of Microbiology, College of Medicine, Yonsei University, Seoul 03722, Republic of Korea
- Vaccine Innovative Technology ALliance (VITAL)-Korea, Yonsei University, Seoul 03721, Republic of Korea
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16
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De Brabander P, Uitterhaegen E, Delmulle T, De Winter K, Soetaert W. Challenges and progress towards industrial recombinant protein production in yeasts: A review. Biotechnol Adv 2023; 64:108121. [PMID: 36775001 DOI: 10.1016/j.biotechadv.2023.108121] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
Recombinant proteins (RP) are widely used as biopharmaceuticals, industrial enzymes, or sustainable food source. Yeasts, with their ability to produce complex proteins through a broad variety of cheap carbon sources, have emerged as promising eukaryotic production hosts. As such, the prevalence of yeasts as favourable production organisms in commercial RP production is expected to increase. Yet, with the selection of a robust production host on the one hand, successful scale-up is dependent on a thorough understanding of the challenging environment and limitations of large-scale bioreactors on the other hand. In the present work, several prominent yeast species, including Saccharomyces cerevisiae, Pichia pastoris, Yarrowia lipolytica, Kluyveromyces lactis and Kluyveromyces marxianus are reviewed for their current state and performance in commercial RP production. Thereafter, the impact of principal process control parameters, including dissolved oxygen, pH, substrate concentration, and temperature, on large-scale RP production are discussed. Finally, technical challenges of process scale-up are identified. To that end, process intensification strategies to enhance industrial feasibility are summarized, specifically highlighting fermentation strategies to ensure sufficient cooling capacity, overcome oxygen limitation, and increase protein quality and productivity. As such, this review aims to contribute to the pursuit of sustainable yeast-based RP production.
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Affiliation(s)
- Pieter De Brabander
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium
| | - Evelien Uitterhaegen
- Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium
| | - Tom Delmulle
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Karel De Winter
- Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium.
| | - Wim Soetaert
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium
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17
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Pouresmaeil M, Azizi-Dargahlou S. Factors involved in heterologous expression of proteins in E. coli host. Arch Microbiol 2023; 205:212. [PMID: 37120438 PMCID: PMC10148705 DOI: 10.1007/s00203-023-03541-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/26/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023]
Abstract
The production of recombinant proteins is one of the most significant achievements of biotechnology in the last century. These proteins are produced in the eukaryotic or prokaryotic heterologous hosts. By increasing the omics data especially related to different heterologous hosts as well as the presence of new amenable genetic engineering tools, we can artificially engineer heterologous hosts to produce recombinant proteins in sufficient quantities. Numerous recombinant proteins have been produced and applied in various industries, and the global recombinant proteins market size is expected to be cast to reach USD 2.4 billion by 2027. Therefore, identifying the weakness and strengths of heterologous hosts is critical to optimize the large-scale biosynthesis of recombinant proteins. E. coli is one of the popular hosts to produce recombinant proteins. Scientists reported some bottlenecks in this host, and due to the increasing demand for the production of recombinant proteins, there is an urgent need to improve this host. In this review, we first provide general information about the E. coli host and compare it with other hosts. In the next step, we describe the factors involved in the expression of the recombinant proteins in E. coli. Successful expression of recombinant proteins in E. coli requires a complete elucidation of these factors. Here, the characteristics of each factor will be fully described, and this information can help to improve the heterologous expression of recombinant proteins in E. coli.
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Affiliation(s)
- Mahin Pouresmaeil
- Agricultural Biotechnology, Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Shahnam Azizi-Dargahlou
- Agricultural Biotechnology, Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran.
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18
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Raoufi E, Hosseini F, Onagh B, Salehi-Shadkami M, Mehrali M, Mohsenzadegan M, Ho JQ, Bigdelou B, Sepand MR, Webster TJ, Zanganeh S, Farajollahi MM. Designing and developing a sensitive and specific SARS-CoV-2 RBD IgG detection kit for identifying positive human samples. Clin Chim Acta 2023; 542:117279. [PMID: 36871661 PMCID: PMC9985519 DOI: 10.1016/j.cca.2023.117279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/07/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND More than 3 y into the coronavirus 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to undergo mutations. In this context, the Receptor Binding Domain (RBD) is the most antigenic region among the SARS-CoV-2 Spike protein and has emerged as a promising candidate for immunological development. We designed an IgG-based indirect enzyme-linked immunoassay (ELISA) kit based on recombinant RBD, which was produced from the laboratory to 10 L industry scales in Pichia pastoris. METHODS A recombinant-RBD comprising 283 residues (31 kDa) was constructed after epitope analyses. The target gene was initially cloned into an Escherichia coli TOP10 genotype and transformed into Pichia pastoris CBS7435 muts for protein production. Production was scaled up in a 10 L fermenter after a 1 L shake-flask cultivation. The product was ultrafiltered and purified using ion-exchange chromatography. IgG-positive human sera for SARS-CoV-2 were employed by an ELISA test to evaluate the antigenicity and specific binding of the produced protein. RESULTS Bioreactor cultivation yielded 4 g/l of the target protein after 160 h of fermentation, and ion-exchange chromatography indicated a purity > 95%. A human serum ELISA test was performed in 4 parts, and the ROC area under the curve (AUC) was > 0.96 for each part. The mean specificity and sensitivity of each part was 100% and 91.5%, respectively. CONCLUSION A highly specific and sensitive IgG-based serologic kit was developed for improved diagnostic purposes in patients with COVID-19 after generating an RBD antigen in Pichia pastoris at laboratory and 10 L fermentation scales.
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Affiliation(s)
- Ehsan Raoufi
- Department of Medical Biotechnology, Iran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Hosseini
- Department of Medical Biotechnology, Iran University of Medical Sciences, Tehran, Iran
| | - Bahman Onagh
- Department of Biochemistry, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Marjan Mehrali
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Monireh Mohsenzadegan
- Department of Medical Laboratory Science, Iran University of Medical Sciences, Tehran, Iran
| | - Jim Q Ho
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Banafsheh Bigdelou
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, MA, United States
| | - Mohammad Reza Sepand
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, MA, United States
| | - Thomas J Webster
- School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin, China; School of Engineering, Saveetha University, Chennai, India; Program in Materials Science, UFPI, Teresina, Brazil
| | - Steven Zanganeh
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, MA, United States.
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19
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Lee J, Lee SK, Park JS, Lee KR. Plant-made pharmaceuticals: exploring studies for the production of recombinant protein in plants and assessing challenges ahead. PLANT BIOTECHNOLOGY REPORTS 2023; 17:53-65. [PMID: 36820221 PMCID: PMC9931573 DOI: 10.1007/s11816-023-00821-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/16/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
The production of pharmaceutical compounds in plants is attracting increasing attention, as plant-based systems can be less expensive, safer, and more scalable than mammalian, yeast, bacterial, and insect cell expression systems. Here, we review the history and current status of plant-made pharmaceuticals. Producing pharmaceuticals in plants requires pairing the appropriate plant species with suitable transformation technology. Pharmaceuticals have been produced in tobacco, cereals, legumes, fruits, and vegetables via nuclear transformation, chloroplast transformation, transient expression, and transformation of suspension cell cultures. Despite this wide range of species and methods used, most such efforts have involved the nuclear transformation of tobacco. Tobacco readily generates large amounts of biomass, easily accepts foreign genes, and is amenable to stable gene expression via nuclear transformation. Although vaccines, antibodies, and therapeutic proteins have been produced in plants, such pharmaceuticals are not readily utilized by humans due to differences in glycosylation, and few such compounds have been approved due to a lack of clinical data. In addition, achieving an adequate immune response using plant-made pharmaceuticals can be difficult due to low rates of production compared to other expression systems. Various technologies have recently been developed to help overcome these limitations; however, plant systems are expected to increasingly become widely used expression systems for recombinant protein production.
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Affiliation(s)
- Juho Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874 Republic of Korea
| | - Seon-Kyeong Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874 Republic of Korea
| | - Jong-Sug Park
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874 Republic of Korea
| | - Kyeong-Ryeol Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874 Republic of Korea
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20
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Saccharomyces cerevisiae cis-acting DNA sequences curation pipeline (Sc-cADSs-CP): Master transcription factors prediction in yeasts. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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How CW, Ong YS, Low SS, Pandey A, Show PL, Foo JB. How far have we explored fungi to fight cancer? Semin Cancer Biol 2022; 86:976-989. [PMID: 33737109 DOI: 10.1016/j.semcancer.2021.03.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/21/2021] [Accepted: 03/13/2021] [Indexed: 01/01/2023]
Abstract
The use of fungal cultures have been well documented in human history. Although its used in healthcare, like penicillin and statins, have saved countless of lives, but there is still no fungal products that are specifically indicated for cancers. Research into fungal-derived materials to curb cancers in the recent decades have made a considerable progress in terms of drug delivery vehicles, anticancer active ingredients and cancer immunotherapy. Various parts of the organisms have successfully been exploited to achieve specific tasks. Apart from the identification of novel anticancer compound from fungi, its native capsular structure can also be used as drug cargo to achieve higher oral bioavailability. This review summarises the anticancer potential of fungal-derived materials, highlighting the role of capsular polysaccharides, proteins, and other structures in variety of innovative utilities to fit the current pharmaceutical technology. Many bioactive compounds isolated from fungi have also been formulated into nanoparticles to achieve greater anticancer activity. The progress of fungal compounds and their analogues in clinical trials is also highlighted. In addition, the potential of various fungal species to be developed for anticancer immunotherapy are also discussed.
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Affiliation(s)
- Chee Wun How
- School of Pharmacy, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia
| | - Yong Sze Ong
- School of Pharmacy, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia
| | - Sze Shin Low
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia
| | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, 226 001, India
| | - Pau Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia.
| | - Jhi Biau Foo
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University, 1, Jalan Taylors, 47500, Subang Jaya, Selangor, Malaysia; Centre for Drug Discovery and Molecular Pharmacology (CDDMP), Faculty of Health & Medical Sciences, Taylor's University, 1, Jalan Taylors, 47500, Subang Jaya, Selangor, Malaysia.
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22
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Liu Y, Feng J, Pan H, Zhang X, Zhang Y. Genetically engineered bacterium: Principles, practices, and prospects. Front Microbiol 2022; 13:997587. [PMID: 36312915 PMCID: PMC9606703 DOI: 10.3389/fmicb.2022.997587] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/23/2022] [Indexed: 12/24/2022] Open
Abstract
Advances in synthetic biology and the clinical application of bacteriotherapy enable the use of genetically engineered bacteria (GEB) to combat various diseases. GEB act as a small 'machine factory' in the intestine or other tissues to continuously produce heterologous proteins or molecular compounds and, thus, diagnose or cure disease or work as an adjuvant reagent for disease treatment by regulating the immune system. Although the achievements of GEBs in the treatment or adjuvant therapy of diseases are promising, the practical implementation of this new therapeutic modality remains a grand challenge, especially at the initial stage. In this review, we introduce the development of GEBs and their advantages in disease management, summarize the latest research advances in microbial genetic techniques, and discuss their administration routes, performance indicators and the limitations of GEBs used as platforms for disease management. We also present several examples of GEB applications in the treatment of cancers and metabolic diseases and further highlight their great potential for clinical application in the near future.
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Affiliation(s)
- Yiting Liu
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Jing Feng
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Hangcheng Pan
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Xiuwei Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Yunlei Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
- Central Laboratory, Translational Medicine Research Center, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
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23
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Deo S, Turton KL, Kainth T, Kumar A, Wieden HJ. Strategies for improving antimicrobial peptide production. Biotechnol Adv 2022; 59:107968. [PMID: 35489657 DOI: 10.1016/j.biotechadv.2022.107968] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/18/2022] [Accepted: 04/25/2022] [Indexed: 01/10/2023]
Abstract
Antimicrobial peptides (AMPs) found in a wide range of animal, insect, and plant species are host defense peptides forming an integral part of their innate immunity. Although the exact mode of action of some AMPs is yet to be deciphered, many exhibit membrane lytic activity or interact with intracellular targets. The ever-growing threat of antibiotic resistance has brought attention to research on AMPs to enhance their clinical use as a therapeutic alternative. AMPs have several advantages over antibiotics such as broad range of antimicrobial activities including anti-fungal, anti-viral and anti-bacterial, and have not reported to contribute to resistance development. Despite the numerous studies to develop efficient production methods for AMPs, limitations including low yield, degradation, and loss of activity persists in many recombinant approaches. In this review, we outline available approaches for AMP production and various expression systems used to achieve higher yield and quality. In addition, recent advances in recombinant strategies, suitable fusion protein partners, and other molecular engineering strategies for improved AMP production are surveyed.
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Affiliation(s)
- Soumya Deo
- Department of Microbiology, Buller building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Kristi L Turton
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Dr. W., Lethbridge, AB T1K 3M4, Canada
| | - Tajinder Kainth
- Department of Microbiology, Buller building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ayush Kumar
- Department of Microbiology, Buller building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Hans-Joachim Wieden
- Department of Microbiology, Buller building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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24
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Chen Y, Zhang R, Zhang W, Xu Y. Alanine aminopeptidase from Bacillus licheniformis E7 expressed in Bacillus subtilis efficiently hydrolyzes soy protein to small peptides and free amino acids. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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Fu X, Huang Y, Shen Y. Improving the Efficiency and Orthogonality of Genetic Code Expansion. BIODESIGN RESEARCH 2022; 2022:9896125. [PMID: 37850140 PMCID: PMC10521639 DOI: 10.34133/2022/9896125] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/20/2022] [Indexed: 10/19/2023] Open
Abstract
The site-specific incorporation of the noncanonical amino acid (ncAA) into proteins via genetic code expansion (GCE) has enabled the development of new and powerful ways to learn, regulate, and evolve biological functions in vivo. However, cellular biosynthesis of ncAA-containing proteins with high efficiency and fidelity is a formidable challenge. In this review, we summarize up-to-date progress towards improving the efficiency and orthogonality of GCE and enhancing intracellular compatibility of introduced translation machinery in the living cells by creation and optimization of orthogonal translation components, constructing genomically recoded organism (GRO), utilization of unnatural base pairs (UBP) and quadruplet codons (four-base codons), and spatial separation of orthogonal translation.
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Affiliation(s)
- Xian Fu
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120China
| | - Yijian Huang
- BGI-Shenzhen, Shenzhen 518083, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Shen
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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Cho JS, Oh HJ, Jang YE, Kim HJ, Kim A, Song J, 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] [MESH Headings] [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 pro-peptide, 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 pro-peptide after the final stage increased by 190% compared to that of the original pro-peptide. Although hG-CSF was used as the model protein in the current study, this strategy is applicable 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 EngineeringKorea UniversitySeoulKorea
| | - Hye Ji Oh
- Department of Chemical and Biological Engineering, College of EngineeringKorea UniversitySeoulKorea
| | - Young Eun Jang
- Department of Chemical and Biological Engineering, College of EngineeringKorea UniversitySeoulKorea
| | - Hyun Jin Kim
- Department of Chemical and Biological Engineering, College of EngineeringKorea UniversitySeoulKorea
| | - Areum Kim
- Department of Chemical and Biological Engineering, College of EngineeringKorea UniversitySeoulKorea
| | - Jong‐Am Song
- Department of Chemical and Biological Engineering, College of EngineeringKorea UniversitySeoulKorea
| | - Eun Jung Lee
- Department of Chemical Engineering, School of Applied Chemical EngineeringKyungpook National UniversityDaeguKorea
| | - Jeewon Lee
- Department of Chemical and Biological Engineering, College of EngineeringKorea UniversitySeoulKorea
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Designing and characterization of a SARS-CoV-2 immunogen with receptor binding motif grafted on a protein scaffold: An epitope-focused vaccine approach. Int J Biol Macromol 2022; 209:1359-1367. [PMID: 35469951 PMCID: PMC9033297 DOI: 10.1016/j.ijbiomac.2022.04.148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 12/24/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has a significant burden on the economy and healthcare around the world. Vaccines are the most effective tools to fight infectious diseases by containing the spread of the disease. The current vaccines against SARS-CoV-2 are mostly based on the spike protein of SARS-CoV-2, which is large and has many immune-dominant non-neutralizing epitopes that may effectively skew the antibody response towards non-neutralizing antibodies. Here, we have explored the possibility of immune-focusing the receptor binding motif (RBM) of the spike protein of SARS-CoV-2 that induces mostly neutralizing antibodies in natural infection or in vacinees. The result shows that the scaffolded RBM can bind to Angiotensin Converting Enzyme 2 (ACE2) although with low affinity and induces a strong antibody response in mice. The immunized sera can bind both, the receptor binding domain (RBD) and the spike protein, which holds the RBM in its natural context. Sera from the immunized mice showed robust interferon γ response but poor neutralization of SARS-CoV-2 suggesting presence of a predominant T cell epitope on scaffolded RBM. Together, we provide a strategy for inducing strong antigenic T cell response which could be exploited further for future vaccine designing and development against SARS-CoV-2 infection.
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Heterologous protein expression enhancement of Komagataella phaffii by ammonium formate induction based on transcriptomic analysis. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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29
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New opportunities for genetic code expansion in synthetic yeast. Curr Opin Biotechnol 2022; 75:102691. [DOI: 10.1016/j.copbio.2022.102691] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/23/2021] [Accepted: 01/18/2022] [Indexed: 12/19/2022]
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Tan Y, Chen L, Li K, Lou B, Liu Y, Liu Z. Yeast as carrier for drug delivery and vaccine construction. J Control Release 2022; 346:358-379. [PMID: 35483637 DOI: 10.1016/j.jconrel.2022.04.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/19/2022] [Accepted: 04/19/2022] [Indexed: 12/16/2022]
Abstract
Yeast has been employed as an effective derived drug carrier as a unicellular microorganism. Many research works have been devoted to the encapsulation of nucleic acid compounds, insoluble small molecule drugs, small molecules, liposomes, polymers, and various nanoparticles in yeast for the treatment of disease. Recombinant yeast-based vaccine carriers (WYV) have played a major role in the development of vaccines. Herein, the latest reports on the application of yeast carriers and the development of related research are summarized, a conceptual description of gastrointestinal absorption of yeast carriers, as well as the various package forms of different drug molecules and nanoparticles in yeast carriers are introduced. In addition, the advantages and development of recombinant yeast vaccine carriers for the disease, veterinary and aquaculture applications are discussed. Moreover, the current challenges and future directions of yeast carriers are proposed.
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Affiliation(s)
- Yifu Tan
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan Province, PR China
| | - Liwei Chen
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan Province, PR China
| | - Ke Li
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Beibei Lou
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan Province, PR China.
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China; Molecular Imaging Research Center of Central South University, Changsha 410008, Hunan, PR China.
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31
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Lima LF, Sousa MGDC, Rodrigues GR, de Oliveira KBS, Pereira AM, da Costa A, Machado R, Franco OL, Dias SC. Elastin-like Polypeptides in Development of Nanomaterials for Application in the Medical Field. FRONTIERS IN NANOTECHNOLOGY 2022. [DOI: 10.3389/fnano.2022.874790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Elastin-like polypeptides (ELPs) are biopolymers formed by amino acid sequences derived from tropoelastin. These biomolecules can be soluble below critical temperatures, forming aggregates at higher temperatures, which makes them an interesting source for the design of different nanobiomaterials. These nanobiomaterials can be obtained from heterologous expression in several organisms such as bacteria, fungi, and plants. Thanks to the many advantages of ELPs, they have been used in the biomedical field to develop nanoparticles, nanofibers, and nanocomposites. These nanostructures can be used in multiple applications such as drug delivery systems, treatments of type 2 diabetes, cardiovascular diseases, tissue repair, and cancer therapy. Thus, this review aims to shed some light on the main advances in elastin-like-based nanomaterials, their possible expression forms, and importance to the medical field.
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Liu Q, Song L, Peng Q, Zhu Q, Shi X, Xu M, Wang Q, Zhang Y, Cai M. A programmable high-expression yeast platform responsive to user-defined signals. SCIENCE ADVANCES 2022; 8:eabl5166. [PMID: 35148182 PMCID: PMC8836803 DOI: 10.1126/sciadv.abl5166] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Rapidly growing yeasts with appropriate posttranslational modifications are favored hosts for protein production in the biopharmaceutical industry. However, limited production capacity and intricate transcription regulation restrict their application and adaptability. Here, we describe a programmable high-expression yeast platform, SynPic-X, which responds to defined signals and is broadly applicable. We demonstrated that a synthetic improved transcriptional signal amplification device (iTSAD) with a bacterial-yeast transactivator and bacterial-yeast promoter markedly increased expression capacity in Pichia pastoris. CRISPR activation and interference devices were designed to strictly regulate iTSAD in response to defined signals. Engineered switches were then constructed to exemplify the response of SynPic-X to exogenous signals. Expression of α-amylase by SynPic-R, a specific SynPic-X, in a bioreactor proved a methanol-free high-production process of recombinant protein. Our SynPic-X platform provides opportunities for protein production in customizable yeast hosts with high expression and regulatory flexibility.
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Affiliation(s)
- Qi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Lili Song
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiangqiang Peng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiaoyun Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xiaona Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Mingqiang Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai 200237, China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Corresponding author.
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Coetzee G, Smith JJ, Görgens JF. Influence of codon optimization, promoter, and strain selection on the heterologous production of a β-fructofuranosidase from Aspergillus fijiensis ATCC 20611 in Pichia pastoris. Folia Microbiol (Praha) 2022; 67:339-350. [PMID: 35133569 DOI: 10.1007/s12223-022-00947-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 01/01/2022] [Indexed: 12/21/2022]
Abstract
Fructooligosaccharides (FOS) are compounds possessing various health properties and are added to functional foods as prebiotics. The commercial production of FOS is done through the enzymatic transfructolysation of sucrose by β-fructofuranosidases which is found in various organisms of which Aureobasidium pullulans and Aspergillus niger are the most well known. This study overexpressed two differently codon-optimized variations of the Aspergillus fijiensis β-fructofuranosidase-encoding gene (fopA) under the transcriptional control of either the alcohol oxidase (AOX1) or glyceraldehyde-3-phosphate dehydrogenase (GAP) promoters. When cultivated in shake flasks, the two codon-optimized variants displayed similar volumetric enzyme activities when expressed under control of the same promoter with the GAP strains producing 11.7 U/ml and 12.7 U/ml, respectively, and the AOX1 strains 95.8 U/ml and 98.6 U/ml, respectively. However, the highest production levels were achieved for both codon-optimized genes when expressed under control of the AOX1 promoter. The AOX1 promoter was superior to the GAP promoter in bioreactor cultivations for both codon-optimized genes with 13,702 U/ml and 2718 U/ml for the AOX1 promoter for ATUM and GeneArt®, respectively, and 6057 U/ml and 1790 U/ml for the GAP promoter for ATUM and GeneArt®, respectively. The ATUM-optimized gene produced higher enzyme activities when compared to the one from GeneArt®, under the control of both promoters.
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Affiliation(s)
- Gerhardt Coetzee
- Department of Process Engineering, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
| | - Jacques J Smith
- Department of Process Engineering, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Johann F Görgens
- Department of Process Engineering, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
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34
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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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35
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Pérez ALA, Piva LC, Fulber JPC, de Moraes LMP, De Marco JL, Vieira HLA, Coelho CM, Reis VCB, Torres FAG. Optogenetic strategies for the control of gene expression in yeasts. Biotechnol Adv 2021; 54:107839. [PMID: 34592347 DOI: 10.1016/j.biotechadv.2021.107839] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 09/07/2021] [Accepted: 09/22/2021] [Indexed: 12/18/2022]
Abstract
Optogenetics involves the use of light to control cellular functions and has become increasingly popular in various areas of research, especially in the precise control of gene expression. While this technology is already well established in neurobiology and basic research, its use in bioprocess development is still emerging. Some optogenetic switches have been implemented in yeasts for different purposes, taking advantage of a wide repertoire of biological parts and relatively easy genetic manipulation. In this review, we cover the current strategies used for the construction of yeast strains to be used in optogenetically controlled protein or metabolite production, as well as the operational aspects to be considered for the scale-up of this type of process. Finally, we discuss the main applications of optogenetic switches in yeast systems and highlight the main advantages and challenges of bioprocess development considering future directions for this field.
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Affiliation(s)
- Ana Laura A Pérez
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Luiza C Piva
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Julia P C Fulber
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Lidia M P de Moraes
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Janice L De Marco
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Hugo L A Vieira
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Cintia M Coelho
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Viviane C B Reis
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Fernando A G Torres
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Bloco K, 1° andar, Universidade de Brasília, Brasília 70910-900, Brazil.
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Ardila-Leal LD, Poutou-Piñales RA, Pedroza-Rodríguez AM, Quevedo-Hidalgo BE. A Brief History of Colour, the Environmental Impact of Synthetic Dyes and Removal by Using Laccases. Molecules 2021; 26:3813. [PMID: 34206669 PMCID: PMC8270347 DOI: 10.3390/molecules26133813] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/12/2021] [Accepted: 06/16/2021] [Indexed: 12/07/2022] Open
Abstract
The history of colour is fascinating from a social and artistic viewpoint because it shows the way; use; and importance acquired. The use of colours date back to the Stone Age (the first news of cave paintings); colour has contributed to the social and symbolic development of civilizations. Colour has been associated with hierarchy; power and leadership in some of them. The advent of synthetic dyes has revolutionized the colour industry; and due to their low cost; their use has spread to different industrial sectors. Although the percentage of coloured wastewater discharged by the textile; food; pharmaceutical; cosmetic; and paper industries; among other productive areas; are unknown; the toxic effect and ecological implications of this discharged into water bodies are harmful. This review briefly shows the social and artistic history surrounding the discovery and use of natural and synthetic dyes. We summarise the environmental impact caused by the discharge of untreated or poorly treated coloured wastewater to water bodies; which has led to physical; chemical and biological treatments to reduce the colour units so as important physicochemical parameters. We also focus on laccase utility (EC 1.10.3.2), for discolouration enzymatic treatment of coloured wastewater, before its discharge into water bodies. Laccases (p-diphenol: oxidoreductase dioxide) are multicopper oxidoreductase enzymes widely distributed in plants, insects, bacteria, and fungi. Fungal laccases have employed for wastewater colour removal due to their high redox potential. This review includes an analysis of the stability of laccases, the factors that influence production at high scales to achieve discolouration of high volumes of contaminated wastewater, the biotechnological impact of laccases, and the degradation routes that some dyes may follow when using the laccase for colour removal.
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Affiliation(s)
- Leidy D. Ardila-Leal
- Grupo de Biotecnología Ambiental e Industrial (GBAI), Laboratorio de Biotecnología Molecular, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana (PUJ), Bogotá 110-23, DC, Colombia;
| | - Raúl A. Poutou-Piñales
- Grupo de Biotecnología Ambiental e Industrial (GBAI), Laboratorio de Biotecnología Molecular, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana (PUJ), Bogotá 110-23, DC, Colombia;
| | - Aura M. Pedroza-Rodríguez
- Grupo de Biotecnología Ambiental e Industrial (GBAI), Laboratorio de Microbiología Ambiental y de Suelos, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana (PUJ), Bogotá 110-23, DC, Colombia;
| | - Balkys E. Quevedo-Hidalgo
- Grupo de Biotecnología Ambiental e Industrial (GBAI), Laboratorio de Biotecnología Aplicada, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana (PUJ), Bogotá 110-23, DC, Colombia;
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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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Palm D, Uzoni A, Simon F, Fischer M, Coogan A, Tucha O, Thome J, Faltraco F. Evolutionary conservations, changes of circadian rhythms and their effect on circadian disturbances and therapeutic approaches. Neurosci Biobehav Rev 2021; 128:21-34. [PMID: 34102148 DOI: 10.1016/j.neubiorev.2021.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 02/04/2021] [Accepted: 06/01/2021] [Indexed: 12/21/2022]
Abstract
The circadian rhythm is essential for the interaction of all living organisms with their environments. Several processes, such as thermoregulation, metabolism, cognition and memory, are regulated by the internal clock. Disturbances in the circadian rhythm have been shown to lead to the development of neuropsychiatric disorders, including attention-deficit hyperactivity disorder (ADHD). Interestingly, the mechanism of the circadian rhythms has been conserved in many different species, and misalignment between circadian rhythms and the environment results in evolutionary regression and lifespan reduction. This review summarises the conserved mechanism of the internal clock and its major interspecies differences. In addition, it focuses on effects the circadian rhythm disturbances, especially in cases of ADHD, and describes the possibility of recombinant proteins generated by eukaryotic expression systems as therapeutic agents as well as CRISPR/Cas9 technology as a potential tool for research and therapy. The aim is to give an overview about the evolutionary conserved mechanism as well as the changes of the circadian clock. Furthermore, current knowledge about circadian rhythm disturbances and therapeutic approaches is discussed.
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Affiliation(s)
- Denise Palm
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Adriana Uzoni
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Frederick Simon
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Matthias Fischer
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Andrew Coogan
- Department of Psychology, Maynooth University, National University of Ireland, Ireland
| | - Oliver Tucha
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Johannes Thome
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Frank Faltraco
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany.
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Contribution of yeast models to virus research. Appl Microbiol Biotechnol 2021; 105:4855-4878. [PMID: 34086116 PMCID: PMC8175935 DOI: 10.1007/s00253-021-11331-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 12/14/2022]
Abstract
Abstract Time and again, yeast has proven to be a vital model system to understand various crucial basic biology questions. Studies related to viruses are no exception to this. This simple eukaryotic organism is an invaluable model for studying fundamental cellular processes altered in the host cell due to viral infection or expression of viral proteins. Mechanisms of infection of several RNA and relatively few DNA viruses have been studied in yeast to date. Yeast is used for studying several aspects related to the replication of a virus, such as localization of viral proteins, interaction with host proteins, cellular effects on the host, etc. The development of novel techniques based on high-throughput analysis of libraries, availability of toolboxes for genetic manipulation, and a compact genome makes yeast a good choice for such studies. In this review, we provide an overview of the studies that have used yeast as a model system and have advanced our understanding of several important viruses. Key points • Yeast, a simple eukaryote, is an important model organism for studies related to viruses. • Several aspects of both DNA and RNA viruses of plants and animals are investigated using the yeast model. • Apart from the insights obtained on virus biology, yeast is also extensively used for antiviral development.
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Piraine REA, Gonçalves VS, Dos Santos Junior AG, Cunha RC, de Albuquerque PMM, Conrad NL, Leite FPL. Expression cassette and plasmid construction for Yeast Surface Display in Saccharomyces cerevisiae. Biotechnol Lett 2021; 43:1649-1657. [PMID: 33934257 DOI: 10.1007/s10529-021-03142-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/23/2021] [Indexed: 12/16/2022]
Abstract
OBJECTIVES Develop a Cell Surface Display system in Saccharomyces cerevisiae, based on the construction of an expression cassette for pYES2 plasmid. RESULTS The construction of an expression cassette containing the α-factor signal peptide and the C-terminal portion of the α-agglutinin protein was made and its sequence inserted into a plasmid named pYES2/gDαAgglutinin. The construction allows surface display of bovine herpesvirus type 5 (BoHV-5) glycoprotein D (gD) on S. cerevisiae BY4741 strain. Recombinant protein expression was confirmed by dot blot, and indirect immunofluorescence using monoclonal anti-histidine antibodies and polyclonal antibodies from mice experimentally vaccinated with a recombinant gD. CONCLUSIONS These results demonstrate that the approach and plasmid used represent not only an effective system for immobilizing proteins on the yeast cell surface, as well as a platform for immunobiologicals development.
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Affiliation(s)
- Renan Eugênio Araujo Piraine
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Vitória Sequeira Gonçalves
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | | | - Rodrigo Casquero Cunha
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil.,Programa de Pós-Graduação em Veterinária, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | | | - Neida Lucia Conrad
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Fábio Pereira Leivas Leite
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil. .,Programa de Pós-Graduação em Veterinária, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil.
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Li B, Wang Y, Xue L, Lu S. Heterologous Expression and Application of Multicopper Oxidases from Enterococcus spp. for Degradation of Biogenic Amines. Protein Pept Lett 2021; 28:183-194. [PMID: 32543357 DOI: 10.2174/0929866527666200616160859] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Biogenic amines are harmful to human health at a certain extent. As a kind of biogenic amine oxidase, multicopper oxidase can be used to degrade them. Currently, the literature about enzyme from Enterococcus spp. are limited, and recombinant multicopper oxidase might be an effective way to degrade biogenic amines. OBJECTIVE (i) Select and identify strains that can degrade biogenic amines, (ii) overexpress enzyme from Enterococcus spp., (iii) measure gene expression and probe amine-degradation differences among strains (native, E. coli DH5α, and L. delbruckii), and (iv) examine the biochemical properties of recombinant multicopper oxidase, (v) apply the recombinant enzyme into smoked horsemeat sausage. METHODS Reverse transcription PCR and high-performance liquid chromatography were performed to examine gene expression and amine degradation rate. RESULTS The results demonstrated that target enzymes were successfully overexpressed, accompanied by increased amine-degrading activity (P <0.05). Gene from E. faecalis M5B was expressed in L. delbrueckii resulted in degradation rates for phenylethylamine, putrescine, histamine and tyramine of 54%, 52%, 70% and 40%, respectively, significantly higher than achieved by other recombinant strains. CONCLUSION In this work, gene expression levels were higher in recombinant M5B than recombinant M2B, regardless of host. E. coli is more stable to express multicopper oxidase. Besides, the amine-degrading ability was markedly increased in the two recombinant strains. After prolonged incubation, the recombinant enzyme could degrade three amines, and it displayed high alkali resistance and thermostability.
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Affiliation(s)
- Binbin Li
- College of Food Science, Shihezi University, Shihezi 832000, China
| | - Yuan Wang
- College of Food Science, Shihezi University, Shihezi 832000, China
| | - Linlin Xue
- College of Food Science, Shihezi University, Shihezi 832000, China
| | - Shiling Lu
- College of Food Science, Shihezi University, Shihezi 832000, China
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Aza P, Molpeceres G, de Salas F, Camarero S. Design of an improved universal signal peptide based on the α-factor mating secretion signal for enzyme production in yeast. Cell Mol Life Sci 2021; 78:3691-3707. [PMID: 33687500 PMCID: PMC8038962 DOI: 10.1007/s00018-021-03793-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 11/26/2022]
Abstract
Saccharomyces cerevisiae plays an important role in the heterologous expression of an array of proteins due to its easy manipulation, low requirements and ability for protein post-translational modifications. The implementation of the preproleader secretion signal of the α-factor mating pheromone from this yeast contributes to increase the production yields by targeting the foreign protein to the extracellular environment. The use of this signal peptide combined with enzyme-directed evolution allowed us to achieve the otherwise difficult functional expression of fungal laccases in S. cerevisiae, obtaining different evolved α-factor preproleader sequences that enhance laccase secretion. However, the design of a universal signal peptide to enhance the production of heterologous proteins in S. cerevisiae is a pending challenge. We describe here the optimisation of the α-factor preproleader to improve recombinant enzyme production in S. cerevisiae through two parallel engineering strategies: a bottom-up design over the native α-factor preproleader (αnat) and a top-down design over the fittest evolved signal peptide obtained in our lab (α9H2 leader). The goal was to analyse the effect of mutations accumulated in the signal sequence throughout iterations of directed evolution, or of other reported mutations, and their possible epistatic interactions. Both approaches agreed in the positive synergism of four mutations (Aα9D, Aα20T, Lα42S, Dα83E) contained in the final optimised leader (αOPT), which notably enhanced the secretion of several fungal oxidoreductases and hydrolases. Additionally, we suggest a guideline to further drive the heterologous production of a particular enzyme based on combinatorial saturation mutagenesis of positions 86th and 87th of the αOPT leader fused to the target protein.
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Affiliation(s)
- Pablo Aza
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Gonzalo Molpeceres
- 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
| | - Susana Camarero
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain.
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Bhatwa A, Wang W, Hassan YI, Abraham N, Li XZ, Zhou T. Challenges Associated With the Formation of Recombinant Protein Inclusion Bodies in Escherichia coli and Strategies to Address Them for Industrial Applications. Front Bioeng Biotechnol 2021; 9:630551. [PMID: 33644021 PMCID: PMC7902521 DOI: 10.3389/fbioe.2021.630551] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
Recombinant proteins are becoming increasingly important for industrial applications, where Escherichia coli is the most widely used bacterial host for their production. However, the formation of inclusion bodies is a frequently encountered challenge for producing soluble and functional recombinant proteins. To overcome this hurdle, different strategies have been developed through adjusting growth conditions, engineering host strains of E. coli, altering expression vectors, and modifying the proteins of interest. These approaches will be comprehensively highlighted with some of the new developments in this review. Additionally, the unique features of protein inclusion bodies, the mechanism and influencing factors of their formation, and their potential advantages will also be discussed.
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Affiliation(s)
- Arshpreet Bhatwa
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Weijun Wang
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Yousef I. Hassan
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Nadine Abraham
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Xiu-Zhen Li
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Ting Zhou
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
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Miao T, Basit A, Wen J, Liu J, Zheng F, Cao Y, Jiang W. High efficient degradation of glucan/glucomannan to cello-/mannan-oligosaccharide by endoglucanase via tetrasaccharide as intermediate. Food Chem 2021; 350:129175. [PMID: 33610847 DOI: 10.1016/j.foodchem.2021.129175] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/27/2020] [Accepted: 01/19/2021] [Indexed: 12/19/2022]
Abstract
Here, we report an efficient endoglucanase from Aureobasidium pullulans (termed ApCel5A) was expressed in Pichia pastoris. ApCel5A shows two different enzyme activities of endoglucanase (1270 U/mg) and mannanase (31.2 U/mg). Through engineering the signal peptide and fed-batch fermentation, the enzyme activity of endoglucanase was improved to 6.63-folds, totally. Its efficient synergism with Celluclast 1.5 L, excellent tolerance to low pH (2.5), cholate and protease suggests potential application in bioresources, food and feed industries. Site-directed mutagenesis experiments present that ApCel5A residues Glu245 and Glu358 are key catalytic sites, while Asp118, Asp122, Asp198 and Asp314 play an auxiliary role. More importantly, ApCel5A display high degradation efficiency of glucan and glucomannan substrates by using tetrasaccharide contained reducing end of glucose residue as an intermediate. This study elucidated the effective methods to improve an endoglucanase expression and detailed catalytic mechanism for degradation of various substrates, which provides a new insight for endoglucanase application.
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Affiliation(s)
- Ting Miao
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Abdul Basit
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Department of Microbiology and Molecular Genetics, Faculty of Life Sciences, University of Okara, Punjab 56300, Pakistan
| | - Jiaqi Wen
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Junquan Liu
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Fengzhen Zheng
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yunhe Cao
- State Key Laboratory of Animal Nutrition, China Agricultural, University, Beijing, China.
| | - Wei Jiang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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Aza P, de Salas F, Molpeceres G, Rodríguez-Escribano D, de la Fuente I, Camarero S. Protein Engineering Approaches to Enhance Fungal Laccase Production in S. cerevisiae. Int J Mol Sci 2021; 22:ijms22031157. [PMID: 33503813 PMCID: PMC7866195 DOI: 10.3390/ijms22031157] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 12/03/2022] Open
Abstract
Laccases secreted by saprotrophic basidiomycete fungi are versatile biocatalysts able to oxidize a wide range of aromatic compounds using oxygen as the sole requirement. Saccharomyces cerevisiae is a preferred host for engineering fungal laccases. To assist the difficult secretion of active enzymes by yeast, the native signal peptide is usually replaced by the preproleader of S. cerevisiae alfa mating factor (MFα1). However, in most cases, only basal enzyme levels are obtained. During directed evolution in S. cerevisiae of laccases fused to the α-factor preproleader, we demonstrated that mutations accumulated in the signal peptide notably raised enzyme secretion. Here we describe different protein engineering approaches carried out to enhance the laccase activity detected in the liquid extracts of S. cerevisiae cultures. We demonstrate the improved secretion of native and engineered laccases by using the fittest mutated α-factor preproleader obtained through successive laccase evolution campaigns in our lab. Special attention is also paid to the role of protein N-glycosylation in laccase production and properties, and to the introduction of conserved amino acids through consensus design enabling the expression of certain laccases otherwise not produced by the yeast. Finally, we revise the contribution of mutations accumulated in laccase coding sequence (CDS) during previous directed evolution campaigns that facilitate enzyme production.
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de Jesús-Pires C, Ferreira-Neto JRC, Pacifico Bezerra-Neto J, Kido EA, de Oliveira Silva RL, Pandolfi V, Wanderley-Nogueira AC, Binneck E, da Costa AF, Pio-Ribeiro G, Pereira-Andrade G, Sittolin IM, Freire-Filho F, Benko-Iseppon AM. Plant Thaumatin-like Proteins: Function, Evolution and Biotechnological Applications. Curr Protein Pept Sci 2021; 21:36-51. [PMID: 30887921 DOI: 10.2174/1389203720666190318164905] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/01/2019] [Accepted: 03/11/2019] [Indexed: 12/30/2022]
Abstract
Thaumatin-like proteins (TLPs) are a highly complex protein family associated with host defense and developmental processes in plants, animals, and fungi. They are highly diverse in angiosperms, for which they are classified as the PR-5 (Pathogenesis-Related-5) protein family. In plants, TLPs have a variety of properties associated with their structural diversity. They are mostly associated with responses to biotic stresses, in addition to some predicted activities under drought and osmotic stresses. The present review covers aspects related to the structure, evolution, gene expression, and biotechnological potential of TLPs. The efficiency of the discovery of new TLPs is below its potential, considering the availability of omics data. Furthermore, we present an exemplary bioinformatics annotation procedure that was applied to cowpea (Vigna unguiculata) transcriptome, including libraries of two tissues (root and leaf), and two stress types (biotic/abiotic) generated using different sequencing approaches. Even without using genomic sequences, the pipeline uncovered 56 TLP candidates in both tissues and stresses. Interestingly, abiotic stress (root dehydration) was associated with a high number of modulated TLP isoforms. The nomenclature used so far for TLPs was also evaluated, considering TLP structure and possible functions identified to date. It is clear that plant TLPs are promising candidates for breeding purposes and for plant transformation aiming a better performance under biotic and abiotic stresses. The development of new therapeutic drugs against human fungal pathogens also deserves attention. Despite that, applications derived from TLP molecules are still below their potential, as it is evident in our review.
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Affiliation(s)
- Carolline de Jesús-Pires
- Departamento de Genetica, Centro de Biociencias, Universidade Federal de Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | | | - João Pacifico Bezerra-Neto
- Departamento de Genetica, Centro de Biociencias, Universidade Federal de Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | - Ederson Akio Kido
- Departamento de Genetica, Centro de Biociencias, Universidade Federal de Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | | | - Valesca Pandolfi
- Departamento de Genetica, Centro de Biociencias, Universidade Federal de Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | | | - Eliseu Binneck
- Empresa Brasileira de Pesquisa Agropecuaria, Embrapa Soja, Londrina, Parana, Brazil
| | | | - Gilvan Pio-Ribeiro
- Departamento de Agronomia/Fitossanidade, Universidade Federal Rural de Pernambuco (UFRPE), Recife, Pernambuco, Brazil
| | - Genira Pereira-Andrade
- Departamento de Agronomia/Fitossanidade, Universidade Federal Rural de Pernambuco (UFRPE), Recife, Pernambuco, Brazil
| | - Ilza Maria Sittolin
- Empresa Brasileira de Pesquisa Agropecuaria, Embrapa Meio-Norte, Teresina, Piaui, Brazil
| | - Francisco Freire-Filho
- Empresa Brasileira de Pesquisa Agropecuaria, Embrapa Amazonia Oriental, Belem, Para, Brazil
| | - Ana Maria Benko-Iseppon
- Departamento de Genetica, Centro de Biociencias, Universidade Federal de Pernambuco (UFPE), Recife, Pernambuco, Brazil
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Enhanced human lysozyme production by Pichia pastoris via periodic glycerol and dissolved oxygen concentrations control. Appl Microbiol Biotechnol 2021; 105:1041-1050. [PMID: 33443631 DOI: 10.1007/s00253-021-11100-9] [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: 09/29/2020] [Revised: 12/26/2020] [Accepted: 01/05/2021] [Indexed: 10/22/2022]
Abstract
In human lysozyme (hLYZ) production by Pichia pastoris, the glycerol fed-batch phase was generally implemented under the environment of "oxygen sufficient-glycerol limited" to achieve high cell-density cultivation during the cell growth phase. However, the structural and functional components in P. pastoris cells were irreversible damaged with more and more reactive oxygen species (ROS) accumulation when cells were exposed to the oxygen sufficient environments for long time, leading to a failure of hLYZ expression. In this study, a novel periodic glycerol and dissolved oxygen concentration (DO) control strategy was proposed to solve these problems. This strategy periodically switched the cultivation environments from "oxygen sufficient-glycerol limited" to "oxygen limited-glycerol sufficient" for 5 cycles. When using this strategy: (1) the highest dry cell weight (DCW) of 143.02 g-DCW/L and the lowest distribution of glycerol towards to cell maintenance (0.0400 1/h) were achieved during the glycerol feeding phase by maintaining ROS levels below 48.39 Fluorescence intensity/g-DCW; (2) the adaption time of P. pastoris cells to methanol induction environments was shortened for about 50%; (3) P. pastoris cell metabolic activities reflected by the activities of alcohol oxidase, formaldehyde dehydrogenase, formate dehydrogenase, and methanol consumption rate, etc., in the successive induction phase were largely enhanced; (4) hLYZ activity reached the highest level of 2.45 × 105 IU/mL, which was about 2-fold than that obtained with the strategy of "oxygen sufficient-glycerol limited," when the same methanol induction strategy was adopted. KEY POINTS: • A novel periodic glycerol feeding strategy proposed/used for P. pastoris cell growth. • Higher cell density was obtained by controlling ROS at low level via this strategy. • The highest hLYZ activity was achieved when initiating induction at higher cell density.
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Arbeitman CR, Auge G, Blaustein M, Bredeston L, Corapi ES, Craig PO, Cossio LA, Dain L, D’Alessio C, Elias F, Fernández NB, Gándola YB, Gasulla J, Gorojovsky N, Gudesblat GE, Herrera MG, Ibañez LI, Idrovo T, Rando MI, Kamenetzky L, Nadra AD, Noseda DG, Paván CH, Pavan MF, Pignataro MF, Roman E, Ruberto LAM, Rubinstein N, Santos J, Velazquez F, Zelada AM. Structural and functional comparison of SARS-CoV-2-spike receptor binding domain produced in Pichia pastoris and mammalian cells. Sci Rep 2020; 10:21779. [PMID: 33311634 PMCID: PMC7732851 DOI: 10.1038/s41598-020-78711-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/25/2020] [Indexed: 12/13/2022] Open
Abstract
The yeast Pichia pastoris is a cost-effective and easily scalable system for recombinant protein production. In this work we compared the conformation of the receptor binding domain (RBD) from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Spike protein expressed in P. pastoris and in the well established HEK-293T mammalian cell system. RBD obtained from both yeast and mammalian cells was properly folded, as indicated by UV-absorption, circular dichroism and tryptophan fluorescence. They also had similar stability, as indicated by temperature-induced unfolding (observed Tm were 50 °C and 52 °C for RBD produced in P. pastoris and HEK-293T cells, respectively). Moreover, the stability of both variants was similarly reduced when the ionic strength was increased, in agreement with a computational analysis predicting that a set of ionic interactions may stabilize RBD structure. Further characterization by high-performance liquid chromatography, size-exclusion chromatography and mass spectrometry revealed a higher heterogeneity of RBD expressed in P. pastoris relative to that produced in HEK-293T cells, which disappeared after enzymatic removal of glycans. The production of RBD in P. pastoris was scaled-up in a bioreactor, with yields above 45 mg/L of 90% pure protein, thus potentially allowing large scale immunizations to produce neutralizing antibodies, as well as the large scale production of serological tests for SARS-CoV-2.
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Che Z, Cao X, Chen G, Liang Z. An effective combination of codon optimization, gene dosage, and process optimization for high-level production of fibrinolytic enzyme in Komagataella phaffii (Pichia pastoris). BMC Biotechnol 2020; 20:63. [PMID: 33276774 PMCID: PMC7716587 DOI: 10.1186/s12896-020-00654-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/05/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND As a main drug for diseased thrombus, some clinically used thrombolytic agents have various disadvantages, safer novel thrombolytic agents are of great demand. This study aimed to achieve high and efficient production of a fibrinolytic enzyme with superior enzymatic properties, by a combination strategy of codon optimization, gene dosage and process optimization in Komagataella phaffii (K. phaffii). RESULTS After codon optimization, the fibase from a marine Bacillus subtilis was expressed and secreted in K. phaffii GS115. Recombinant strains harboring different copies of the fib gene (fib-nc) were successfully obtained via Geneticin (0.25-4 mg/ml) screening on minimal dextrose selection plates and assessment via real-time quantitative PCR. The respective levels of fibase produced by strains expressing fib-5.4c, fib-6c, fib-8c, fib-9c, and fib-12c were 4428, 5781, 7323, 7930, and 2472 U/ml. Levels increased as the copy number increased from 4 to 9, but decreased dramatically at copy number 12. After high cell density fermentation optimization, the highest fibase activity of the strain expressing fib-9c was 7930 U/ml in a shake flask and increased to 12,690 U/ml after 3 days of continuous culture in a 5-L fermenter, which is one of the highest levels of production reported. The recombinant fibase was maximally active at pH 9.0 and 45 °C, and was remarkably stable at pH levels ranging from 5 to 10 and temperatures up to 50 °C. As a metal-dependent serine protease, fibase did not cause hemolysis in vitro and preferentially degraded fibrin directly. CONCLUSIONS The combination of codon optimization, gene dosage, and process optimization described herein could be used for the expression of other therapeutic proteins difficult to express. The characteristics of the recombinant fibase suggest that it has potential applications for thrombosis prevention and therapy.
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Affiliation(s)
- Zhiqun Che
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Xiaoyan Cao
- College of Agriculture and Forestry Science, Linyi University, Linyi, 276000, China
| | - Guiguang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Zhiqun Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
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50
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Ethanol fed-batch bioreactor operation to enhance therapeutic protein production in Pichia pastoris under hybrid-architectured ADH2 promoter. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107782] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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