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Moon H, Min K, Winarto J, Shin S, Jeon H, Song DG, Son H. Proteomic Analysis of Cell Wall Proteins with Various Linkages in Fusarium graminearum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6028-6039. [PMID: 38457781 DOI: 10.1021/acs.jafc.3c07746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
The fungal cell wall, primarily comprising a glucan-chitin matrix and cell wall proteins (CWPs), serves as a key mediator for fungal interactions with the environment and plays a pivotal role in virulence. In this study, we employed a comprehensive proteomics approach to analyze the CWPs in the plant pathogenic fungus Fusarium graminearum. Our methodology successfully extracted and identified 1373 CWPs, highlighting their complex linkages, including noncovalent bonds, disulfide bridges, alkali-sensitive linkages, and glycosylphosphatidylinositol (GPI) anchors. A significant subset of these proteins, enriched in Gene Ontology terms, suggest multifunctional roles of CWPs. Through the integration of transcriptomic and proteomic data, we observed differential expression patterns of CWPs across developmental stages. Specifically, we focused on two genes, Fca7 and Cpd1, which were upregulated in planta, and confirmed their localization predominantly outside the plasma membrane, primarily in the cell wall and periplasmic space. The disruption of FCA7 reduced virulence on wheat, aligning with previous findings and underscoring its significance. Overall, our findings offer a comprehensive proteomic profile of CWPs in F. graminearum, laying the groundwork for a deeper understanding of their roles in the development and interactions with host plants.
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Affiliation(s)
- Heeji Moon
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Kyunghun Min
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Department of Plant Science, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
| | - Jessica Winarto
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST) Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea
- Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
| | - Soobin Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Hosung Jeon
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Dae-Geun Song
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST) Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea
- Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
| | - Hokyoung Son
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
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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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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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Extension of O-Linked Mannosylation in the Golgi Apparatus Is Critical for Cell Wall Integrity Signaling and Interaction with Host Cells in Cryptococcus neoformans Pathogenesis. mBio 2022; 13:e0211222. [PMID: 36409123 PMCID: PMC9765558 DOI: 10.1128/mbio.02112-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The human-pathogenic yeast Cryptococcus neoformans assembles two types of O-linked glycans on its proteins. In this study, we identified and functionally characterized the C. neoformans CAP6 gene, encoding an α1,3-mannosyltransferase responsible for the second mannose addition to minor O-glycans containing xylose in the Golgi apparatus. Two cell surface sensor proteins, Wml1 (WSC/Mid2-like) and Wml2, were found to be independent substrates of Cap6-mediated minor or Ktr3-mediated major O-mannosylation, respectively. The double deletion of KTR3 and CAP6 (ktr3Δ cap6Δ) completely blocked the mannose addition at the second position of O-glycans, resulting in the accumulation of proteins with O-glycans carrying only a single mannose. Tunicamycin (TM)-induced phosphorylation of the Mpk1 mitogen-activated protein kinase (MAPK) was greatly decreased in both ktr3Δ cap6Δ and wml1Δ wml2Δ strains. Transcriptome profiling of the ktr3Δ cap6Δ strain upon TM treatment revealed decreased expression of genes involved in the Mpk1-dependent cell wall integrity (CWI) pathway. Consistent with its defective growth under several stress conditions, the ktr3Δ cap6Δ strain was avirulent in a mouse model of cryptococcosis. Associated with this virulence defect, the ktr3Δ cap6Δ strain showed decreased adhesion to lung epithelial cells, decreased proliferation within macrophages, and reduced transcytosis of the blood-brain barrier (BBB). Notably, the ktr3Δ cap6Δ strain showed reduced induction of the host immune response and defective trafficking of ergosterol, an immunoreactive fungal molecule. In conclusion, O-glycan extension in the Golgi apparatus plays critical roles in various pathobiological processes, such as CWI signaling and stress resistance and interaction with host cells in C. neoformans. IMPORTANCE Cryptococcus neoformans assembles two types of O-linked glycans on its surface proteins, the more abundant major O-glycans that do not contain xylose residues and minor O-glycans containing xylose. Here, we demonstrate the role of the Cap6 α1,3-mannosyltransferase in the synthesis of minor O-glycans. Previously proposed to be involved in capsule biosynthesis, Cap6 works with the related Ktr3 α1,2-mannosyltransferase to synthesize O-glycans on their target proteins. We also identified two novel C. neoformans stress sensors that require Ktr3- and Cap6-mediated posttranslational modification for full function. Accordingly, the ktr3Δ cap6Δ double O-glycan mutant strain displays defects in stress signaling pathways, CWI, and ergosterol trafficking. Furthermore, the ktr3Δ cap6Δ strain is completely avirulent in a mouse infection model. Together, these results demonstrate critical roles for O-glycosylation in fungal pathogenesis. As there are no human homologs for Cap6 or Ktr3, these fungus-specific mannosyltransferases are novel targets for antifungal therapy.
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Zahrl RJ, Prielhofer R, Ata Ö, Baumann K, Mattanovich D, Gasser B. Pushing and pulling proteins into the yeast secretory pathway enhances recombinant protein secretion. Metab Eng 2022; 74:36-48. [PMID: 36057427 DOI: 10.1016/j.ymben.2022.08.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022]
Abstract
Yeasts and especially Pichia pastoris (syn Komagataella spp.) are popular microbial expression systems for the production of recombinant proteins. One of the key advantages of yeast host systems is their ability to secrete the recombinant protein into the culture media. However, secretion of some recombinant proteins is less efficient. These proteins include antibody fragments such as Fabs or scFvs. We have recently identified translocation of nascent Fab fragments from the cytosol into the endoplasmic reticulum (ER) as one major bottleneck. Conceptually, this bottleneck requires engineering to increase the flux of recombinant proteins at the translocation step by pushing on the cytosolic side and pulling on the ER side. This engineering strategy is well-known in the field of metabolic engineering. To apply the push-and-pull strategy to recombinant protein secretion, we chose to modulate the cytosolic and ER Hsp70 cycles, which have a key impact on the translocation process. After identifying the relevant candidate factors of the Hsp70 cycles, we combined the push-and-pull factors in a single strain and achieved synergistic effects for antibody fragment secretion. With this concept we were able to successfully engineer strains and improve protein secretion up to 5-fold for different model protein classes. Overall, titers of more than 1.3 g/L Fab and scFv were reached in bioreactor cultivations.
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Affiliation(s)
- Richard J Zahrl
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Roland Prielhofer
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Özge Ata
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Kristin Baumann
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Diethard Mattanovich
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Brigitte Gasser
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria.
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6
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Ata Ö, Ergün BG, Fickers P, Heistinger L, Mattanovich D, Rebnegger C, Gasser B. What makes Komagataella phaffii non-conventional? FEMS Yeast Res 2021; 21:6440159. [PMID: 34849756 PMCID: PMC8709784 DOI: 10.1093/femsyr/foab059] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/23/2021] [Indexed: 12/30/2022] Open
Abstract
The important industrial protein production host Komagataella phaffii (syn Pichia pastoris) is classified as a non-conventional yeast. But what exactly makes K. phaffii non-conventional? In this review, we set out to address the main differences to the 'conventional' yeast Saccharomyces cerevisiae, but also pinpoint differences to other non-conventional yeasts used in biotechnology. Apart from its methylotrophic lifestyle, K. phaffii is a Crabtree-negative yeast species. But even within the methylotrophs, K. phaffii possesses distinct regulatory features such as glycerol-repression of the methanol-utilization pathway or the lack of nitrate assimilation. Rewiring of the transcriptional networks regulating carbon (and nitrogen) source utilization clearly contributes to our understanding of genetic events occurring during evolution of yeast species. The mechanisms of mating-type switching and the triggers of morphogenic phenotypes represent further examples for how K. phaffii is distinguished from the model yeast S. cerevisiae. With respect to heterologous protein production, K. phaffii features high secretory capacity but secretes only low amounts of endogenous proteins. Different to S. cerevisiae, the Golgi apparatus of K. phaffii is stacked like in mammals. While it is tempting to speculate that Golgi architecture is correlated to the high secretion levels or the different N-glycan structures observed in K. phaffii, there is recent evidence against this. We conclude that K. phaffii is a yeast with unique features that has a lot of potential to explore both fundamental research questions and industrial applications.
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Affiliation(s)
- Özge Ata
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
| | - Burcu Gündüz Ergün
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara, Turkey.,Biotechnology Research Center, Ministry of Agriculture and Forestry, Ankara, Turkey
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Av. de la Faculté 2B, 5030 Gembloux, Belgium
| | - Lina Heistinger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Christian Doppler Laboratory for Innovative Immunotherapeutics, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
| | - Corinna Rebnegger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Christian Doppler Laboratory for Growth-Decoupled Protein Production in Yeast, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Biotechnology Research Center, Ministry of Agriculture and Forestry, Ankara, Turkey
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Calatayud M, Börner RA, Ghyselinck J, Verstrepen L, Medts JD, den Abbeele PV, Boulangé CL, Priour S, Marzorati M, Damak S. Water Kefir and Derived Pasteurized Beverages Modulate Gut Microbiota, Intestinal Permeability and Cytokine Production In Vitro. Nutrients 2021; 13:nu13113897. [PMID: 34836151 PMCID: PMC8625349 DOI: 10.3390/nu13113897] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 01/08/2023] Open
Abstract
Fermentation is an ancient food preservation process, and fermented products have been traditionally consumed in different cultures worldwide over the years. The interplay between human gut microbiota, diet and host health is widely recognized. Diet is one of the main factors modulating gut microbiota potentially with beneficial effects on human health. Fermented dairy products have received much attention, but other sources of probiotic delivery through food received far less attention. In this research, a combination of in vitro tools mimicking colonic fermentation and the intestinal epithelium have been applied to study the effect of different pasteurized and non-pasteurized water kefir products on gut microbiota, epithelial barrier function and immunomodulation. Water kefir increased beneficial short-chain fatty acid production at the microbial level, reduced detrimental proteolytic fermentation compounds and increased Bifidobacterium genus abundance. The observed benefits are enhanced by pasteurization. Pasteurized products also had a significant effect at the host level, improving inflammation-induced intestinal epithelial barrier disruption and increasing IL-10 and IL-1β compared to the control condition. Our data support the potential health benefits of water kefir and demonstrate that pasteurization, performed to prolong shelf life and stability of the product, also enhanced these benefits.
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Affiliation(s)
- Marta Calatayud
- ProDigest, Technologiepark 82, 9052 Zwijnaarde, Belgium; (M.C.); (J.G.); (L.V.); (J.D.M.); (P.V.d.A.)
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Rosa Aragao Börner
- Nestlé Institute of Health Sciences, and Nestlé Institute of Material Sciences, Nestlé Research, Société des Produits Nestlé S.A., Vers-chez-les-Blanc, 1000 Lausanne, Switzerland; (C.L.B.); (S.P.); (S.D.)
- Correspondence: (R.A.B.); (M.M.)
| | - Jonas Ghyselinck
- ProDigest, Technologiepark 82, 9052 Zwijnaarde, Belgium; (M.C.); (J.G.); (L.V.); (J.D.M.); (P.V.d.A.)
| | - Lynn Verstrepen
- ProDigest, Technologiepark 82, 9052 Zwijnaarde, Belgium; (M.C.); (J.G.); (L.V.); (J.D.M.); (P.V.d.A.)
| | - Jelle De Medts
- ProDigest, Technologiepark 82, 9052 Zwijnaarde, Belgium; (M.C.); (J.G.); (L.V.); (J.D.M.); (P.V.d.A.)
| | - Pieter Van den Abbeele
- ProDigest, Technologiepark 82, 9052 Zwijnaarde, Belgium; (M.C.); (J.G.); (L.V.); (J.D.M.); (P.V.d.A.)
| | - Claire L. Boulangé
- Nestlé Institute of Health Sciences, and Nestlé Institute of Material Sciences, Nestlé Research, Société des Produits Nestlé S.A., Vers-chez-les-Blanc, 1000 Lausanne, Switzerland; (C.L.B.); (S.P.); (S.D.)
| | - Sarah Priour
- Nestlé Institute of Health Sciences, and Nestlé Institute of Material Sciences, Nestlé Research, Société des Produits Nestlé S.A., Vers-chez-les-Blanc, 1000 Lausanne, Switzerland; (C.L.B.); (S.P.); (S.D.)
| | - Massimo Marzorati
- ProDigest, Technologiepark 82, 9052 Zwijnaarde, Belgium; (M.C.); (J.G.); (L.V.); (J.D.M.); (P.V.d.A.)
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
- Correspondence: (R.A.B.); (M.M.)
| | - Sami Damak
- Nestlé Institute of Health Sciences, and Nestlé Institute of Material Sciences, Nestlé Research, Société des Produits Nestlé S.A., Vers-chez-les-Blanc, 1000 Lausanne, Switzerland; (C.L.B.); (S.P.); (S.D.)
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8
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Yeast-produced RBD-based recombinant protein vaccines elicit broadly neutralizing antibodies and durable protective immunity against SARS-CoV-2 infection. Cell Discov 2021; 7:71. [PMID: 34408130 PMCID: PMC8372230 DOI: 10.1038/s41421-021-00315-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/21/2021] [Indexed: 12/15/2022] Open
Abstract
Massive production of efficacious SARS-CoV-2 vaccines is essential for controlling the ongoing COVID-19 pandemic. We report here the preclinical development of yeast-produced receptor-binding domain (RBD)-based recombinant protein SARS-CoV-2 vaccines. We found that monomeric RBD of SARS-CoV-2 could be efficiently produced as a secreted protein from transformed Pichia pastoris (P. pastoris) yeast. Yeast-derived RBD-monomer possessed functional conformation and was able to elicit protective level of neutralizing antibodies in mice. We further designed and expressed a genetically linked dimeric RBD protein in yeast. The engineered dimeric RBD was more potent than the monomeric RBD in inducing long-lasting neutralizing antibodies. Mice immunized with either monomeric RBD or dimeric RBD were effectively protected from live SARS-CoV-2 virus challenge even at 18 weeks after the last vaccine dose. Importantly, we found that the antisera raised against the RBD of a single SARS-CoV-2 prototype strain could effectively neutralize the two predominant circulating variants B.1.1.7 and B.1.351, implying broad-spectrum protective potential of the RBD-based vaccines. Our data demonstrate that yeast-derived RBD-based recombinant SARS-CoV-2 vaccines are feasible and efficacious, opening up a new avenue for rapid and cost-effective production of SARS-CoV-2 vaccines to achieve global immunization.
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Kim JY, Joo WH, Shin DS, Lee YI, Teo CF, Lim JM. Metabolic labeling of glycans with isotopic glucose for quantitative glycomics in yeast. Anal Biochem 2021; 621:114152. [PMID: 33726981 DOI: 10.1016/j.ab.2021.114152] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/23/2021] [Accepted: 03/02/2021] [Indexed: 12/29/2022]
Abstract
Changes in glycan levels could directly affect the biochemical properties of glycoproteins and thus influence their physiological functions. In order to decode the correlation of glycan prevalence with their physiological contribution, many mass spectrometry (MS) and stable isotope labeling-based methods have been developed for the relative quantification of glycans. In this study, we expand the quantitative glycomic toolbox with the addition of optimized Metabolic Isotope Labeling of Polysaccharides with Isotopic Glucose (MILPIG) approach in baker's yeast (Saccharomyces cerevisiae). We demonstrate that culturing baker's yeast in the presence of carbon-13 labeled glucose (1-13C1) leads to effective incorporation of carbon-13 to both N-linked and O-linked glycans. We established that metabolic incorporation of isotope-labeled glucose at a concentration of 5 mg/mL for three days is required for an accurate quantitative analysis with optimal isotopic cluster distribution of glycans. To validate the robustness of the method, we performed the analysis by 1:1 mixing of normal and isotope-labeled glycans, and obtained excellent linear calibration curves from various analytes. Finally, we quantitated the inhibitory effect of tunicamycin, a N-linked glycosylation inhibitor, to glycan expression profile in yeast.
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Affiliation(s)
- Ji-Yeon Kim
- Department of Chemistry, Changwon National University, Changwon, 51140, Republic of Korea
| | - Woo Hong Joo
- Department of Biology, Changwon National University, Changwon, 51140, Republic of Korea
| | - Dong-Soo Shin
- Department of Chemistry, Changwon National University, Changwon, 51140, Republic of Korea
| | - Yong-Ill Lee
- Department of Chemistry, Changwon National University, Changwon, 51140, Republic of Korea
| | - Chin Fen Teo
- Departments of Physiology, Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Jae-Min Lim
- Department of Chemistry, Changwon National University, Changwon, 51140, Republic of Korea.
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Harvey DJ. NEGATIVE ION MASS SPECTROMETRY FOR THE ANALYSIS OF N-LINKED GLYCANS. MASS SPECTROMETRY REVIEWS 2020; 39:586-679. [PMID: 32329121 DOI: 10.1002/mas.21622] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/13/2019] [Accepted: 12/22/2019] [Indexed: 05/03/2023]
Abstract
N-glycans from glycoproteins are complex, branched structures whose structural determination presents many analytical problems. Mass spectrometry, usually conducted in positive ion mode, often requires extensive sample manipulation, usually by derivatization such as permethylation, to provide the necessary structure-revealing fragment ions. The newer but, so far, lesser used negative ion techniques, on the contrary, provide a wealth of structural information not present in positive ion spectra that greatly simplify the analysis of these compounds and can usually be conducted without the need for derivatization. This review describes the use of negative ion mass spectrometry for the structural analysis of N-linked glycans and emphasises the many advantages that can be gained by this mode of operation. Biosynthesis and structures of the compounds are described followed by methods for release of the glycans from the protein. Methods for ionization are discussed with emphasis on matrix-assisted laser desorption/ionization (MALDI) and methods for producing negative ions from neutral compounds. Acidic glycans naturally give deprotonated species under most ionization conditions. Fragmentation of negative ions is discussed next with particular reference to those ions that are diagnostic for specific features such as the branching topology of the glycans and substitution positions of moieties such as fucose and sulfate, features that are often difficult to identify easily by conventional techniques such as positive ion fragmentation and exoglycosidase digestions. The advantages of negative over positive ions for this structural work are emphasised with an example of a series of glycans where all other methods failed to produce a structure. Fragmentation of derivatized glycans is discussed next, both with respect to derivatives at the reducing terminus of the molecules, and to methods for neutralization of the acidic groups on sialic acids to both stabilize them for MALDI analysis and to produce the diagnostic fragments seen with the neutral glycans. The use of ion mobility, combined with conventional mass spectrometry is described with emphasis on its use to extract clean glycan spectra both before and after fragmentation, to separate isomers and its use to extract additional information from separated fragment ions. A section on applications follows with examples of the identification of novel structures from lower organisms and tables listing the use of negative ions for structural identification of specific glycoproteins, glycans from viruses and uses in the biopharmaceutical industry and in medicine. The review concludes with a summary of the advantages and disadvantages of the technique. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, United Kingdom
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11
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Genome-wide functional analysis of phosphatases in the pathogenic fungus Cryptococcus neoformans. Nat Commun 2020; 11:4212. [PMID: 32839469 PMCID: PMC7445287 DOI: 10.1038/s41467-020-18028-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
Phosphatases, together with kinases and transcription factors, are key components in cellular signalling networks. Here, we present a systematic functional analysis of the phosphatases in Cryptococcus neoformans, a fungal pathogen that causes life-threatening fungal meningoencephalitis. We analyse 230 signature-tagged mutant strains for 114 putative phosphatases under 30 distinct in vitro growth conditions, revealing at least one function for 60 of these proteins. Large-scale virulence and infectivity assays using insect and mouse models indicate roles in pathogenicity for 31 phosphatases involved in various processes such as thermotolerance, melanin and capsule production, stress responses, O-mannosylation, or retromer function. Notably, phosphatases Xpp1, Ssu72, Siw14, and Sit4 promote blood-brain barrier adhesion and crossing by C. neoformans. Together with our previous systematic studies of transcription factors and kinases, our results provide comprehensive insight into the pathobiological signalling circuitry of C. neoformans. Phosphatases are key components in cellular signalling networks. Here, the authors present a systematic functional analysis of phosphatases of the fungal pathogen Cryptococcus neoformans, revealing roles in virulence, stress responses, O-mannosylation, retromer function and other processes.
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12
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Thak EJ, Lee SB, Xu-Vanpala S, Lee DJ, Chung SY, Bahn YS, Oh DB, Shinohara ML, Kang HA. Core N-Glycan Structures Are Critical for the Pathogenicity of Cryptococcus neoformans by Modulating Host Cell Death. mBio 2020; 11:e00711-20. [PMID: 32398313 PMCID: PMC7218283 DOI: 10.1128/mbio.00711-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/13/2020] [Indexed: 12/17/2022] Open
Abstract
Cryptococcus neoformans is a human-pathogenic fungal pathogen that causes life-threatening meningoencephalitis in immunocompromised individuals. To investigate the roles of N-glycan core structure in cryptococcal pathogenicity, we constructed mutant strains of C. neoformans with defects in the assembly of lipid-linked N-glycans in the luminal side of the endoplasmic reticulum (ER). Deletion of ALG3 (alg3Δ), which encodes dolichyl-phosphate-mannose (Dol-P-Man)-dependent α-1,3-mannosyltransferase, resulted in the production of truncated neutral N-glycans carrying five mannose residues as a major species. Despite moderate or nondetectable defects in virulence-associated phenotypes in vitro, the alg3Δ mutant was avirulent in a mouse model of systemic cryptococcosis. Notably, the mutant did not show defects in early stages of host cell interaction during infection, including attachment to lung epithelial cells, opsonic/nonopsonic phagocytosis, and manipulation of phagosome acidification. However, the ability to drive macrophage cell death was greatly decreased in this mutant, without loss of cell wall remodeling capacity. Furthermore, deletion of ALG9 and ALG12, encoding Dol-P-Man-dependent α-1,2-mannosyltransferases and α-1,6-mannosyltransferases, generating truncated core N-glycans with six and seven mannose residues, respectively, also displayed remarkably reduced macrophage cell death and in vivo virulence. However, secretion levels of interleukin-1β (IL-1β) were not reduced in the bone marrow-derived dendritic cells obtained from Asc- and Gsdmd-deficient mice infected with the alg3Δ mutant strain, excluding the possibility that pyroptosis is a main host cell death pathway dependent on intact core N-glycans. Our results demonstrated N-glycan structures as a critical feature in modulating death of host cells, which is exploited by as a strategy for host cell escape for dissemination of C. neoformansIMPORTANCE We previously reported that the outer mannose chains of N-glycans are dispensable for the virulence of C. neoformans, which is in stark contrast to findings for the other human-pathogenic yeast, Candida albicans Here, we present evidence that an intact core N-glycan structure is required for C. neoformans pathogenicity by systematically analyzing alg3Δ, alg9Δ, and alg12Δ strains that have defects in lipid-linked N-glycan assembly and in in vivo virulence. The alg null mutants producing truncated core N-glycans were defective in inducing host cell death after phagocytosis, which is triggered as a mechanism of pulmonary escape and dissemination of C. neoformans, thus becoming inactive in causing fatal infection. The results clearly demonstrated the critical features of the N-glycan structure in mediating the interaction with host cells during fungal infection. The delineation of the roles of protein glycosylation in fungal pathogenesis not only provides insight into the glycan-based fungal infection mechanism but also will aid in the development of novel antifungal agents.
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Affiliation(s)
- Eun Jung Thak
- Department of Life Science, Chung-Ang University, Seoul, South Korea
| | - Su-Bin Lee
- Department of Life Science, Chung-Ang University, Seoul, South Korea
| | - Shengjie Xu-Vanpala
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Dong-Jik Lee
- Department of Life Science, Chung-Ang University, Seoul, South Korea
| | - Seung-Yeon Chung
- Department of Life Science, Chung-Ang University, Seoul, South Korea
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Doo-Byoung Oh
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Mari L Shinohara
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Microbiology and Molecular Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Hyun Ah Kang
- Department of Life Science, Chung-Ang University, Seoul, South Korea
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13
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Thak EJ, Yoo SJ, Moon HY, Kang HA. Yeast synthetic biology for designed cell factories producing secretory recombinant proteins. FEMS Yeast Res 2020; 20:5721243. [DOI: 10.1093/femsyr/foaa009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/30/2020] [Indexed: 12/17/2022] Open
Abstract
ABSTRACT
Yeasts are prominent hosts for the production of recombinant proteins from industrial enzymes to therapeutic proteins. Particularly, the similarity of protein secretion pathways between these unicellular eukaryotic microorganisms and higher eukaryotic organisms has made them a preferential host to produce secretory recombinant proteins. However, there are several bottlenecks, in terms of quality and quantity, restricting their use as secretory recombinant protein production hosts. In this mini-review, we discuss recent developments in synthetic biology approaches to constructing yeast cell factories endowed with enhanced capacities of protein folding and secretion as well as designed targeted post-translational modification process functions. We focus on the new genetic tools for optimizing secretory protein expression, such as codon-optimized synthetic genes, combinatory synthetic signal peptides and copy number-controllable integration systems, and the advanced cellular engineering strategies, including endoplasmic reticulum and protein trafficking pathway engineering, synthetic glycosylation, and cell wall engineering, for improving the quality and yield of secretory recombinant proteins.
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Affiliation(s)
- Eun Jung Thak
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Su Jin Yoo
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hye Yun Moon
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hyun Ah Kang
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
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14
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Maldonado-Carmona N, Vázquez-Hernández M, Patiño Chávez OJ, Rodríguez-Luna SD, Jiménez Rodríguez O, Sanchez S, Ceapă CD. Impact of ∼omics in the detection and validation of potential anti-infective drugs. Curr Opin Pharmacol 2019; 48:1-7. [PMID: 30921690 DOI: 10.1016/j.coph.2019.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 12/25/2022]
Abstract
New anti-infective drugs are an unmet necessity of modern medicine. The use of ∼omics technologies has exponentially increased the knowledge on active anti-infective structures, where to search for them and their mechanisms of action. Research involving extreme and unique environments (such as endophytes) revealed their potential for many yet unknown active molecules. This work intends to review a recent research involving discovery of secondary metabolites with an established anti-infective action which was mediated by one of the ∼omics sciences: genomics, proteomics, transcriptomics, metabolomics, glycomics or their combinations, as well as the software at the base of these discoveries.
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Affiliation(s)
- Nidia Maldonado-Carmona
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), CDMX, 04510, Mexico
| | - Melissa Vázquez-Hernández
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), CDMX, 04510, Mexico
| | - Osiris Jair Patiño Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), CDMX, 04510, Mexico
| | - Stefany Daniela Rodríguez-Luna
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), CDMX, 04510, Mexico
| | - Omar Jiménez Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), CDMX, 04510, Mexico
| | - Sergio Sanchez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), CDMX, 04510, Mexico.
| | - Corina Diana Ceapă
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), CDMX, 04510, Mexico.
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15
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Ikegami T. Hydrophilic interaction chromatography for the analysis of biopharmaceutical drugs and therapeutic peptides: A review based on the separation characteristics of the hydrophilic interaction chromatography phases. J Sep Sci 2019; 42:130-213. [DOI: 10.1002/jssc.201801074] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 11/17/2018] [Accepted: 11/18/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Tohru Ikegami
- Faculty of Molecular Chemistry and Engineering; Kyoto Institute of Technology; Kyoto Japan
- Institute of Pharmaceutical Sciences; Pharmaceutical (Bio-) Analysis; Eberhard-Karls Universität Tübingen; Tübingen Germany
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16
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Yoo SJ, Moon HY, Kang HA. Screening and Selection of Production Strains: Secretory Protein Expression and Analysis in Hansenula polymorpha. Methods Mol Biol 2019; 1923:133-151. [PMID: 30737738 DOI: 10.1007/978-1-4939-9024-5_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The thermotolerant methylotrophic yeast Hansenula polymorpha has been used as a host for the high-level production of recombinant proteins from industrial enzymes to therapeutic proteins. Despite favorable characteristics of the H. polymorpha-based platform for application to heterologous gene expression, several problems and limitations, such as over-glycosylation and proteolytic degradation, can be encountered in the development of production strains for secretory proteins. Here, H. polymorpha genetic tools and host strains, developed for authentic processing and modification of secretory recombinant proteins, are introduced with the analytical protocols.
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Affiliation(s)
- Su Jin Yoo
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hye Yun Moon
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hyun Ah Kang
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, Republic of Korea.
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