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Velappan N, Biryukov SS, Rill NO, Klimko CP, Rosario-Acevedo R, Shoe JL, Hunter M, Dankmeyer JL, Fetterer DP, Bedinger D, Phipps ME, Watt AJ, Abergel RJ, Dichosa A, Kozimor SA, Cote CK, Lillo AM. Characterization of two affinity matured Anti-Yersinia pestis F1 human antibodies with medical countermeasure potential. PLoS One 2024; 19:e0305034. [PMID: 38954719 PMCID: PMC11218954 DOI: 10.1371/journal.pone.0305034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 05/23/2024] [Indexed: 07/04/2024] Open
Abstract
Yersinia pestis, the causative agent of plague and a biological threat agent, presents an urgent need for novel medical countermeasures due to documented cases of naturally acquired antibiotic resistance and potential person-to-person spread during a pneumonic infection. Immunotherapy has been proposed as a way to circumvent current and future antibiotic resistance. Here, we describe the development and characterization of two affinity matured human antibodies (αF1Ig AM2 and αF1Ig AM8) that promote survival of mice after exposure to aerosolized Y. pestis. We share details of the error prone PCR and yeast display technology-based affinity maturation process that we used. The resultant matured antibodies have nanomolar affinity for Y. pestis F1 antigen, are produced in high yield, and are resilient to 37°C stress for up to 6 months. Importantly, in vitro assays using a murine macrophage cell line demonstrated that αF1Ig AM2 and αF1Ig AM8 are opsonic. Even more importantly, in vivo studies using pneumonic plague mouse models showed that 100% of the mice receiving 500 μg of IgGs αF1Ig AM2 and αF1Ig AM8 survived lethal challenge with aerosolized Y. pestis CO92. Combined, these results provide evidence of the quality and robustness of αF1Ig AM2 and αF1Ig AM8 and support their development as potential medical countermeasures against plague.
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Affiliation(s)
- Nileena Velappan
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Sergei S. Biryukov
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Nathaniel O. Rill
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Christopher P. Klimko
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Raysa Rosario-Acevedo
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Jennifer L. Shoe
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Melissa Hunter
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Jennifer L. Dankmeyer
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - David P. Fetterer
- Biostatisitics Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | | | - Mary E. Phipps
- Los Alamos National Laboratory, Center Alamos for Integrated Nanotechnologies, Los Alamos, NM, United States of America
| | - Austin J. Watt
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Rebecca J. Abergel
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Nuclear Engineering, University of California, Berkeley, CA, United States of America
| | - Armand Dichosa
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Stosh A. Kozimor
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Christopher K. Cote
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America
| | - Antonietta M. Lillo
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
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2
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Yu YA, Lien WJ, Lin WC, Pan YC, Huang SW, Mou CY, Hu CMJ, Mou KY. High-Affinity Superantigen-Based Trifunctional Immune Cell Engager Synergizes NK and T Cell Activation for Tumor Suppression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2310204. [PMID: 38937984 DOI: 10.1002/advs.202310204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 06/14/2024] [Indexed: 06/29/2024]
Abstract
The development of immune cell engagers (ICEs) can be limited by logistical and functional restrictions associated with fusion protein designs, thus limiting immune cell recruitment to solid tumors. Herein, a high affinity superantigen-based multivalent ICE is developed for simultaneous activation and recruitment of NK and T cells for tumor treatment. Yeast library-based directed evolution is adopted to identify superantigen variants possessing enhanced binding affinity to immunoreceptors expressed on human T cells and NK cells. High-affinity superantigens exhibiting improved immune-stimulatory activities are then incorporated into a superantigen-based tri-functional yeast-display-enhanced multivalent immune cell engager (STYMIE), which is functionalized with a nanobody, a Neo-2/15 cytokine, and an Fc domain for tumor targeting, immune stimulation, and prolonged circulation, respectively. Intravenous administration of STYMIE enhances NK and T cell recruitment into solid tumors, leading to enhanced inhibition in multiple tumor models. The study offers design principles for multifunctional ICEs.
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Affiliation(s)
- Yao-An Yu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
- Doctoral Degree Program of Translational Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, 112, Taiwan
| | - Wan-Ju Lien
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Wen-Ching Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Chung Pan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Sin-Wei Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Chung-Yuan Mou
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Che-Ming Jack Hu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
- Doctoral Degree Program of Translational Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, 112, Taiwan
- Biomedical Translation Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Kurt Yun Mou
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
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3
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Liang Y, Luo H, Li X, Liu S, Habib A, Liu B, Huang J, Wang J, Yi H, Hu B, Zheng L, Xie J, Zhu N. PD-L1 targeted peptide demonstrates potent antitumor and immunomodulatory activity in cancer immunotherapy. Front Immunol 2024; 15:1367040. [PMID: 38745661 PMCID: PMC11091243 DOI: 10.3389/fimmu.2024.1367040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024] Open
Abstract
Background In recent years, immunotherapy has been emerging as a promising alternative therapeutic method for cancer patients, offering potential benefits. The expression of PD-L1 by tumors can inhibit the T-cell response to the tumor and allow the tumor to evade immune surveillance. To address this issue, cancer immunotherapy has shown promise in disrupting the interaction between PD-L1 and its ligand PD-1. Methods We used mirror-image phage display technology in our experiment to screen and determine PD-L1 specific affinity peptides (PPL-C). Using CT26 cells, we established a transplanted mouse tumor model to evaluate the inhibitory effects of PPL-C on tumor growth in vivo. We also demonstrated that PPL-C inhibited the differentiation of T regulatory cells (Tregs) and regulated the production of cytokines. Results In vitro, PPL-C has a strong affinity for PD-L1, with a binding rate of 0.75 μM. An activation assay using T cells and mixed lymphocytes demonstrated that PPL-C inhibits the interaction between PD-1 and PD-L1. PPL-C or an anti-PD-L1 antibody significantly reduced the rate of tumor mass development in mice compared to those given a control peptide (78% versus 77%, respectively). The results of this study demonstrate that PPL-C prevents or retards tumor growth. Further, immunotherapy with PPL-C enhances lymphocyte cytotoxicity and promotes proliferation in CT26-bearing mice. Conclusion PPL-C exhibited antitumor and immunoregulatory properties in the colon cancer. Therefore, PPL-C peptides of low molecular weight could serve as effective cancer immunotherapy.
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Affiliation(s)
- Yulai Liang
- Laboratory of Molecular Immunology, State Key Lab of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Huazao Luo
- Laboratory of Molecular Immunology, State Key Lab of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Xue Li
- Laboratory of Molecular Immunology, State Key Lab of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuang Liu
- Renal Division, Department of Internal Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Arslan Habib
- Laboratory of Molecular Immunology, State Key Lab of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Baoxiu Liu
- Laboratory of Molecular Immunology, State Key Lab of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiansheng Huang
- Laboratory of Molecular Immunology, State Key Lab of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jingbo Wang
- Laboratory of Molecular Immunology, State Key Lab of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Han Yi
- Laboratory of Molecular Immunology, State Key Lab of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Bo Hu
- Laboratory of Molecular Immunology, State Key Lab of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Liuhai Zheng
- Laboratory of Molecular Immunology, State Key Lab of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jun Xie
- Laboratory of Molecular Immunology, State Key Lab of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Naishuo Zhu
- Laboratory of Molecular Immunology, State Key Lab of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Institute of Biomedical Sciences, School of Life Sciences, Fudan University, Shanghai, China
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4
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Gao S, Zuo W, Kang C, Zou Z, Zhang K, Qiu J, Shang X, Li J, Zhang Y, Zuo Q, Zhao Y, Jin M. Saccharomyces cerevisiae oral immunization in mice using multi-antigen of the African swine fever virus elicits a robust immune response. Front Immunol 2024; 15:1373656. [PMID: 38742108 PMCID: PMC11089227 DOI: 10.3389/fimmu.2024.1373656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 04/05/2024] [Indexed: 05/16/2024] Open
Abstract
African swine fever virus (ASFV) is one of the most complex viruses. ASFV is a serious threat to the global swine industry because no commercial vaccines against this virus are currently available except in Vietnam. Moreover, ASFV is highly stable in the environment and can survive in water, feed, and aerosols for a long time. ASFV is transmitted through the digestive and respiratory tract. Mucosal immunity is the first line of defense against ASFV. Saccharomyces cerevisiae (SC), which has been certified by the U.S. Food and Drug Administration and has a generally recognized as safe status in the food industry, was used for oral immunization in this study. ASFV antigens were effectively expressed in recombinant SC strains with high DNA copy numbers and stable growth though surface display technology and chromosome engineering (δ-integration). The recombinant SC strains containing eight ASFV antigens-KP177R, E183L, E199L, CP204L, E248R, EP402R, B602L, and B646L- induced strong humoral and mucosal immune responses in mice. There was no antigenic competition, and these antigens induced Th1 and Th2 cellular immune responses. Therefore, the oral immunization strategy using recombinant SC strains containing multiple ASFV antigens demonstrate potential for future testing in swine, including challenge studies to evaluate its efficacy as a vaccine against ASFV.
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Affiliation(s)
- Shuo Gao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Wenfeng Zuo
- Research Institute of Wuhan Keqian Biology Co., Ltd, Wuhan, China
| | - Chao Kang
- Research Institute of Wuhan Keqian Biology Co., Ltd, Wuhan, China
| | - Zhong Zou
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Kaiqi Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Jun Qiu
- College of Animal Sciences, Yangtze University, Jingzhou, Hubei, China
| | - Xiaomin Shang
- Research Institute of Wuhan Keqian Biology Co., Ltd, Wuhan, China
| | - Jingjing Li
- Research Institute of Wuhan Keqian Biology Co., Ltd, Wuhan, China
| | - Yuanfeng Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Research Institute of Wuhan Keqian Biology Co., Ltd, Wuhan, China
| | - Qi Zuo
- Research Institute of Wuhan Keqian Biology Co., Ltd, Wuhan, China
| | - Ya Zhao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Meilin Jin
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
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5
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Deichmann M, Hansson FG, Jensen ED. Yeast-based screening platforms to understand and improve human health. Trends Biotechnol 2024:S0167-7799(24)00095-7. [PMID: 38677901 DOI: 10.1016/j.tibtech.2024.04.003] [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: 12/30/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/29/2024]
Abstract
Detailed molecular understanding of the human organism is essential to develop effective therapies. Saccharomyces cerevisiae has been used extensively for acquiring insights into important aspects of human health, such as studying genetics and cell-cell communication, elucidating protein-protein interaction (PPI) networks, and investigating human G protein-coupled receptor (hGPCR) signaling. We highlight recent advances and opportunities of yeast-based technologies for cost-efficient chemical library screening on hGPCRs, accelerated deciphering of PPI networks with mating-based screening and selection, and accurate cell-cell communication with human immune cells. Overall, yeast-based technologies constitute an important platform to support basic understanding and innovative applications towards improving human health.
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Affiliation(s)
- Marcus Deichmann
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Frederik G Hansson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Emil D Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
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6
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O’Riordan N, Jurić V, O’Neill SK, Roche AP, Young PW. A Yeast Modular Cloning (MoClo) Toolkit Expansion for Optimization of Heterologous Protein Secretion and Surface Display in Saccharomyces cerevisiae. ACS Synth Biol 2024; 13:1246-1258. [PMID: 38483353 PMCID: PMC11036508 DOI: 10.1021/acssynbio.3c00743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 04/20/2024]
Abstract
Saccharomyces cerevisiae is an attractive host for the expression of secreted proteins in a biotechnology context. Unfortunately, many heterologous proteins fail to enter, or efficiently progress through, the secretory pathway, resulting in poor yields. Similarly, yeast surface display has become a widely used technique in protein engineering but achieving sufficient levels of surface expression of recombinant proteins is often challenging. Signal peptides (SPs) and translational fusion partners (TFPs) can be used to direct heterologous proteins through the yeast secretory pathway, however, selection of the optimal secretion promoting sequence is largely a process of trial and error. The yeast modular cloning (MoClo) toolkit utilizes type IIS restriction enzymes to facilitate an efficient assembly of expression vectors from standardized parts. We have expanded this toolkit to enable the efficient incorporation of a panel of 16 well-characterized SPs and TFPs and five surface display anchor proteins into S. cerevisiae expression cassettes. The secretion promoting signals are validated by using five different proteins of interest. Comparison of intracellular and secreted protein levels reveals the optimal secretion promoting sequence for each individual protein. Large, protein of interest-specific variations in secretion efficiency are observed. SP sequences are also used with the five surface display anchors, and the combination of SP and anchor protein proves critical for efficient surface display. These observations highlight the value of the described panel of MoClo compatible parts to allow facile screening of SPs and TFPs and anchor proteins for optimal secretion and/or surface display of a given protein of interest in S. cerevisiae.
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Affiliation(s)
- Nicola
M. O’Riordan
- School
of Biochemistry and Cell Biology, University
College Cork, Cork T12 YN60, Ireland
| | - Vanja Jurić
- School
of Biochemistry and Cell Biology, University
College Cork, Cork T12 YN60, Ireland
- AMBER
Centre, Environmental Research Institute, University College Cork, Cork T23 XE10, Ireland
| | - Sarah K. O’Neill
- School
of Biochemistry and Cell Biology, University
College Cork, Cork T12 YN60, Ireland
| | - Aoife P. Roche
- School
of Biochemistry and Cell Biology, University
College Cork, Cork T12 YN60, Ireland
| | - Paul W. Young
- School
of Biochemistry and Cell Biology, University
College Cork, Cork T12 YN60, Ireland
- AMBER
Centre, Environmental Research Institute, University College Cork, Cork T23 XE10, Ireland
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7
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Ma XY, Coleman B, Prabhu P, Yang M, Wen F. Engineering Compositionally Uniform Yeast Whole-Cell Biocatalysts with Maximized Surface Enzyme Density for Cellulosic Biofuel Production. ACS Synth Biol 2024; 13:1225-1236. [PMID: 38551819 DOI: 10.1021/acssynbio.3c00669] [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] [Indexed: 04/20/2024]
Abstract
In recent decades, whole-cell biocatalysis has played an increasingly important role in the food, pharmaceutical, and energy sector. One promising application is the use of ethanologenic yeast displaying minicellulosomes on the cell surface to combine cellulose hydrolysis and fermentation into a single step for consolidated bioprocessing. However, cellulosic ethanol production using existing yeast whole-cell biocatalysts (yWCBs) has not reached industrial feasibility due to their inefficient cellulose hydrolysis. As prior studies have demonstrated enzyme density on the yWCB surface to be one of the most important parameters for enhancing cellulose hydrolysis, we sought to maximize this parameter at both the population and single-cell levels in yWCBs displaying tetrafunctional minicellulosomes. At the population level, enzyme density is limited by the presence of a nondisplay population constituting 25-50% of all cells. In this study, we identified the cause to be plasmid loss and successfully eliminated the nondisplay population to generate compositionally uniform yWCBs. At the single-cell level, we demonstrate that enzyme density is limited by molecular crowding, which hinders minicellulosome assembly. By adjusting the integrated gene copy number, we obtained yWCBs of tunable enzyme display levels. This tunability allowed us to avoid the crowding-limited regime and achieve a maximum enzyme density per cell. As a result, the best strain showed a cellulose-to-ethanol yield of 4.92 g/g, corresponding to 96% of the theoretical maximum and near-complete conversion (∼96%) of the starting cellulose (1% PASC). Our holistic engineering strategy that combines a population and single-cell level approach is broadly applicable to enhance the WCB performance in other biocatalytic cascade schemes.
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Affiliation(s)
- Xiao Yin Ma
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bryan Coleman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ponnandy Prabhu
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Margaret Yang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
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8
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Muñoz-Muñoz PLA, Terán-Ramírez C, Mares-Alejandre RE, Márquez-González AB, Madero-Ayala PA, Meléndez-López SG, Ramos-Ibarra MA. Surface Engineering of Escherichia coli to Display Its Phytase (AppA) and Functional Analysis of Enzyme Activities. Curr Issues Mol Biol 2024; 46:3424-3437. [PMID: 38666945 PMCID: PMC11048855 DOI: 10.3390/cimb46040215] [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: 03/18/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Escherichia coli phytase (AppA) is widely used as an exogenous enzyme in monogastric animal feed mainly because of its ability to degrade phytic acid or its salt (phytate), a natural source of phosphorus. Currently, successful recombinant production of soluble AppA has been achieved by gene overexpression using both bacterial and yeast systems. However, some methods for the biomembrane immobilization of phytases (including AppA), such as surface display on yeast cells and bacterial spores, have been investigated to avoid expensive enzyme purification processes. This study explored a homologous protein production approach for displaying AppA on the cell surface of E. coli by engineering its outer membrane (OM) for extracellular expression. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of total bacterial lysates and immunofluorescence microscopy of non-permeabilized cells revealed protein expression, whereas activity assays using whole cells or OM fractions indicated functional enzyme display, as evidenced by consistent hydrolytic rates on typical substrates (i.e., p-nitrophenyl phosphate and phytic acid). Furthermore, the in vitro results obtained using a simple method to simulate the gastrointestinal tract of poultry suggest that the whole-cell biocatalyst has potential as a feed additive. Overall, our findings support the notion that biomembrane-immobilized enzymes are reliable for the hydrolysis of poorly digestible substrates relevant to animal nutrition.
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Affiliation(s)
- Patricia L. A. Muñoz-Muñoz
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, BCN, Mexico; (P.L.A.M.-M.); (C.T.-R.); (R.E.M.-A.); (A.B.M.-G.); (P.A.M.-A.); (S.G.M.-L.)
| | - Celina Terán-Ramírez
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, BCN, Mexico; (P.L.A.M.-M.); (C.T.-R.); (R.E.M.-A.); (A.B.M.-G.); (P.A.M.-A.); (S.G.M.-L.)
- Biochemical Sciences Graduate Program (Doctorate Studies), National Autonomous University of Mexico, Cuernavaca 62210, MOR, Mexico
| | - Rosa E. Mares-Alejandre
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, BCN, Mexico; (P.L.A.M.-M.); (C.T.-R.); (R.E.M.-A.); (A.B.M.-G.); (P.A.M.-A.); (S.G.M.-L.)
| | - Ariana B. Márquez-González
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, BCN, Mexico; (P.L.A.M.-M.); (C.T.-R.); (R.E.M.-A.); (A.B.M.-G.); (P.A.M.-A.); (S.G.M.-L.)
- Biological and Biomedical Sciences Graduate Program (Doctorate Studies), University of North Carolina, Chapel Hill, NC 27599, USA
| | - Pablo A. Madero-Ayala
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, BCN, Mexico; (P.L.A.M.-M.); (C.T.-R.); (R.E.M.-A.); (A.B.M.-G.); (P.A.M.-A.); (S.G.M.-L.)
- Science and Engineering Graduate Program (Doctorate Studies), Autonomous University of Baja California, Tijuana 22390, BCN, Mexico
| | - Samuel G. Meléndez-López
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, BCN, Mexico; (P.L.A.M.-M.); (C.T.-R.); (R.E.M.-A.); (A.B.M.-G.); (P.A.M.-A.); (S.G.M.-L.)
| | - Marco A. Ramos-Ibarra
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, BCN, Mexico; (P.L.A.M.-M.); (C.T.-R.); (R.E.M.-A.); (A.B.M.-G.); (P.A.M.-A.); (S.G.M.-L.)
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9
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Zhang L, Tan L, Liu M, Chen Y, Yang Y, Zhang Y, Zhao G. Quantitative measurement of cell-surface displayed proteins based on split-GFP assembly. Microb Cell Fact 2024; 23:108. [PMID: 38609965 PMCID: PMC11015686 DOI: 10.1186/s12934-024-02386-1] [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: 01/12/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Microbial cell surface display technology allows immobilizing proteins on the cell surface by fusing them to anchoring motifs, thereby endowing the cells with diverse functionalities. However, the assessment of successful protein display and the quantification of displayed proteins remain challenging. The green fluorescent protein (GFP) can be split into two non-fluorescent fragments, while they spontaneously assemble and emit fluorescence when brought together through complementation. Based on split-GFP assembly, we aim to: (1) confirm the success display of passenger proteins, (2) quantify the number of passenger proteins displayed on individual cells. RESULTS In this study, we propose two innovative methods based on split-green fluorescent protein (split-GFP), named GFP1-10/GFP11 and GFP1-9/GFP10-11 assembly, for the purpose of confirming successful display and quantifying the number of proteins displayed on individual cells. We evaluated the display efficiency of SUMO and ubiquitin using different anchor proteins to demonstrate the feasibility of the two split-GFP assembly systems. To measure the display efficiency of functional proteins, laccase expression was measured using the split-GFP assembly system by co-displaying GFP11 or GFP10-11 tags, respectively. CONCLUSIONS Our study provides two split-GFP based methods that enable qualitative and quantitative analyses of individual cell display efficiency with a simple workflow, thus facilitating further comprehensive investigations into microbial cell surface display technology. Both split-GFP assembly systems offer a one-step procedure with minimal cost, simplifying the fluorescence analysis of surface-displaying cells.
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Affiliation(s)
- Li Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, 410083, PR China
| | - Ling Tan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
| | - Meizi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
| | - Yunhong Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Yu Yang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, 410083, PR China.
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China.
| | - Guoping Zhao
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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10
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Martinusen SG, Denard CA. Leveraging yeast sequestration to study and engineer posttranslational modification enzymes. Biotechnol Bioeng 2024; 121:903-914. [PMID: 38079116 PMCID: PMC11229454 DOI: 10.1002/bit.28621] [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: 05/17/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 02/20/2024]
Abstract
Enzymes that catalyze posttranslational modifications (PTMs) of peptides and proteins (PTM-enzymes)-proteases, protein ligases, oxidoreductases, kinases, and other transferases-are foundational to our understanding of health and disease and empower applications in chemical biology, synthetic biology, and biomedicine. To fully harness the potential of PTM-enzymes, there is a critical need to decipher their enzymatic and biological mechanisms, develop molecules that can probe and modulate them, and endow them with improved and novel functions. These objectives are contingent upon implementation of high-throughput functional screens and selections that interrogate large sequence libraries to isolate desired PTM-enzyme properties. This review discusses the principles of Saccharomyces cerevisiae organelle sequestration to study and engineer PTM-enzymes. These include outer membrane sequestration, specifically methods that modify yeast surface display, and cytoplasmic sequestration based on enzyme-mediated transcription activation. Furthermore, we present a detailed discussion of yeast endoplasmic reticulum sequestration for the first time. Where appropriate, we highlight the major features and limitations of different systems, specifically how they can measure and control enzyme catalytic efficiencies. Taken together, yeast-based high-throughput sequestration approaches significantly lower the barrier to understanding how PTM-enzymes function and how to reprogram them.
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Affiliation(s)
- Samantha G Martinusen
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Carl A Denard
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
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11
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Mustafa MI, Alzebair AA, Mohammed A. Development of Recombinant Antibody by Yeast Surface Display Technology. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2024; 6:100174. [PMID: 38318280 PMCID: PMC10839864 DOI: 10.1016/j.crphar.2024.100174] [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: 12/02/2023] [Accepted: 01/13/2024] [Indexed: 02/07/2024] Open
Abstract
Recombinant antibodies have emerged as powerful tools in various fields, including therapeutics, diagnostics, and research applications. The selection of high-affinity antibodies with desired specificity is a crucial step in the development of recombinant antibody-based products. In recent years, yeast surface display technology has gained significant attention as a robust and versatile platform for antibody selection. This graphical review provides an overview of the yeast surface display technology and its applications in recombinant antibody selection. We discuss the key components involved in the construction of yeast surface display libraries, including the antibody gene libraries, yeast host strains, and display vectors. Furthermore, we highlight the strategies employed for affinity maturation and optimization of recombinant antibodies using yeast surface display. Finally, we discuss the advantages and limitations of this technology compared to other antibody selection methods. Overall, yeast surface display technology offers a powerful and efficient approach for the selection of recombinant antibodies, enabling the rapid generation of high-affinity antibodies for various applications.
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Affiliation(s)
- Mujahed I. Mustafa
- Department of Biotechnology, College of Applied and Industrial Sciences, University of Bahri, Khartoum, Sudan
| | - Awad A. Alzebair
- Department of Biotechnology, School of Life Sciences and Technology, Omdurman Islamic University, Omdurman, Sudan
| | - Ahmed Mohammed
- Department of Biotechnology, School of Life Sciences and Technology, Omdurman Islamic University, Omdurman, Sudan
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12
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Zeke A, Alexa A, Reményi A. Discovery and Characterization of Linear Motif Mediated Protein-Protein Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:59-71. [PMID: 38507200 DOI: 10.1007/978-3-031-52193-5_5] [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: 03/22/2024]
Abstract
There are myriads of protein-protein complexes that form within the cell. In addition to classical binding events between globular domains, many protein-protein interactions involve short disordered protein regions. The latter contain so-called linear motifs binding specifically to ordered protein domain surfaces. Linear binding motifs are classified based on their consensus sequence, where only a few amino acids are conserved. In this chapter we will review experimental and in silico techniques that can be used for the discovery and characterization of linear motif mediated protein-protein complexes involved in cellular signaling, protein level and gene expression regulation.
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Affiliation(s)
- András Zeke
- Institute of Organic Chemistry, HUN-REN Research Center for Natural Sciences, Budapest, Hungary
| | - Anita Alexa
- Institute of Organic Chemistry, HUN-REN Research Center for Natural Sciences, Budapest, Hungary
| | - Attila Reményi
- Institute of Organic Chemistry, HUN-REN Research Center for Natural Sciences, Budapest, Hungary.
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13
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Belluati A, Happel D, Erbe M, Kirchner N, Szelwicka A, Bloch A, Berner V, Christmann A, Hertel B, Pardehkhorram R, Reyhani A, Kolmar H, Bruns N. Self-decorating cells via surface-initiated enzymatic controlled radical polymerization. NANOSCALE 2023; 15:19486-19492. [PMID: 38051112 DOI: 10.1039/d3nr04008a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Through the innovative use of surface-displayed horseradish peroxidase, this work explores the enzymatic catalysis of both bioRAFT polymerization and bioATRP to prompt polymer synthesis on the surface of Saccharomyces cerevisiae cells, with bioATRP outperforming bioRAFT polymerization. The resulting surface modification of living yeast cells with synthetic polymers allows for a significant change in yeast phenotype, including growth profile, aggregation characteristics, and conjugation of non-native enzymes to the clickable polymers on the cell surface, opening new avenues in bioorthogonal cell-surface engineering.
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Affiliation(s)
- Andrea Belluati
- Department of Chemistry, Technical University of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany.
- Centre for Synthetic Biology, Technical University of Darmstadt, Merckstraße 25, 64283 Darmstadt, Germany
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glashow G1 1XL, UK
| | - Dominic Happel
- Department of Chemistry, Technical University of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany.
| | - Malte Erbe
- Department of Chemistry, Technical University of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany.
| | - Nicole Kirchner
- Department of Chemistry, Technical University of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany.
| | - Anna Szelwicka
- Department of Chemistry, Technical University of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany.
| | - Adrian Bloch
- Department of Chemistry, Technical University of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany.
| | - Valeria Berner
- Department of Chemistry, Technical University of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany.
| | - Andreas Christmann
- Department of Chemistry, Technical University of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany.
| | - Brigitte Hertel
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany
| | - Raheleh Pardehkhorram
- Department of Chemistry, Technical University of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany.
| | - Amin Reyhani
- Department of Chemistry, Technical University of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany.
| | - Harald Kolmar
- Department of Chemistry, Technical University of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany.
- Centre for Synthetic Biology, Technical University of Darmstadt, Merckstraße 25, 64283 Darmstadt, Germany
| | - Nico Bruns
- Department of Chemistry, Technical University of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany.
- Centre for Synthetic Biology, Technical University of Darmstadt, Merckstraße 25, 64283 Darmstadt, Germany
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glashow G1 1XL, UK
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14
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Kizerwetter M, Pietz K, Tomasovic LM, Spangler JB. Empowering gene delivery with protein engineering platforms. Gene Ther 2023; 30:775-782. [PMID: 36529795 PMCID: PMC10277311 DOI: 10.1038/s41434-022-00379-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
The repertoire of therapeutic proteins has been substantially augmented by molecular engineering approaches, which have seen remarkable advancement in recent years. In particular, advances in directed evolution technologies have empowered the development of custom-designed proteins with novel and disease-relevant functions. Whereas engineered proteins have typically been administered through systemic injection of the purified molecule, exciting progress in gene delivery affords the opportunity to elicit sustained production of the engineered proteins by targeted cells in the host organism. Combining developments at the leading edge of protein engineering and gene delivery has catapulted a new wave of molecular and cellular therapy approaches, which harbor great promise for personalized and precision medicine. This mini-review outlines currently used display platforms for protein evolution and describes recent examples of how the resulting engineered proteins have been incorporated into DNA- and cell-based therapeutic platforms, both in vitro and in vivo. Collectively, the strategies detailed herein provide a framework for synthesizing molecular engineering workflows with gene therapy systems for a breadth of applications in research and medicine.
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Affiliation(s)
- Monika Kizerwetter
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD, USA
| | - Kevin Pietz
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD, USA
| | - Luke M Tomasovic
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD, USA
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jamie B Spangler
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD, USA.
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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15
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Shoari A, Khalili-Tanha G, Coban MA, Radisky ES. Structure and computation-guided yeast surface display for the evolution of TIMP-based matrix metalloproteinase inhibitors. Front Mol Biosci 2023; 10:1321956. [PMID: 38074088 PMCID: PMC10702220 DOI: 10.3389/fmolb.2023.1321956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 11/13/2023] [Indexed: 01/03/2024] Open
Abstract
The study of protein-protein interactions (PPIs) and the engineering of protein-based inhibitors often employ two distinct strategies. One approach leverages the power of combinatorial libraries, displaying large ensembles of mutant proteins, for example, on the yeast cell surface, to select binders. Another approach harnesses computational modeling, sifting through an astronomically large number of protein sequences and attempting to predict the impact of mutations on PPI binding energy. Individually, each approach has inherent limitations, but when combined, they generate superior outcomes across diverse protein engineering endeavors. This synergistic integration of approaches aids in identifying novel binders and inhibitors, fine-tuning specificity and affinity for known binding partners, and detailed mapping of binding epitopes. It can also provide insight into the specificity profiles of varied PPIs. Here, we outline strategies for directing the evolution of tissue inhibitors of metalloproteinases (TIMPs), which act as natural inhibitors of matrix metalloproteinases (MMPs). We highlight examples wherein design of combinatorial TIMP libraries using structural and computational insights and screening these libraries of variants using yeast surface display (YSD), has successfully optimized for MMP binding and selectivity, and conferred insight into the PPIs involved.
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Affiliation(s)
| | | | | | - Evette S. Radisky
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, United States
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16
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Loock M, Antunes LB, Heslop RT, De Lauri AA, Brito Lira A, Cestari I. High-Efficiency Transformation and Expression of Genomic Libraries in Yeast. Methods Protoc 2023; 6:89. [PMID: 37736972 PMCID: PMC10514863 DOI: 10.3390/mps6050089] [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: 08/08/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023] Open
Abstract
Saccharomyces cerevisiae is a powerful system for the expression of genome-wide or combinatorial libraries for diverse types of screening. However, expressing large libraries in yeast requires high-efficiency transformation and controlled expression. Transformation of yeast using electroporation methods is more efficient than chemical methods; however, protocols described for electroporation require large amounts of linearized plasmid DNA and often yield approximately 106 cfu/µg of plasmid DNA. We optimized the electroporation of yeast cells for the expression of whole-genome libraries to yield up to 108 cfu/µg plasmid DNA. The protocol generates sufficient transformants for 10-100× coverage of diverse genome libraries with small amounts of genomic libraries (0.1 µg of DNA per reaction) and provides guidance on calculations to estimate library size coverage and transformation efficiency. It describes the preparation of electrocompetent yeast cells with lithium acetate and dithiothreitol conditioning step and the transformation of cells by electroporation with carrier DNA. We validated the protocol using three yeast surface display libraries and demonstrated using nanopore sequencing that libraries' size and diversity are preserved. Moreover, expression analysis confirmed library functionality and the method's efficacy. Hence, this protocol yields a sufficient representation of the genome of interest for downstream screening purposes while limiting the amount of the genomic library required.
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Affiliation(s)
- Mira Loock
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, QC H9X 3V9, Canada
| | | | - Rhiannon T Heslop
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, QC H9X 3V9, Canada
- Infectious Diseases and One Health Consortium, Faculté de Pharmacie de Tours, 31, Avenue Monge, 37200 Tours, France
| | | | - Andressa Brito Lira
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, QC H9X 3V9, Canada
- Program of Postgraduate Studies in Natural Products and Synthetic Bioactives, Federal University of Paraıba, João Pessoa 58051-900, Brazil
| | - Igor Cestari
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, QC H9X 3V9, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada
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17
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Lim HT, Kok BH, Leow CY, Leow CH. Exploring shark VNAR antibody against infectious diseases using phage display technology. FISH & SHELLFISH IMMUNOLOGY 2023; 140:108986. [PMID: 37541634 DOI: 10.1016/j.fsi.2023.108986] [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: 03/23/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]
Abstract
Antibody with high affinity and specificity to antigen has widely used as a tool to combat various diseases. The variable domain of immunoglobulin new antigen receptor (VNAR) naturally found in shark contains autonomous function as single-domain antibody. Due to its excellent characteristics, the small, non-complex, and highly stable have made shark VNAR can acquires the antigen-binding capability that might not be reached by conventional antibody. Phage display technology enables shark VNAR to be presented on the surface of phage, allowing the exploration of shark VNAR as an alternative antibody format to target antigens from various infectious diseases. The application of phage-displayed shark VNAR in antibody library and biopanning eventually leads to the discovery and isolation of antigen-specific VNARs with diagnostic and therapeutic potential towards infectious diseases. This review provides an overview of the shark VNAR antibody, the types of phage display technology with comparison to the other types of display system, as well as the application and case studies of phage-displayed shark VNAR antibodies against infectious diseases.
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Affiliation(s)
- Hui Ting Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
| | - Boon Hui Kok
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
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18
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Mallik BB, Stanislaw J, Alawathurage TM, Khmelinskaia A. De Novo Design of Polyhedral Protein Assemblies: Before and After the AI Revolution. Chembiochem 2023; 24:e202300117. [PMID: 37014094 DOI: 10.1002/cbic.202300117] [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: 02/15/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 04/05/2023]
Abstract
Self-assembling polyhedral protein biomaterials have gained attention as engineering targets owing to their naturally evolved sophisticated functions, ranging from protecting macromolecules from the environment to spatially controlling biochemical reactions. Precise computational design of de novo protein polyhedra is possible through two main types of approaches: methods from first principles, using physical and geometrical rules, and more recent data-driven methods based on artificial intelligence (AI), including deep learning (DL). Here, we retrospect first principle- and AI-based approaches for designing finite polyhedral protein assemblies, as well as advances in the structure prediction of such assemblies. We further highlight the possible applications of these materials and explore how the presented approaches can be combined to overcome current challenges and to advance the design of functional protein-based biomaterials.
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Affiliation(s)
- Bhoomika Basu Mallik
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Jenna Stanislaw
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Tharindu Madhusankha Alawathurage
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Alena Khmelinskaia
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
- Current address: Department of Chemistry, Ludwig Maximillian University, 80539, Munich, Germany
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19
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Wang H, Zhou R, Xu F, Yang K, Zheng L, Zhao P, Shi G, Dai L, Xu C, Yu L, Li Z, Wang J, Wang J. Beyond canonical PROTAC: biological targeted protein degradation (bioTPD). Biomater Res 2023; 27:72. [PMID: 37480049 PMCID: PMC10362593 DOI: 10.1186/s40824-023-00385-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/21/2023] [Indexed: 07/23/2023] Open
Abstract
Targeted protein degradation (TPD) is an emerging therapeutic strategy with the potential to modulate disease-associated proteins that have previously been considered undruggable, by employing the host destruction machinery. The exploration and discovery of cellular degradation pathways, including but not limited to proteasomes and lysosome pathways as well as their degraders, is an area of active research. Since the concept of proteolysis-targeting chimeras (PROTACs) was introduced in 2001, the paradigm of TPD has been greatly expanded and moved from academia to industry for clinical translation, with small-molecule TPD being particularly represented. As an indispensable part of TPD, biological TPD (bioTPD) technologies including peptide-, fusion protein-, antibody-, nucleic acid-based bioTPD and others have also emerged and undergone significant advancement in recent years, demonstrating unique and promising activities beyond those of conventional small-molecule TPD. In this review, we provide an overview of recent advances in bioTPD technologies, summarize their compositional features and potential applications, and briefly discuss their drawbacks. Moreover, we present some strategies to improve the delivery efficacy of bioTPD, addressing their challenges in further clinical development.
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Affiliation(s)
- Huifang Wang
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Runhua Zhou
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China
| | - Fushan Xu
- The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Kongjun Yang
- The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Liuhai Zheng
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Pan Zhao
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Guangwei Shi
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China
| | - Lingyun Dai
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Chengchao Xu
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
| | - Le Yu
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China.
| | - Zhijie Li
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China.
| | - Jianhong Wang
- Shenzhen Mental Health Center, Shenzhen Kangning Hospital, Shenzhen, 518020, Guangdong, P. R. China.
| | - Jigang Wang
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China.
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China.
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China.
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20
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Lahiri P, Martin MS, Lino BR, Scheck RA, Van Deventer JA. Dual Noncanonical Amino Acid Incorporation Enabling Chemoselective Protein Modification at Two Distinct Sites in Yeast. Biochemistry 2023; 62:2098-2114. [PMID: 37377426 PMCID: PMC11146674 DOI: 10.1021/acs.biochem.2c00711] [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] [Indexed: 06/29/2023]
Abstract
Incorporation of more than one noncanonical amino acid (ncAA) within a single protein endows the resulting construct with multiple useful features such as augmented molecular recognition or covalent cross-linking capabilities. Herein, for the first time, we demonstrate the incorporation of two chemically distinct ncAAs into proteins biosynthesized in Saccharomyces cerevisiae. To complement ncAA incorporation in response to the amber (TAG) stop codon in yeast, we evaluated opal (TGA) stop codon suppression using three distinct orthogonal translation systems. We observed selective TGA readthrough without detectable cross-reactivity from host translation components. Readthrough efficiency at TGA was modulated by factors including the local nucleotide environment, gene deletions related to the translation process, and the identity of the suppressor tRNA. These observations facilitated systematic investigation of dual ncAA incorporation in both intracellular and yeast-displayed protein constructs, where we observed efficiencies up to 6% of wild-type protein controls. The successful display of doubly substituted proteins enabled the exploration of two critical applications on the yeast surface─(A) antigen binding functionality and (B) chemoselective modification with two distinct chemical probes through sequential application of two bioorthogonal click chemistry reactions. Lastly, by utilizing a soluble form of a doubly substituted construct, we validated the dual incorporation system using mass spectrometry and demonstrated the feasibility of conducting selective labeling of the two ncAAs sequentially using a "single-pot" approach. Overall, our work facilitates the addition of a 22nd amino acid to the genetic code of yeast and expands the scope of applications of ncAAs for basic biological research and drug discovery.
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Affiliation(s)
- Priyanka Lahiri
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Meghan S. Martin
- Chemistry Department, Tufts University, Medford, Massachusetts 02155, USA
| | - Briana R. Lino
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Rebecca A. Scheck
- Chemistry Department, Tufts University, Medford, Massachusetts 02155, USA
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
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21
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Feng X, Wang H. Emerging Landscape of Nanobodies and Their Neutralizing Applications against SARS-CoV-2 Virus. ACS Pharmacol Transl Sci 2023; 6:925-942. [PMID: 37470012 PMCID: PMC10275483 DOI: 10.1021/acsptsci.3c00042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Indexed: 07/21/2023]
Abstract
The new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the coronavirus disease 2019 (COVID-19) has significantly altered people's way of life. Despite widespread knowledge of vaccination, mask use, and avoidance of close contact, COVID-19 is still spreading around the world. Numerous research teams are examining the SARS-CoV-2 infection process to discover strategies to identify, prevent, and treat COVID-19 to limit the spread of this chronic coronavirus illness and restore lives to normalcy. Nanobodies have advantages over polyclonal and monoclonal antibodies (Ab) and Ab fragments, including reduced size, high stability, simplicity in manufacture, compatibility with genetic engineering methods, and lack of solubility and aggregation issues. Recent studies have shown that nanobodies that target the SARS-CoV-2 receptor-binding domain and disrupt ACE2 interactions are helpful in the prevention and treatment of SARS-CoV-2-infected animal models, despite the lack of evidence in human patients. The creation and evaluation of nanobodies, as well as their diagnostic and therapeutic applications against COVID-19, are discussed in this paper.
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Affiliation(s)
- Xuemei Feng
- Department
of Microbiology and Immunology, College
of Medicine and Health Science, China Three Gorges University, Yichang 443002, China
| | - Hu Wang
- Department
of Microbiology and Immunology, College
of Medicine and Health Science, China Three Gorges University, Yichang 443002, China
- Institute
of Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore 21215, United States
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22
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Konakbayeva D, Karlsson AJ. Strategies and opportunities for engineering antifungal peptides for therapeutic applications. Curr Opin Biotechnol 2023; 81:102926. [PMID: 37028003 PMCID: PMC10229436 DOI: 10.1016/j.copbio.2023.102926] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 04/09/2023]
Abstract
Antifungal peptides (AFPs) are widely described as promising prospects to treat and prevent fungal infections, though they are far less studied than their antibacterial counterparts. Although promising, AFPs have practical limitations that have hindered their use as therapeutics. Rational design and combinatorial engineering are powerful protein engineering strategies with much potential to address the limitations of AFPs by designing peptides with improved physiochemical and biological characteristics. We examine how rational design and combinatorial engineering approaches have already been used to improve the properties of AFPs and propose key opportunities for applying these strategies to push the design and application of AFPs forward.
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Affiliation(s)
- Dinara Konakbayeva
- Department of Chemical and Biomolecular Engineering, University of Maryland, 2113 Chemical and Nuclear Engineering Building (#090), 4418 Stadium Drive, College Park, MD 20742, USA
| | - Amy J Karlsson
- Department of Chemical and Biomolecular Engineering, University of Maryland, 2113 Chemical and Nuclear Engineering Building (#090), 4418 Stadium Drive, College Park, MD 20742, USA.
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23
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Heslop R, Gao M, Brito Lira A, Sternlieb T, Loock M, Sanghi SR, Cestari I. Genome-Wide Libraries for Protozoan Pathogen Drug Target Screening Using Yeast Surface Display. ACS Infect Dis 2023; 9:1078-1091. [PMID: 37083339 PMCID: PMC10187560 DOI: 10.1021/acsinfecdis.2c00568] [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: 11/11/2022] [Indexed: 04/22/2023]
Abstract
The lack of genetic tools to manipulate protozoan pathogens has limited the use of genome-wide approaches to identify drug or vaccine targets and understand these organisms' biology. We have developed an efficient method to construct genome-wide libraries for yeast surface display (YSD) and developed a YSD fitness screen (YSD-FS) to identify drug targets. We show the efficacy of our method by generating genome-wide libraries for Trypanosoma brucei, Trypanosoma cruzi, and Giardia lamblia parasites. Each library has a diversity of ∼105 to 106 clones, representing ∼6- to 30-fold of the parasite's genome. Nanopore sequencing confirmed the libraries' genome coverage with multiple clones for each parasite gene. Western blot and imaging analysis confirmed surface expression of the G. lamblia library proteins in yeast. Using the YSD-FS assay, we identified bonafide interactors of metronidazole, a drug used to treat protozoan and bacterial infections. We also found enrichment in nucleotide-binding domain sequences associated with yeast increased fitness to metronidazole, indicating that this drug might target multiple enzymes containing nucleotide-binding domains. The libraries are valuable biological resources for discovering drug or vaccine targets, ligand receptors, protein-protein interactions, and pathogen-host interactions. The library assembly approach can be applied to other organisms or expression systems, and the YSD-FS assay might help identify new drug targets in protozoan pathogens.
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Affiliation(s)
- Rhiannon Heslop
- Institute
of Parasitology, McGill University, Ste Anne de Bellevue, Montreal, QC H9X 3V9, Canada
- Faculté
de Pharmacie de Tours, 31, Avenue Monge, 37200 Tours, France
| | - Mengjin Gao
- Institute
of Parasitology, McGill University, Ste Anne de Bellevue, Montreal, QC H9X 3V9, Canada
| | - Andressa Brito Lira
- Institute
of Parasitology, McGill University, Ste Anne de Bellevue, Montreal, QC H9X 3V9, Canada
| | - Tamara Sternlieb
- Institute
of Parasitology, McGill University, Ste Anne de Bellevue, Montreal, QC H9X 3V9, Canada
| | - Mira Loock
- Institute
of Parasitology, McGill University, Ste Anne de Bellevue, Montreal, QC H9X 3V9, Canada
| | - Sahil Rao Sanghi
- Institute
of Parasitology, McGill University, Ste Anne de Bellevue, Montreal, QC H9X 3V9, Canada
| | - Igor Cestari
- Institute
of Parasitology, McGill University, Ste Anne de Bellevue, Montreal, QC H9X 3V9, Canada
- Division
of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada
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24
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Bhavya G, De Britto S, Satapute P, Geetha N, Jogaiah S. Biofabricated yeast: super-soldier for detoxification of heavy metals. World J Microbiol Biotechnol 2023; 39:148. [PMID: 37022650 DOI: 10.1007/s11274-023-03596-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/27/2023] [Indexed: 04/07/2023]
Abstract
The advances in nanotechnology have shown enormous impacts in environmental technology as a potent weapon for degradation of toxic organic pollutants and detoxification of heavy metals. It is either by in-situ or ex-situ adaptive strategies. Mycoremediation of environmental pollutants has been a success story of the past decade, by employing the wide arsenal of biological capabilities of fungi. Recently, the proficiency and uniqueness of yeast cell surface alterations have encouraged the generation of engineered yeast cells as dye degraders, heavy metal reduction and its recovery, and also as detoxifiers of various hazardous xenobiotic compounds. As a step forward, recent trends in research are towards developing biologically engineered living materials as potent, biocompatible and reusable hybrid nanomaterials. They include chitosan-yeast nanofibers, nanomats, nanopaper, biosilica hybrids, and TiO2-yeast nanocomposites. The nano-hybrid materials contribute significantly as supportive stabilizer, and entrappers, which enhances the biofabricated yeast cells' functionality. This field serves as an eco-friendly cutting-edge cocktail research area. In this review, we highlight recent research on biofabricated yeast cells and yeast-based biofabricated molecules, as potent heavy metals, toxic chemical detoxifiers, and their probable mechanistic properties with future application perspectives.
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Affiliation(s)
- Gurulingaiah Bhavya
- Nanobiotechnology laboratory, Department of Biotechnology, University of Mysore, Manasagangotri, Mysuru, Karnataka, 570006, India
| | - Savitha De Britto
- Division of Biological Sciences, School of Science and Technology, University of Goroka, 441, Goroka, Papua New Guinea
| | - Praveen Satapute
- Laboratory of Plant Healthcare and Diagnostics, Department of Biotechnology and Microbiology, Karnatak University, Dharwad, PG, Karnataka, 580 003, India
| | - Nagaraja Geetha
- Nanobiotechnology laboratory, Department of Biotechnology, University of Mysore, Manasagangotri, Mysuru, Karnataka, 570006, India
| | - Sudisha Jogaiah
- Laboratory of Plant Healthcare and Diagnostics, Department of Biotechnology and Microbiology, Karnatak University, Dharwad, PG, Karnataka, 580 003, India.
- Department of Environmental Science, Central University of Kerala, Tejaswini Hills, Periye (PO), Kasaragod (DT), Periye, Kerala, 671316, India.
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25
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Lu SY, Liu S, Patel MH, Glenzinski KM, Skory CD. Saccharomyces cerevisiae surface display of endolysin LysKB317 for control of bacterial contamination in corn ethanol fermentations. Front Bioeng Biotechnol 2023; 11:1162720. [PMID: 37091344 PMCID: PMC10117863 DOI: 10.3389/fbioe.2023.1162720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/20/2023] [Indexed: 04/09/2023] Open
Abstract
Control of bacterial contamination in bioethanol fermentation facilities has traditionally relied on chemical-based products such as hop acids and use of antibiotics. Recent emphasis on antibiotic stewardship has prompted new research into the development of alternative approaches to microbial remediation strategies. We recently described a recombinant peptidoglycan hydrolase, endolysin LysKB317, which inhibited Limosilactobacillus fermentum strains in corn mash fermentation. Here, Saccharomyces cerevisiae EBY100 was used to anchor recombinant LysKB317 using cell surface display with the a-agglutinin proteins Aga1p–Aga2p. Immunostaining and confocal fluorescence were used for localization of the extracellular interface of the cells. Yeast surface-expressed endolysin demonstrated an 83.8% decrease in bacterial cell counts compared to a 9.5% decrease in control yeast. Recombinant S. cerevisiae expressing LysKB317 used for small-scale corn mash fermentation, when infected with L. fermentum, could proactively control bacterial infection for 72 h with at least 1-log fold reduction. Analysis of fermentation products showed improved ethanol concentrations from 3.4% to at least 5.9% compared to the infection-only control and reduced levels of lactic and acetic acid from 34.7 mM to 13.8 mM and 25.5 mM to 18.1 mM, respectively. In an optimized yeast surface display system, proactive treatment of bacterial contaminants by endolysin LysKB317 can improve fermentation efficiency in the presence of L. fermentum contamination.
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Affiliation(s)
- Shao-Yeh Lu
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, Peoria, IL, United States
- *Correspondence: Shao-Yeh Lu,
| | - Siqing Liu
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, Peoria, IL, United States
| | - Maulik H. Patel
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, United States
| | - Kristina M. Glenzinski
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, Peoria, IL, United States
| | - Christopher D. Skory
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, Peoria, IL, United States
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26
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Jin BK, Odongo S, Radwanska M, Magez S. NANOBODIES®: A Review of Diagnostic and Therapeutic Applications. Int J Mol Sci 2023; 24:5994. [PMID: 36983063 PMCID: PMC10057852 DOI: 10.3390/ijms24065994] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
NANOBODY® (a registered trademark of Ablynx N.V) molecules (Nbs), also referred to as single domain-based VHHs, are antibody fragments derived from heavy-chain only IgG antibodies found in the Camelidae family. Due to their small size, simple structure, high antigen binding affinity, and remarkable stability in extreme conditions, nanobodies possess the potential to overcome several of the limitations of conventional monoclonal antibodies. For many years, nanobodies have been of great interest in a wide variety of research fields, particularly in the diagnosis and treatment of diseases. This culminated in the approval of the world's first nanobody based drug (Caplacizumab) in 2018 with others following soon thereafter. This review will provide an overview, with examples, of (i) the structure and advantages of nanobodies compared to conventional monoclonal antibodies, (ii) methods used to generate and produce antigen-specific nanobodies, (iii) applications for diagnostics, and (iv) ongoing clinical trials for nanobody therapeutics as well as promising candidates for clinical development.
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Affiliation(s)
- Bo-kyung Jin
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon 21985, Republic of Korea
| | - Steven Odongo
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon 21985, Republic of Korea
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala 7062, Uganda
- Center for Biosecurity and Global Health, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala 7062, Uganda
| | - Magdalena Radwanska
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon 21985, Republic of Korea
- Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Stefan Magez
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon 21985, Republic of Korea
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
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27
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Heinzelman P, Romero PA. Directed evolution of angiotensin-converting enzyme 2 (ACE2) peptidase activity profiles for therapeutic applications. Protein Sci 2023; 32:e4597. [PMID: 36794431 PMCID: PMC10019445 DOI: 10.1002/pro.4597] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/19/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023]
Abstract
Angiotensin-Converting Enzyme 2 (ACE2) has been investigated for its ability to beneficially modulate the Angiotensin receptor (ATR) therapeutic axis to treat multiple human diseases. Its broad substrate scope and diverse physiological roles however, limit its potential as a therapeutic agent. In this work, we address this limitation by establishing a yeast display-based liquid chromatography screen that enabled use of directed evolution to discover ACE2 variants that possess both wildtype or greater Ang-II hydrolytic activity and improved specificity toward Ang-II relative to the off-target peptide substrate Apelin-13. To obtain these results, we screened ACE2 active site libraries to reveal three substitution-tolerant positions (M360, T371 and Y510) that can be mutated to enhance ACE2's activity profile and followed up on these hits with focused double mutant libraries to further improve the enzyme. Relative to wildtype ACE2, our top variant (T371L/Y510Ile) displayed a sevenfold increase in Ang-II turnover number (kcat ), a sixfold diminished catalytic efficiency (kcat /Km ) on Apelin-13, and an overall decreased activity on other ACE2 substrates that were not directly assayed in the directed evolution screen. At physiologically relevant substrate concentrations, T371L/Y510Ile hydrolyzes as much or more Ang-II than wildtype ACE2 with concomitant Ang-II:Apelin-13 specificity improvements reaching 30-fold. Our efforts have delivered ATR axis-acting therapeutic candidates with relevance to both established and unexplored ACE2 therapeutic applications and provide a foundation for further ACE2 engineering efforts. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Pete Heinzelman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Philip A Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.,Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
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28
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Lopez-Morales J, Vanella R, Kovacevic G, Santos MS, Nash MA. Titrating Avidity of Yeast-Displayed Proteins Using a Transcriptional Regulator. ACS Synth Biol 2023; 12:419-431. [PMID: 36728831 PMCID: PMC9942200 DOI: 10.1021/acssynbio.2c00351] [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] [Indexed: 02/03/2023]
Abstract
Yeast surface display is a valuable tool for protein engineering and directed evolution; however, significant variability in the copy number (i.e., avidity) of displayed variants on the yeast cell wall complicates screening and selection campaigns. Here, we report an engineered titratable display platform that modulates the avidity of Aga2-fusion proteins on the yeast cell wall dependent on the concentration of the anhydrotetracycline (aTc) inducer. Our design is based on a genomic Aga1 gene copy and an episomal Aga2-fusion construct both under the control of an aTc-dependent transcriptional regulator that enables stoichiometric and titratable expression, secretion, and display of Aga2-fusion proteins. We demonstrate tunable display levels over 2-3 orders of magnitude for various model proteins, including glucose oxidase enzyme variants, mechanostable dockerin-binding domains, and anti-PDL1 affibody domains. By regulating the copy number of displayed proteins, we demonstrate the effects of titratable avidity levels on several specific phenotypic activities, including enzyme activity and cell adhesion to surfaces under shear flow. Finally, we show that titrating down the display level allows yeast-based binding affinity measurements to be performed in a regime that avoids ligand depletion effects while maintaining small sample volumes, avoiding a well-known artifact in yeast-based binding assays. The ability to titrate the multivalency of proteins on the yeast cell wall through simple inducer control will benefit protein engineering and directed evolution methodology relying on yeast display for broad classes of therapeutic and diagnostic proteins of interest.
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Affiliation(s)
- Joanan Lopez-Morales
- Department
of Chemistry, University of Basel, Basel 4058, Switzerland,Swiss
Nanoscience Institute, University of Basel, Basel 4056, Switzerland,Department
of Biosystems Science and Engineering, ETH
Zurich, Basel 4058, Switzerland
| | - Rosario Vanella
- Department
of Chemistry, University of Basel, Basel 4058, Switzerland,Department
of Biosystems Science and Engineering, ETH
Zurich, Basel 4058, Switzerland
| | - Gordana Kovacevic
- Department
of Chemistry, University of Basel, Basel 4058, Switzerland,Department
of Biosystems Science and Engineering, ETH
Zurich, Basel 4058, Switzerland
| | - Mariana Sá Santos
- Department
of Chemistry, University of Basel, Basel 4058, Switzerland,Department
of Biosystems Science and Engineering, ETH
Zurich, Basel 4058, Switzerland
| | - Michael A. Nash
- Department
of Chemistry, University of Basel, Basel 4058, Switzerland,Swiss
Nanoscience Institute, University of Basel, Basel 4056, Switzerland,Department
of Biosystems Science and Engineering, ETH
Zurich, Basel 4058, Switzerland,
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29
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Lei M, Trivedi VD, Nair NU, Lee K, Van Deventer JA. Flow cytometric evaluation of yeast-bacterial cell-cell interactions. Biotechnol Bioeng 2023; 120:399-408. [PMID: 36259110 PMCID: PMC10072783 DOI: 10.1002/bit.28253] [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: 06/10/2022] [Revised: 09/23/2022] [Accepted: 10/09/2022] [Indexed: 01/13/2023]
Abstract
Synthetic cell-cell interaction systems can be useful for understanding multicellular communities or for screening binding molecules. We adapt a previously characterized set of synthetic cognate nanobody-antigen pairs to a yeast-bacteria coincubation format and use flow cytometry to evaluate cell-cell interactions mediated by binding between surface-displayed molecules. We further use fluorescence-activated cell sorting to enrich a specific yeast-displayed nanobody within a mixed yeast-display population. Finally, we demonstrate that this system supports the characterization of a therapeutically relevant nanobody-antigen interaction: a previously discovered nanobody that binds to the intimin protein expressed on the surface of enterohemorrhagic Escherichia coli. Overall, our findings indicate that the yeast-bacteria format supports efficient evaluation of ligand-target interactions. With further development, this format may facilitate systematic characterization and high-throughput discovery of bacterial surface-binding molecules.
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Affiliation(s)
- Ming Lei
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155
| | - Vikas D. Trivedi
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155
| | - Nikhil U. Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155
| | - Kyongbum Lee
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155
| | - James A. Van Deventer
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155
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30
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Mieczkowski C, Zhang X, Lee D, Nguyen K, Lv W, Wang Y, Zhang Y, Way J, Gries JM. Blueprint for antibody biologics developability. MAbs 2023; 15:2185924. [PMID: 36880643 PMCID: PMC10012935 DOI: 10.1080/19420862.2023.2185924] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Large-molecule antibody biologics have revolutionized medicine owing to their superior target specificity, pharmacokinetic and pharmacodynamic properties, safety and toxicity profiles, and amenability to versatile engineering. In this review, we focus on preclinical antibody developability, including its definition, scope, and key activities from hit to lead optimization and selection. This includes generation, computational and in silico approaches, molecular engineering, production, analytical and biophysical characterization, stability and forced degradation studies, and process and formulation assessments. More recently, it is apparent these activities not only affect lead selection and manufacturability, but ultimately correlate with clinical progression and success. Emerging developability workflows and strategies are explored as part of a blueprint for developability success that includes an overview of the four major molecular properties that affect all developability outcomes: 1) conformational, 2) chemical, 3) colloidal, and 4) other interactions. We also examine risk assessment and mitigation strategies that increase the likelihood of success for moving the right candidate into the clinic.
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Affiliation(s)
- Carl Mieczkowski
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Xuejin Zhang
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Dana Lee
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Khanh Nguyen
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Wei Lv
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Yanling Wang
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Yue Zhang
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Jackie Way
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Jean-Michel Gries
- President, Discovery Research, Hengenix Biotech, Inc, Milpitas, CA, USA
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31
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Duan F, Sun T, Zhang J, Wang K, Wen Y, Lu L. Recent innovations in immobilization of β-galactosidases for industrial and therapeutic applications. Biotechnol Adv 2022; 61:108053. [DOI: 10.1016/j.biotechadv.2022.108053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022]
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32
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Massey OW, Suphioglu C. Taking a Breather: Advances in Interleukin 5 Inhibition for Asthma Relief. Int J Mol Sci 2022; 23:ijms231911166. [PMID: 36232470 PMCID: PMC9569507 DOI: 10.3390/ijms231911166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/05/2022] [Accepted: 09/15/2022] [Indexed: 11/26/2022] Open
Abstract
Interleukin 5 (IL-5) is a major cytokine responsible for eosinophil proliferation, migration and degranulation. Eosinophils play a considerable role in the manifestation of type 2 asthma, and therefore this makes IL-5 a unique and clinically important target for therapeutic intervention. Due to the critical role that IL-5 plays in all areas of eosinophil activity, it has been identified and targeted by three therapeutics, Mepolizumab, Benralizumab and Reslizumab. This review describes the IL-5 pathway and presents the clinical trial history of the three IL-5 inhibitors, to provide insight into the role of IL-5 in clinical asthma presentation. Additionally, this review aims to foster further investigation into the IL-5 pathway by describing current novel therapeutic discovery strategies with monoclonal antibodies.
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Affiliation(s)
- Oliver William Massey
- NeuroAllergy Research Laboratory (NARL), School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, 75 Pigdons Road, Geelong, VIC 3216, Australia
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, 75 Pigdons Road, Geelong, VIC 3216, Australia
| | - Cenk Suphioglu
- NeuroAllergy Research Laboratory (NARL), School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, 75 Pigdons Road, Geelong, VIC 3216, Australia
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, 75 Pigdons Road, Geelong, VIC 3216, Australia
- Correspondence:
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33
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Cruz CJG, Kil R, Wong S, Dacquay LC, Mirano-Bascos D, Rivera PT, McMillen DR. Malarial Antibody Detection with an Engineered Yeast Agglutination Assay. ACS Synth Biol 2022; 11:2938-2946. [PMID: 35861604 DOI: 10.1021/acssynbio.2c00160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Malaria, a disease caused by the Plasmodium parasite carried by Anopheles mosquitoes, is commonly diagnosed by microscopy of peripheral blood smears and with rapid diagnostic tests. Both methods show limited detection of low parasitemia that may maintain transmission and hinder malaria elimination. We have developed a novel agglutination assay in which modified Saccharomyces cerevisiae cells act as antigen-displaying bead-like particles to capture malaria antibodies. The Epidermal Growth Factor-1 like domain (EGF1) of the Plasmodium falciparum merozoite surface protein-1 (PfMSP-119) was displayed on the yeast surface and shown to be capable of binding antimalaria antibodies. Mixed with a second yeast strain displaying the Z domain of Protein A from Staphylococcus aureus and allowed to settle in a round-bottomed well, the yeast produce a visually distinctive agglutination test result: a tight "button" at a low level of malarial antibodies, and a diffuse "sheet" when higher antibody levels are present. Positive agglutination results were observed in malaria-positive human serum to a serum dilution of 1:100 to 1:125. Since the yeast cells are inexpensive to produce, the test may be amenable to local production in regions seeking malaria surveillance information to guide their elimination programs.
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Affiliation(s)
- Criselda Jean G Cruz
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,College of Medicine, University of the Philippines Manila, Manila 1108, Philippines
| | - Richard Kil
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Stanley Wong
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Louis C Dacquay
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Denise Mirano-Bascos
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Pilarita T Rivera
- College of Medicine, University of the Philippines Manila, Manila 1108, Philippines.,Department of Parasitology, College of Public Health, University of the Philippines Manila, Manila 1000, Philippines
| | - David R McMillen
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
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Dominant Negative Mutants of Human Immunodeficiency Virus Type 1 Viral Infectivity Factor (Vif) Disrupt Core-Binding Factor Beta-Vif Interaction. J Virol 2022; 96:e0055522. [PMID: 35950859 PMCID: PMC9472641 DOI: 10.1128/jvi.00555-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Apolipoprotein B mRNA-editing catalytic polypeptide-like 3 family members (APOBEC3s) are host restriction factors that inhibit viral replication. Viral infectivity factor (Vif), a human immunodeficiency virus type 1 (HIV-1) accessory protein, mediates the degradation of APOBEC3s by forming the Vif-E3 complex, in which core-binding factor beta (CBFβ) is an essential molecular chaperone. Here, we screened nonfunctional Vif mutants with high affinity for CBFβ to inhibit HIV-1 in a dominant negative manner. We applied the yeast surface display technology to express Vif random mutant libraries, and mutants showing high CBFβ affinity were screened using flow cytometry. Most of the screened Vif mutants containing random mutations of different frequencies were able to rescue APOBEC3G (A3G). In the subsequent screening, three of the mutants restricted HIV-1, recovered G-to-A hypermutation, and rescued APOBEC3s. Among them, Vif-6M showed a cross-protection effect toward APOBEC3C, APOBEC3F, and African green monkey A3G. Stable expression of Vif-6M in T lymphocytes inhibited the viral replication in newly HIV-1-infected cells and the chronically infected cell line H9/HXB2. Furthermore, the expression of Vif-6M provided a survival advantage to T lymphocytes infected with HIV-1. These results suggest that dominant negative Vif mutants acting on the Vif-CBFβ target potently restrict HIV-1. IMPORTANCE Antiviral therapy cannot eliminate HIV and exhibits disadvantages such as drug resistance and toxicity. Therefore, novel strategies for inhibiting viral replication in patients with HIV are urgently needed. APOBEC3s in host cells are able to inhibit viral replication but are antagonized by HIV-1 Vif-mediated degradation. Therefore, we screened nonfunctional Vif mutants with high affinity for CBFβ to compete with the wild-type Vif (wtVif) as a potential strategy to assist with HIV-1 treatment. Most screened mutants rescued the expression of A3G in the presence of wtVif, especially Vif-6M, which could protect various APOBEC3s and improve the incorporation of A3G into HIV-1 particles. Transduction of Vif-6M into T lymphocytes inhibited the replication of the newly infected virus and the chronically infected virus. These data suggest that Vif mutants targeting the Vif-CBFβ interaction may be promising in the development of a new AIDS therapeutic strategy.
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35
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Gätjen D, Tomszak F, Dettmann JC, Droste M, Nölle V, Wieczorek M. Design of a novel switchable antibody display system in Pichia pastoris. Appl Microbiol Biotechnol 2022; 106:6209-6224. [PMID: 35953606 DOI: 10.1007/s00253-022-12108-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2022] [Indexed: 12/13/2022]
Abstract
Yeast surface display (YSD) has been shown to represent a powerful tool in the field of antibody discovery and engineering as well as for selection of high producer clones. However, YSD is predominantly applied in Saccharomyces cerevisiae, whereas expression of heterologous proteins is generally favored in the non-canonical yeast Pichia pastoris (Komagataella phaffii). Establishment of surface display in P. pastoris would therefore enable antibody selection and expression in a single host. Here we describe the generation of a Pichia surface display (PSD) system based on antibody expression from episomal plasmids. By screening a diverse set of expression vectors using Design of Experiments (DoE), the effect of different genetic elements on the surface expression of antibody fragments was analyzed. Among the tested genetic elements, we found that the combination of P. pastoris formaldehyde dehydrogenase (FLD1) promoter, S. cerevisiae invertase 2 signal peptide (SUC2), and α-agglutinin cell wall protein (SAG1) including an autonomously replicating sequence of Kluyveromyces lactis (panARS) were contributing most strongly to higher display levels of three tested antibody fragments. Employing this combination resulted in the display of antibody fragments for up to 25% of cells. Despite significantly reduced expression levels in PSD compared to well-established YSD in S. cerevisiae, similar fractions of antigen binding single-chain variable fragments (scFvs) were observed (80% vs. 84%). In addition, plasmid stability assays and flow cytometric analysis demonstrated the efficient plasmid clearance of cells and associated loss of antibody fragment display after removal of selective pressure. KEY POINTS: • First report of antibody display in P. pastoris using episomal plasmids. • Identification of genetic elements conferring highest levels of antibody display. • Comparable antigen binding capacity of displayed scFvs for PSD compared to YSD.
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Affiliation(s)
- Dominic Gätjen
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch, Gladbach, Germany
| | - Florian Tomszak
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch, Gladbach, Germany
| | | | - Miriam Droste
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch, Gladbach, Germany
| | - Volker Nölle
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch, Gladbach, Germany
| | - Marek Wieczorek
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch, Gladbach, Germany.
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36
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Holec PV, Camacho KV, Breuckman KC, Mou J, Birnbaum ME. Proteome-Scale Screening to Identify High-Expression Signal Peptides with Minimal N-Terminus Biases via Yeast Display. ACS Synth Biol 2022; 11:2405-2416. [PMID: 35687717 DOI: 10.1021/acssynbio.2c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Signal peptides are critical for the efficient expression and routing of extracellular and secreted proteins. Most protein production and screening technologies rely upon a relatively small set of signal peptides. Despite their central role in biotechnology, there are limited studies comprehensively examining the interplay between signal peptides and expressed protein sequences. Here, we describe a high-throughput method to screen novel signal peptides that maintain a high degree of surface expression across a range of protein scaffolds with highly variable N-termini. We find that the canonical signal peptide used in yeast surface display, derived from Aga2p, fails to achieve high surface expression for 42.5% of constructs containing diverse N-termini. To circumvent this, we have identified two novel signal peptides derived from endogenous yeast proteins, SRL1 and KISH, which are highly tolerant to diverse N-terminal sequences. This pipeline can be used to expand our understanding of signal peptide function, identify improved signal peptides for protein expression, and refine the computational tools used for signal peptide prediction.
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Affiliation(s)
- Patrick V Holec
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Karen V Camacho
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kathryn C Breuckman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jody Mou
- Harvard-MIT Program in Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael E Birnbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
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37
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Song L, Wu F, Li C, Zhang S. Dietary intake of GDF11 delays the onset of several biomarkers of aging in male mice through anti-oxidant system via Smad2/3 pathway. Biogerontology 2022; 23:341-362. [PMID: 35604508 PMCID: PMC9125541 DOI: 10.1007/s10522-022-09967-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/02/2022] [Indexed: 11/08/2022]
Abstract
Current studies have generated controversy over the age-related change in concentration of growth differentiation factor 11 (GDF11) and its role in the genesis of rejuvenation conditions. In this study, we displayed rGDF11 on the surface of Yarrowic Lipolytica (Y. lipolytica), and proved the bioavailability of the yeast-displayed rGDF11 by oral delivery in aged male mice. On the basis of these findings, we started to explore the anti-aging activity and underlying mechanisms of displayed rGDF11. It was found that dietary intake of displayed rGDF11 had little influence on the body weight and biochemical parameters of aged male mice, but delayed the occurrence and development of age-related biomarkers such as lipofuscin (LF) and senescence-associated-β-galactosidase, and to some extent, prolonged the lifespan of aged male mice. Moreover, we demonstrated once again that dietary intake of displayed rGDF11 enhanced the activity of anti-oxidant enzymes, including catalase (CAT), superoxide dismutase (SOD) and glutathione peroxidase (GPX), reduced the reactive oxygen species (ROS) level, and slowed down the protein oxidation and lipid peroxidation. Importantly, we showed for the first time that rGDF11 enhanced the activity of CAT, SOD and GPX through activation of the Smad2/3 signaling pathway. Our study also provided a simple and safe route for delivery of recombinant GDF11, facilitating its therapeutic application in the future.
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Affiliation(s)
- Lili Song
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Fei Wu
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Congjun Li
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Shicui Zhang
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China.
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38
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Engineering Proteins Containing Noncanonical Amino Acids on the Yeast Surface. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2491:491-559. [PMID: 35482204 DOI: 10.1007/978-1-0716-2285-8_23] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Yeast display has been used to advance many critical research areas, including the discovery of unique protein binders and biological therapeutics. In parallel, noncanonical amino acids (ncAAs) have been used to tailor antibody-drug conjugates and enable discovery of therapeutic leads. Together, these two technologies have allowed for generation of synthetic antibody libraries, where the introduction of ncAAs in yeast-displayed proteins allows for library screening for therapeutically relevant targets. The combination of yeast display with genetically encoded ncAAs increases the available chemistry in proteins and advances applications that require high-throughput strategies. In this chapter, we discuss methods for displaying proteins containing ncAAs on the yeast surface, generating and screening libraries of proteins containing ncAAs, preparing bioconjugates on the yeast surface in large scale, generating and screening libraries of aminoacyl-tRNA synthetases (aaRSs) for encoding ncAAs by using reporter constructs, and characterizing ncAA-containing proteins secreted from yeast. The experimental designs laid out in this chapter are generalizable for discovery of protein binders to a variety of targets and aaRS evolution to continue expanding the genetic code beyond what is currently available in yeast.
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39
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Kovačević G, Elgahwash RGA, Blažić M, Pantić N, Prodanović O, Balaž AM, Prodanović R. Production of fructose and gluconic acid from sucrose with cross-linked yeast cell walls expressing glucose oxidase on the surface. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Abstract
While computational engineering of therapeutic proteins is a desirable goal, in practice the optimization of protein–protein interactions requires substantial experimental intervention. We present here a computational approach that focuses on stabilizing core protein structures rather than engineering the protein–protein interface. Using this approach, we designed thermostabilized interleukin-2 (IL-2) variants that bind tightly to their receptor without experimental optimization, mimicking the properties of the yeast-display engineered IL-2 variant “super-2.” Our results suggest that structure-guided stabilization may be a general method for in silico affinity maturation of protein–protein interactions. Affinity maturation of protein–protein interactions is an important approach in the development of therapeutic proteins such as cytokines. Typical experimental strategies involve targeting the cytokine-receptor interface with combinatorial libraries and then selecting for higher-affinity variants. Mutations to the binding scaffold are usually not considered main drivers for improved affinity. Here we demonstrate that computational design can provide affinity-enhanced variants of interleukin-2 (IL-2) “out of the box” without any requirement for interface engineering. Using a strategy of global IL-2 structural stabilization targeting metastable regions of the three-dimensional structure, rather than the receptor binding interfaces, we computationally designed thermostable IL-2 variants with up to 40-fold higher affinity for IL-2Rβ without any library-based optimization. These IL-2 analogs exhibited CD25-independent activities on T and natural killer (NK) cells both in vitro and in vivo, mimicking the properties of the IL-2 superkine “super-2” that was engineered through yeast surface display [A. M. Levin et al., Nature, 484, 529–533 (2012)]. Structure-guided stabilization of cytokines is a powerful approach to affinity maturation with applications to many cytokine and protein–protein interactions.
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41
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Incorporating, Quantifying, and Leveraging Noncanonical Amino Acids in Yeast. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2394:377-432. [PMID: 35094338 DOI: 10.1007/978-1-0716-1811-0_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Genetic code expansion has allowed for extraordinary advances in enhancing protein chemical diversity and functionality, but there remains a critical need for understanding and engineering genetic code expansion systems for improved efficiency. Incorporation of noncanonical amino acids (ncAAs) at stop codons provides a site-specific method for introducing unique chemistry into proteins, though often at reduced yields compared to wild-type proteins. A powerful platform for ncAA incorporation supports both the expression and evaluation of chemically diverse proteins for a broad range of applications. In yeast, ncAAs have been used to study dynamic cellular processes such as protein-protein interactions and also allow for exploration of eukaryotic-specific biology such as epigenetics. Furthermore, yeast display is an advantageous technology for engineering and screening the properties of proteins in high throughput. The protocols presented in this chapter describe detailed methods for the yeast-based genetic encoding of ncAAs in proteins intracellularly or on the yeast surface. In addition, methods are presented for modifying proteins on the yeast surface using bioorthogonal chemical reactions and evaluating reaction efficiency. Finally, protocols are included for the preparation of libraries that involve genetic code expansion. Libraries of proteins that contain ncAAs or libraries of the cellular machinery required to encode ncAAs can be constructed and screened in high throughput for many biological and chemical applications. Efficient incorporation of ncAAs facilitates elucidation of fundamental eukaryotic biology and advances tools for enzyme and genome engineering to evolve host cells that are better able to accommodate alternative genetic codes.
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42
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Kenny SE, Antaw F, Locke WJ, Howard CB, Korbie D, Trau M. Next-Generation Molecular Discovery: From Bottom-Up In Vivo and In Vitro Approaches to In Silico Top-Down Approaches for Therapeutics Neogenesis. Life (Basel) 2022; 12:life12030363. [PMID: 35330114 PMCID: PMC8950575 DOI: 10.3390/life12030363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/23/2022] [Indexed: 12/02/2022] Open
Abstract
Protein and drug engineering comprises a major part of the medical and research industries, and yet approaches to discovering and understanding therapeutic molecular interactions in biological systems rely on trial and error. The general approach to molecular discovery involves screening large libraries of compounds, proteins, or antibodies, or in vivo antibody generation, which could be considered “bottom-up” approaches to therapeutic discovery. In these bottom-up approaches, a minimal amount is known about the therapeutics at the start of the process, but through meticulous and exhaustive laboratory work, the molecule is characterised in detail. In contrast, the advent of “big data” and access to extensive online databases and machine learning technologies offers promising new avenues to understanding molecular interactions. Artificial intelligence (AI) now has the potential to predict protein structure at an unprecedented accuracy using only the genetic sequence. This predictive approach to characterising molecular structure—when accompanied by high-quality experimental data for model training—has the capacity to invert the process of molecular discovery and characterisation. The process has potential to be transformed into a top-down approach, where new molecules can be designed directly based on the structure of a target and the desired function, rather than performing screening of large libraries of molecular variants. This paper will provide a brief evaluation of bottom-up approaches to discovering and characterising biological molecules and will discuss recent advances towards developing top-down approaches and the prospects of this.
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Affiliation(s)
- Sophie E. Kenny
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner of College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia; (S.E.K.); (F.A.); (C.B.H.)
| | - Fiach Antaw
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner of College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia; (S.E.K.); (F.A.); (C.B.H.)
| | - Warwick J. Locke
- Molecular Diagnostic Solutions, Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Building 101, Clunies Ross Street, Canberra, ACT 2601, Australia;
| | - Christopher B. Howard
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner of College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia; (S.E.K.); (F.A.); (C.B.H.)
| | - Darren Korbie
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner of College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia; (S.E.K.); (F.A.); (C.B.H.)
- Correspondence: (D.K.); (M.T.)
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner of College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia; (S.E.K.); (F.A.); (C.B.H.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence: (D.K.); (M.T.)
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43
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Meanor JN, Keung AJ, Rao BM. Modified Histone Peptides Linked to Magnetic Beads Reduce Binding Specificity. Int J Mol Sci 2022; 23:ijms23031691. [PMID: 35163614 PMCID: PMC8836101 DOI: 10.3390/ijms23031691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/20/2022] [Accepted: 01/29/2022] [Indexed: 12/03/2022] Open
Abstract
Histone post-translational modifications are small chemical changes to the histone protein structure that have cascading effects on diverse cellular functions. Detecting histone modifications and characterizing their binding partners are critical steps in understanding chromatin biochemistry and have been accessed using common reagents such as antibodies, recombinant assays, and FRET-based systems. High-throughput platforms could accelerate work in this field, and also could be used to engineer de novo histone affinity reagents; yet, published studies on their use with histones have been noticeably sparse. Here, we describe specific experimental conditions that affect binding specificities of post-translationally modified histones in classic protein engineering platforms and likely explain the relative difficulty with histone targets in these platforms. We also show that manipulating avidity of binding interactions may improve specificity of binding.
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Affiliation(s)
- Jenna N. Meanor
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC 27606, USA;
| | - Albert J. Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC 27606, USA;
- Correspondence: (A.J.K.); (B.M.R.)
| | - Balaji M. Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC 27606, USA;
- Golden LEAF Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695, USA
- Correspondence: (A.J.K.); (B.M.R.)
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44
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Lin K, Han S, Zheng S. Application of Corynebacterium glutamicum engineering display system in three generations of biorefinery. Microb Cell Fact 2022; 21:14. [PMID: 35090458 PMCID: PMC8796525 DOI: 10.1186/s12934-022-01741-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/09/2022] [Indexed: 11/29/2022] Open
Abstract
The fermentation production of platform chemicals in biorefineries is a sustainable alternative to the current petroleum refining process. The natural advantages of Corynebacterium glutamicum in carbon metabolism have led to C. glutamicum being used as a microbial cell factory that can use various biomass to produce value-added platform chemicals and polymers. In this review, we discussed the use of C. glutamicum surface display engineering bacteria in the three generations of biorefinery resources, and analyzed the C. glutamicum engineering display system in degradation, transport, and metabolic network reconstruction models. These engineering modifications show that the C. glutamicum engineering display system has great potential to become a cell refining factory based on sustainable biomass, and further optimizes the inherent properties of C. glutamicum as a whole-cell biocatalyst. This review will also provide a reference for the direction of future engineering transformation.
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Affiliation(s)
- Kerui Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.
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45
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Abstract
The Tabula Gallus is a proposed project that aims to create a map of every cell type in the chicken body and chick embryos. Chickens (Gallus gallus) are one of the most recognized model animals that recapitulate the development and physiology of mammals. The Tabula Gallus will generate a compendium of single-cell transcriptome data from Gallus gallus, characterize each cell type, and provide tools for the study of the biology of this species, similar to other ongoing cell atlas projects (Tabula Muris and Tabula Sapiens/Human Cell Atlas for mice and humans, respectively). The Tabula Gallus will potentially become an international collaboration between many researchers. This project will be useful for the basic scientific study of Gallus gallus and other birds (e.g., cell biology, molecular biology, developmental biology, neuroscience, physiology, oncology, virology, behavior, ecology, and evolution). It will eventually be beneficial for a better understanding of human health and diseases.
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46
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Carrara SC, Bogen JP, Grzeschik J, Hock B, Kolmar H. Antibody Library Screening Using Yeast Biopanning and Fluorescence-Activated Cell Sorting. Methods Mol Biol 2022; 2491:177-193. [PMID: 35482191 DOI: 10.1007/978-1-0716-2285-8_10] [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: 06/14/2023]
Abstract
Yeast surface display (YSD) emerged as a prominent screening methodology for the isolation of monoclonal antibodies (mAbs) against various antigens. However, phage display remains the gold standard in cell panning-based screenings to isolate mAbs against difficult-to-screen targets, such as G-protein coupled receptors (GPCR) and ion channels. Herein we describe a step-by-step protocol to establish and perform the isolation of mAbs using YSD in a fluorescence-activated cell sorting (FACS)-assisted biopanning manner, yielding a variety of antibodies binding their antigen with high affinity in the natural environment of the cell. Upon mixing antibody-displaying yeast cells with antigen-displaying mammalian cells, complexes are specifically formed and isolated for enrichment of yeast cells encoding binders against the antigen. The utilization of mammalian cells expressing the respective target accounts for accessibility of the epitope and the correct conformation of the antigen. Furthermore, critical characterization methods mandatory for this kind of antibodies are illuminated.
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Affiliation(s)
- Stefania C Carrara
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- Ferring Darmstadt Laboratory, Biologics Technology and Development, Darmstadt, Germany
| | - Jan P Bogen
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- Ferring Darmstadt Laboratory, Biologics Technology and Development, Darmstadt, Germany
| | - Julius Grzeschik
- Ferring Darmstadt Laboratory, Biologics Technology and Development, Darmstadt, Germany
| | - Björn Hock
- Ferring International Center S.A., Saint-Prex, Switzerland
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.
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47
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Raeeszadeh-Sarmazdeh M, Boder ET. Yeast Surface Display: New Opportunities for a Time-Tested Protein Engineering System. Methods Mol Biol 2022; 2491:3-25. [PMID: 35482182 DOI: 10.1007/978-1-0716-2285-8_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Yeast surface display has proven to be a powerful tool for the discovery of antibodies and other novel binding proteins and for engineering the affinity and selectivity of existing proteins for their targets. In the decades since the first demonstrations of the approach, the range of yeast display applications has greatly expanded to include many different protein targets and has grown to encompass methods for rapid protein characterization. Here, we briefly summarize the development of yeast display methodologies and highlight several selected examples of recent applications to timely and challenging protein engineering and characterization problems.
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Affiliation(s)
| | - Eric T Boder
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA.
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48
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Kang BH, Lax BM, Wittrup KD. Yeast Surface Display for Protein Engineering: Library Generation, Screening, and Affinity Maturation. Methods Mol Biol 2022; 2491:29-62. [PMID: 35482183 DOI: 10.1007/978-1-0716-2285-8_2] [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: 06/14/2023]
Abstract
Yeast surface display is a powerful directed evolution method for developing and engineering protein molecules to attain desired properties. Here, updated protocols are presented for purposes of identification of lead binders and their affinity maturation. Large libraries are screened by magnetic bead selections followed by flow cytometric selections. Upon identification and characterization of single clones, their affinities are improved by an iterative process of mutagenesis and fluorescence-activated cell sorting.
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Affiliation(s)
- Byong H Kang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brianna M Lax
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - K Dane Wittrup
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Toumaian MR, Raeeszadeh-Sarmazdeh M. Engineering Tissue Inhibitors of Metalloproteinases Using Yeast Surface Display. Methods Mol Biol 2022; 2491:361-385. [PMID: 35482200 DOI: 10.1007/978-1-0716-2285-8_19] [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] [Indexed: 06/14/2023]
Abstract
Yeast surface display (YSD) has been extensively used for protein design, engineering, and directed evolution in the past two decades. Here, we describe methods for directed evolution of tissue inhibitors of metalloproteinase (TIMP), the natural inhibitors of matrix metalloproteinases (MMPs), through design and generation of a combinatorial library of TIMP mutants and screening the targeted TIMP library of variants toward MMP binding using YSD. This protocol can be adopted to other natural enzyme inhibitors and similar protein binders such as antibodies.
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Affiliation(s)
- Mari R Toumaian
- Chemical and Materials Engineering, University of Nevada, Reno, NV, USA
- Cell and Molecular Biology, University of Nevada, Reno, NV, USA
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50
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Davydova EK. Protein Engineering: Advances in Phage Display for Basic Science and Medical Research. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S146-S110. [PMID: 35501993 PMCID: PMC8802281 DOI: 10.1134/s0006297922140127] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 12/03/2022]
Abstract
Functional Protein Engineering became the hallmark in biomolecule manipulation in the new millennium, building on and surpassing the underlying structural DNA manipulation and recombination techniques developed and employed in the last decades of 20th century. Because of their prominence in almost all biological processes, proteins represent extremely important targets for engineering enhanced or altered properties that can lead to improvements exploitable in healthcare, medicine, research, biotechnology, and industry. Synthetic protein structures and functions can now be designed on a computer and/or evolved using molecular display or directed evolution methods in the laboratory. This review will focus on the recent trends in protein engineering and the impact of this technology on recent progress in science, cancer- and immunotherapies, with the emphasis on the current achievements in basic protein research using synthetic antibody (sABs) produced by phage display pipeline in the Kossiakoff laboratory at the University of Chicago (KossLab). Finally, engineering of the highly specific binding modules, such as variants of Streptococcal protein G with ultra-high orthogonal affinity for natural and engineered antibody scaffolds, and their possible applications as a plug-and-play platform for research and immunotherapy will be described.
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Affiliation(s)
- Elena K Davydova
- The University of Chicago, Department of Biochemistry and Molecular Biology, Chicago, IL 60637, USA.
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