1
|
Li W, Yin F, Bu Z, Liu Y, Zhang Y, Chen X, Li S, Li L, Zhou R, Huang Q. An Engineered Outer Membrane-Defective Escherichia coli Secreting Protective Antigens against Streptococcus suis via the Twin-Arginine Translocation Pathway as a Vaccine. J Microbiol Biotechnol 2022; 32:278-286. [PMID: 35283432 PMCID: PMC9628857 DOI: 10.4014/jmb.2107.07052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/20/2022] [Accepted: 02/09/2022] [Indexed: 12/15/2022]
Abstract
Live bacterial vector vaccines are one of the most promising vaccine types and have the advantages of low cost, flexibility, and good safety. Meanwhile, protein secretion systems have been reported as useful tools to facilitate the release of heterologous antigen proteins from bacterial vectors. The twin-arginine translocation (Tat) system is an important protein export system that transports fully folded proteins in a signal peptide-dependent manner. In this study, we constructed a live vector vaccine using an engineered commensal Escherichia coli strain in which amiA and amiC genes were deleted, resulting in a leaky outer membrane that allows the release of periplasmic proteins to the extracellular environment. The protective antigen proteins SLY, enolase, and Sbp against Streptococcus suis were targeted to the Tat pathway by fusing a Tat signal peptide. Our results showed that by exploiting the Tat pathway and the outer membrane-defective E. coli strain, the antigen proteins were successfully secreted. The strains secreting the antigen proteins were used to vaccinate mice. After S. suis challenge, the vaccinated group showed significantly higher survival and milder clinical symptoms compared with the vector group. Further analysis showed that the mice in the vaccinated group had lower burdens of bacteria load and slighter pathological changes. Our study reports a novel live bacterial vector vaccine that uses the Tat system and provides a new alternative for developing S. suis vaccine.
Collapse
Affiliation(s)
- Wenyu Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China,Shandong Vocational Animal Science and Veterinary College, Weifang, P.R. China
| | - Fan Yin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Zixuan Bu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Yuying Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Yongqing Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Xiabing Chen
- Institute of Animal Husbandry and Veterinary Science, Wuhan Academy of Agricultural Science and Technology, Wuhan 430070, P.R. China
| | - Shaowen Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Lu Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China,Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, P.R. China,International Research Center for Animal Disease, Ministry of Science and Technology, Wuhan 430070, P.R. China,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of China, Wuhan 430070, P.R. China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China,Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, P.R. China,International Research Center for Animal Disease, Ministry of Science and Technology, Wuhan 430070, P.R. China,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of China, Wuhan 430070, P.R. China
| | - Qi Huang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China,Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, P.R. China,International Research Center for Animal Disease, Ministry of Science and Technology, Wuhan 430070, P.R. China,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of China, Wuhan 430070, P.R. China,Corresponding author Phone: +86-27-87281878 Fax: + 86-27-8728 2608 E-mail:
| |
Collapse
|
2
|
Taw MN, Li M, Kim D, Rocco MA, Waraho-Zhmayev D, DeLisa MP. Engineering a Supersecreting Strain of Escherichia coli by Directed Coevolution of the Multiprotein Tat Translocation Machinery. ACS Synth Biol 2021; 10:2947-2958. [PMID: 34757717 DOI: 10.1021/acssynbio.1c00183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Escherichia coli remains one of the preferred hosts for biotechnological protein production due to its robust growth in culture and ease of genetic manipulation. It is often desirable to export recombinant proteins into the periplasmic space for reasons related to proper disulfide bond formation, prevention of aggregation and proteolytic degradation, and ease of purification. One such system for expressing heterologous secreted proteins is the twin-arginine translocation (Tat) pathway, which has the unique advantage of delivering correctly folded proteins into the periplasm. However, transit times for proteins through the Tat translocase, comprised of the TatABC proteins, are much longer than for passage through the SecYEG pore, the translocase associated with the more widely utilized Sec pathway. To date, a high protein flux through the Tat pathway has yet to be demonstrated. To address this shortcoming, we employed a directed coevolution strategy to isolate mutant Tat translocases for their ability to deliver higher quantities of heterologous proteins into the periplasm. Three supersecreting translocases were selected that each exported a panel of recombinant proteins at levels that were significantly greater than those observed for wild-type TatABC or SecYEG translocases. Interestingly, all three of the evolved Tat translocases exhibited quality control suppression, suggesting that increased translocation flux was gained by relaxation of substrate proofreading. Overall, our discovery of more efficient translocase variants paves the way for the use of the Tat system as a powerful complement to the Sec pathway for secreted production of both commodity and high value-added proteins.
Collapse
Affiliation(s)
- May N. Taw
- Department of Microbiology, Cornell University, Ithaca, New York 14853, United States
| | - Mingji Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
| | - Daniel Kim
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
| | - Mark A. Rocco
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
| | - Dujduan Waraho-Zhmayev
- Biological Engineering, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
| | - Matthew P. DeLisa
- Department of Microbiology, Cornell University, Ithaca, New York 14853, United States
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
- Cornell Institute of Biotechnology, Cornell University, 130 Biotechnology Building, Ithaca, New York 14853, United States
| |
Collapse
|
3
|
Gaudet RG, Zhu S, Halder A, Kim BH, Bradfield CJ, Huang S, Xu D, Mamiñska A, Nguyen TN, Lazarou M, Karatekin E, Gupta K, MacMicking JD. A human apolipoprotein L with detergent-like activity kills intracellular pathogens. Science 2021; 373:eabf8113. [PMID: 34437126 PMCID: PMC8422858 DOI: 10.1126/science.abf8113] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/29/2021] [Accepted: 06/03/2021] [Indexed: 12/11/2022]
Abstract
Activation of cell-autonomous defense by the immune cytokine interferon-γ (IFN-γ) is critical to the control of life-threatening infections in humans. IFN-γ induces the expression of hundreds of host proteins in all nucleated cells and tissues, yet many of these proteins remain uncharacterized. We screened 19,050 human genes by CRISPR-Cas9 mutagenesis and identified IFN-γ-induced apolipoprotein L3 (APOL3) as a potent bactericidal agent protecting multiple non-immune barrier cell types against infection. Canonical apolipoproteins typically solubilize mammalian lipids for extracellular transport; APOL3 instead targeted cytosol-invasive bacteria to dissolve their anionic membranes into human-bacterial lipoprotein nanodiscs detected by native mass spectrometry and visualized by single-particle cryo-electron microscopy. Thus, humans have harnessed the detergent-like properties of extracellular apolipoproteins to fashion an intracellular lysin, thereby endowing resident nonimmune cells with a mechanism to achieve sterilizing immunity.
Collapse
Affiliation(s)
- Ryan G Gaudet
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Shiwei Zhu
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Anushka Halder
- Yale Nanobiology Institute, West Haven, CT 06477, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Bae-Hoon Kim
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Clinton J Bradfield
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Shuai Huang
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Dijin Xu
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Agnieszka Mamiñska
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Thanh Ngoc Nguyen
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - Michael Lazarou
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - Erdem Karatekin
- Yale Nanobiology Institute, West Haven, CT 06477, USA
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
- Saints-Pères Paris Institute for the Neurosciences, Centre National de la Recherche Scientifique (CNRS), Université de Paris, F-75006 Paris, France
| | - Kallol Gupta
- Yale Nanobiology Institute, West Haven, CT 06477, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - John D MacMicking
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA.
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| |
Collapse
|
4
|
Valldorf B, Hinz SC, Russo G, Pekar L, Mohr L, Klemm J, Doerner A, Krah S, Hust M, Zielonka S. Antibody display technologies: selecting the cream of the crop. Biol Chem 2021; 403:455-477. [PMID: 33759431 DOI: 10.1515/hsz-2020-0377] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/05/2021] [Indexed: 02/07/2023]
Abstract
Antibody display technologies enable the successful isolation of antigen-specific antibodies with therapeutic potential. The key feature that facilitates the selection of an antibody with prescribed properties is the coupling of the protein variant to its genetic information and is referred to as genotype phenotype coupling. There are several different platform technologies based on prokaryotic organisms as well as strategies employing higher eukaryotes. Among those, phage display is the most established system with more than a dozen of therapeutic antibodies approved for therapy that have been discovered or engineered using this approach. In recent years several other technologies gained a certain level of maturity, most strikingly mammalian display. In this review, we delineate the most important selection systems with respect to antibody generation with an emphasis on recent developments.
Collapse
Affiliation(s)
- Bernhard Valldorf
- Chemical and Pharmaceutical Development, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Steffen C Hinz
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Giulio Russo
- Abcalis GmbH, Inhoffenstrasse 7, D-38124Braunschweig, Germany.,Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Lukas Pekar
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Laura Mohr
- Institute of Cell Biology and Neuroscience and Buchmann Institute for Molecular Life Sciences, University of Frankfurt, Max-von-Laue-Strasse 13, D-60438Frankfurt am Main, Germany
| | - Janina Klemm
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| |
Collapse
|
5
|
Smith SM, Walker KL, Jones AS, Smith CJ, Robinson C. Characterization of a novel method for the production of single-span membrane proteins in Escherichia coli. Biotechnol Bioeng 2018; 116:722-733. [PMID: 30536699 PMCID: PMC6492203 DOI: 10.1002/bit.26895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/26/2018] [Accepted: 12/06/2018] [Indexed: 12/03/2022]
Abstract
The large‐scale production and isolation of recombinant protein is a central element of the biotechnology industry and many of the products have proved extremely beneficial for therapeutic medicine. Escherichia coli is the microorganism of choice for the expression of heterologous proteins for therapeutic application, and a range of high‐value proteins have been targeted to the periplasm using the well characterized Sec protein export pathway. More recently, the ability of the second mainstream protein export system, the twin‐arginine translocase, to transport fully‐folded proteins into the periplasm of not only E. coli, but also other Gram‐negative bacteria, has captured the interest of the biotechnology industry. In this study, we have used a novel approach to block the export of a heterologous Tat substrate in the later stages of the export process, and thereby generate a single‐span membrane protein with the soluble domain positioned on the periplasmic side of the inner membrane. Biochemical and immuno‐electron microscopy approaches were used to investigate the export of human growth hormone by the twin‐arginine translocase, and the generation of a single‐span membrane‐embedded variant. This is the first time that a bonafide biotechnologically relevant protein has been exported by this machinery and visualized directly in this manner. The data presented here demonstrate a novel method for the production of single‐span membrane proteins in E. coli.
Collapse
Affiliation(s)
- Sarah M Smith
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Kelly L Walker
- School of Biosciences, University of Kent, Canterbury, UK
| | | | - Corinne J Smith
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Colin Robinson
- School of Biosciences, University of Kent, Canterbury, UK
| |
Collapse
|
6
|
Glasscock CJ, Yates LE, Jaroentomeechai T, Wilson JD, Merritt JH, Lucks JB, DeLisa MP. A flow cytometric approach to engineering Escherichia coli for improved eukaryotic protein glycosylation. Metab Eng 2018; 47:488-495. [DOI: 10.1016/j.ymben.2018.04.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/17/2018] [Accepted: 04/19/2018] [Indexed: 12/31/2022]
|
7
|
Abstract
The last decade has seen a dramatic increase in the utilization of enzymes as green and sustainable (bio)catalysts in pharmaceutical and industrial applications. This trend has to a significant degree been fueled by advances in scientists' and engineers' ability to customize native enzymes by protein engineering. A review of the literature quickly reveals the tremendous success of this approach; protein engineering has generated enzyme variants with improved catalytic activity, broadened or altered substrate specificity, as well as raised or reversed stereoselectivity. Enzymes have been tailored to retain activity at elevated temperatures and to function in the presence of organic solvents, salts and pH values far from physiological conditions. However, readers unfamiliar with the field will soon encounter the confusingly large number of experimental techniques that have been employed to accomplish these engineering feats. Herein, we use history to guide a brief overview of the major strategies for protein engineering-past, present, and future.
Collapse
Affiliation(s)
- Stefan Lutz
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA, 30322, USA.
| | - Samantha M Iamurri
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA, 30322, USA
| |
Collapse
|
8
|
Julian MC, Li L, Garde S, Wilen R, Tessier PM. Efficient affinity maturation of antibody variable domains requires co-selection of compensatory mutations to maintain thermodynamic stability. Sci Rep 2017; 7:45259. [PMID: 28349921 PMCID: PMC5368667 DOI: 10.1038/srep45259] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/27/2017] [Indexed: 12/31/2022] Open
Abstract
The ability of antibodies to accumulate affinity-enhancing mutations in their complementarity-determining regions (CDRs) without compromising thermodynamic stability is critical to their natural function. However, it is unclear if affinity mutations in the hypervariable CDRs generally impact antibody stability and to what extent additional compensatory mutations are required to maintain stability during affinity maturation. Here we have experimentally and computationally evaluated the functional contributions of mutations acquired by a human variable (VH) domain that was evolved using strong selections for enhanced stability and affinity for the Alzheimer’s Aβ42 peptide. Interestingly, half of the key affinity mutations in the CDRs were destabilizing. Moreover, the destabilizing effects of these mutations were compensated for by a subset of the affinity mutations that were also stabilizing. Our findings demonstrate that the accumulation of both affinity and stability mutations is necessary to maintain thermodynamic stability during extensive mutagenesis and affinity maturation in vitro, which is similar to findings for natural antibodies that are subjected to somatic hypermutation in vivo. These findings for diverse antibodies and antibody fragments specific for unrelated antigens suggest that the formation of the antigen-binding site is generally a destabilizing process and that co-enrichment for compensatory mutations is critical for maintaining thermodynamic stability.
Collapse
Affiliation(s)
- Mark C Julian
- Center for Biotechnology &Interdisciplinary Studies, Isermann Dept. of Chemical &Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Lijuan Li
- Center for Biotechnology &Interdisciplinary Studies, Isermann Dept. of Chemical &Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Shekhar Garde
- Center for Biotechnology &Interdisciplinary Studies, Isermann Dept. of Chemical &Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Rebecca Wilen
- Center for Biotechnology &Interdisciplinary Studies, Isermann Dept. of Chemical &Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Peter M Tessier
- Center for Biotechnology &Interdisciplinary Studies, Isermann Dept. of Chemical &Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| |
Collapse
|
9
|
Moghaddam-Taaheri P, Ikonomova SP, Gong Z, Wisniewski JQ, Karlsson AJ. Bacterial Inner-membrane Display for Screening a Library of Antibody Fragments. J Vis Exp 2016. [PMID: 27805609 PMCID: PMC5092199 DOI: 10.3791/54583] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Antibodies engineered for intracellular function must not only have affinity for their target antigen, but must also be soluble and correctly folded in the cytoplasm. Commonly used methods for the display and screening of recombinant antibody libraries do not incorporate intracellular protein folding quality control, and, thus, the antigen-binding capability and cytoplasmic folding and solubility of antibodies engineered using these methods often must be engineered separately. Here, we describe a protocol to screen a recombinant library of single-chain variable fragment (scFv) antibodies for antigen-binding and proper cytoplasmic folding simultaneously. The method harnesses the intrinsic intracellular folding quality control mechanism of the Escherichia coli twin-arginine translocation (Tat) pathway to display an scFv library on the E. coli inner membrane. The Tat pathway ensures that only soluble, well-folded proteins are transported out of the cytoplasm and displayed on the inner membrane, thereby eliminating poorly folded scFvs prior to interrogation for antigen-binding. Following removal of the outer membrane, the scFvs displayed on the inner membrane are panned against a target antigen immobilized on magnetic beads to isolate scFvs that bind to the target antigen. An enzyme-linked immunosorbent assay (ELISA)-based secondary screen is used to identify the most promising scFvs for additional characterization. Antigen-binding and cytoplasmic solubility can be improved with subsequent rounds of mutagenesis and screening to engineer antibodies with high affinity and high cytoplasmic solubility for intracellular applications.
Collapse
Affiliation(s)
| | | | - Zifan Gong
- Department of Chemical and Biomolecular Engineering, University of Maryland
| | | | - Amy J Karlsson
- Fischell Department of Bioengineering, University of Maryland; Department of Chemical and Biomolecular Engineering, University of Maryland;
| |
Collapse
|
10
|
An Intrabody Drug (rAAV6-INT41) Reduces the Binding of N-Terminal Huntingtin Fragment(s) to DNA to Basal Levels in PC12 Cells and Delays Cognitive Loss in the R6/2 Animal Model. JOURNAL OF NEURODEGENERATIVE DISEASES 2016; 2016:7120753. [PMID: 27595037 PMCID: PMC4995342 DOI: 10.1155/2016/7120753] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/27/2016] [Indexed: 01/01/2023]
Abstract
Huntington's disease (HD) is a fatal progressive disease linked to expansion of glutamine repeats in the huntingtin protein and characterized by the progressive loss of cognitive and motor function. We show that expression of a mutant human huntingtin exon-1-GFP fusion construct results in nonspecific gene dysregulation that is significantly reduced by 50% due to coexpression of INT41, an intrabody specific for the proline-rich region of the huntingtin protein. Using stable PC12 cell lines expressing either inducible human mutant huntingtin (mHtt, Q73) or normal huntingtin (nHtt, Q23), we investigated the effect of rAAV6-INT41, an adeno-associated virus vector with the INT41 coding sequence, on the subcellular distribution of Htt. Compartmental fractionation 8 days after induction of Htt showed a 6-fold increased association of a dominate N-terminal mHtt fragment with DNA compared to N-terminal nHtt. Transduction with rAAV6-INT41 reduced DNA binding of N-terminal mHtt 6.5-fold in the nucleus and reduced nuclear translocation of the detected fragments. Subsequently, when rAAV6-INT41 is delivered to the striatum in the R6/2 mouse model, treated female mice exhibited executive function statistically indistinguishable from wild type, accompanied by reductions in Htt aggregates in the striatum, suggesting that rAAV6-INT41 is promising as a gene therapy for Huntington's disease.
Collapse
|
11
|
Antibody affinity maturation through combining display of two-chain paired antibody and precision flow cytometric sorting. Appl Microbiol Biotechnol 2016; 100:5977-88. [DOI: 10.1007/s00253-016-7472-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 03/13/2016] [Accepted: 03/15/2016] [Indexed: 01/09/2023]
|
12
|
Glasscock C, Lucks J, DeLisa M. Engineered Protein Machines: Emergent Tools for Synthetic Biology. Cell Chem Biol 2016; 23:45-56. [DOI: 10.1016/j.chembiol.2015.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/01/2015] [Accepted: 12/01/2015] [Indexed: 11/25/2022]
|
13
|
Marschall ALJ, Dübel S, Böldicke T. Specific in vivo knockdown of protein function by intrabodies. MAbs 2015; 7:1010-35. [PMID: 26252565 PMCID: PMC4966517 DOI: 10.1080/19420862.2015.1076601] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 07/19/2015] [Accepted: 07/20/2015] [Indexed: 01/02/2023] Open
Abstract
Intracellular antibodies (intrabodies) are recombinant antibody fragments that bind to target proteins expressed inside of the same living cell producing the antibodies. The molecules are commonly used to study the function of the target proteins (i.e., their antigens). The intrabody technology is an attractive alternative to the generation of gene-targeted knockout animals, and complements knockdown techniques such as RNAi, miRNA and small molecule inhibitors, by-passing various limitations and disadvantages of these methods. The advantages of intrabodies include very high specificity for the target, the possibility to knock down several protein isoforms by one intrabody and targeting of specific splice variants or even post-translational modifications. Different types of intrabodies must be designed to target proteins at different locations, typically either in the cytoplasm, in the nucleus or in the endoplasmic reticulum (ER). Most straightforward is the use of intrabodies retained in the ER (ER intrabodies) to knock down the function of proteins passing the ER, which disturbs the function of members of the membrane or plasma proteomes. More effort is needed to functionally knock down cytoplasmic or nuclear proteins because in this case antibodies need to provide an inhibitory effect and must be able to fold in the reducing milieu of the cytoplasm. In this review, we present a broad overview of intrabody technology, as well as applications both of ER and cytoplasmic intrabodies, which have yielded valuable insights in the biology of many targets relevant for drug development, including α-synuclein, TAU, BCR-ABL, ErbB-2, EGFR, HIV gp120, CCR5, IL-2, IL-6, β-amyloid protein and p75NTR. Strategies for the generation of intrabodies and various designs of their applications are also reviewed.
Collapse
Affiliation(s)
- Andrea LJ Marschall
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics; Braunschweig, Germany
| | - Stefan Dübel
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics; Braunschweig, Germany
| | - Thomas Böldicke
- Helmholtz Centre for Infection Research, Recombinant Protein Expression/Intrabody Unit, Helmholtz Centre for Infection Research; Braunschweig, Germany
| |
Collapse
|
14
|
Boock JT, King BC, Taw MN, Conrado RJ, Siu KH, Stark JC, Walker LP, Gibson DM, DeLisa MP. Repurposing a bacterial quality control mechanism to enhance enzyme production in living cells. J Mol Biol 2015; 427:1451-1463. [PMID: 25591491 DOI: 10.1016/j.jmb.2015.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/30/2014] [Accepted: 01/05/2015] [Indexed: 11/25/2022]
Abstract
Heterologous expression of many proteins in bacteria, yeasts, and plants is often limited by low titers of functional protein. To address this problem, we have created a two-tiered directed evolution strategy in Escherichia coli that enables optimization of protein production while maintaining high biological activity. The first tier involves a genetic selection for intracellular protein stability that is based on the folding quality control mechanism inherent to the twin-arginine translocation pathway, while the second is a semi-high-throughput screen for protein function. To demonstrate the utility of this strategy, we isolated variants of the endoglucanase Cel5A, from the plant-pathogenic fungus Fusarium graminearum, whose production was increased by as much as 30-fold over the parental enzyme. This gain in production was attributed to just two amino acid substitutions, and it was isolated after two iterations through the two-tiered approach. There was no significant tradeoff in activity on soluble or insoluble cellulose substrates. Importantly, by combining the folding filter afforded by the twin-arginine translocation quality control mechanism with a function-based screen, we show enrichment for variants with increased protein abundance in a manner that does not compromise catalytic activity, providing a highly soluble parent for engineering of improved or new function.
Collapse
Affiliation(s)
- Jason T Boock
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Brian C King
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - May N Taw
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Robert J Conrado
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Ka-Hei Siu
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Jessica C Stark
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Larry P Walker
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Donna M Gibson
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA; Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture, Ithaca, NY 14853, USA
| | - Matthew P DeLisa
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
15
|
An engineered genetic selection for ternary protein complexes inspired by a natural three-component hitchhiker mechanism. Sci Rep 2014; 4:7570. [PMID: 25531212 PMCID: PMC4273604 DOI: 10.1038/srep07570] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 12/02/2014] [Indexed: 12/29/2022] Open
Abstract
The bacterial twin-arginine translocation (Tat) pathway is well known to translocate correctly folded monomeric and dimeric proteins across the tightly sealed cytoplasmic membrane. We identified a naturally occurring heterotrimer, the Escherichia coli aldehyde oxidoreductase PaoABC, that is co-translocated by the Tat translocase according to a ternary “hitchhiker” mechanism. Specifically, the PaoB and PaoC subunits, each devoid of export signals, are escorted to the periplasm in a piggyback fashion by the Tat signal peptide-containing subunit PaoA. Moreover, export of PaoA was blocked when either PaoB or PaoC was absent, revealing a surprising interdependence for export that is not seen for classical secretory proteins. Inspired by this observation, we created a bacterial three-hybrid selection system that links the formation of ternary protein complexes with antibiotic resistance. As proof-of-concept, a bispecific antibody was employed as an adaptor that physically crosslinked one antigen fused to a Tat export signal with a second antigen fused to TEM-1 β-lactamase (Bla). The resulting non-covalent heterotrimer was exported in a Tat-dependent manner, delivering Bla to the periplasm where it hydrolyzed β-lactam antibiotics. Collectively, these results highlight the remarkable flexibility of the Tat system and its potential for studying and engineering ternary protein interactions in living bacteria.
Collapse
|
16
|
Waraho-Zhmayev D, Meksiriporn B, Portnoff AD, DeLisa MP. Optimizing recombinant antibodies for intracellular function using hitchhiker-mediated survival selection. Protein Eng Des Sel 2014; 27:351-8. [PMID: 25225416 DOI: 10.1093/protein/gzu038] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The 'hitchhiker' mechanism of the bacterial twin-arginine translocation pathway has previously been adapted as a genetic selection for detecting pairwise protein interactions in the cytoplasm of living Escherichia coli cells. Here, we extended this method, called FLI-TRAP, for rapid isolation of intracellular antibodies (intrabodies) in the single-chain Fv format that possess superior traits simply by demanding bacterial growth on high concentrations of antibiotic. Following just a single round of survival-based enrichment using FLI-TRAP, variants of an intrabody against the dimerization domain of the yeast Gcn4p transcription factor were isolated having significantly greater intracellular stability that translated to yield enhancements of >10-fold. Likewise, an intrabody specific for the non-amyloid component region of α-synuclein was isolated that has ~8-fold improved antigen-binding affinity. Collectively, our results illustrate the potential of the FLI-TRAP method for intracellular stabilization and affinity maturation of intrabodies, all without the need for purification or immobilization of the antigen.
Collapse
Affiliation(s)
- Dujduan Waraho-Zhmayev
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi, 126 Pracha-utid Road, Bangmod, Toongkru, Bangkok 10140, Thailand
| | | | - Alyse D Portnoff
- Department of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Matthew P DeLisa
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA Department of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
17
|
Kim DS, Song HN, Nam HJ, Kim SG, Park YS, Park JC, Woo EJ, Lim HK. Directed evolution of human heavy chain variable domain (VH) using in vivo protein fitness filter. PLoS One 2014; 9:e98178. [PMID: 24892548 PMCID: PMC4043505 DOI: 10.1371/journal.pone.0098178] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/29/2014] [Indexed: 12/30/2022] Open
Abstract
Human immunoglobulin heavy chain variable domains (VH) are promising scaffolds for antigen binding. However, VH is an unstable and aggregation-prone protein, hindering its use for therapeutic purposes. To evolve the VH domain, we performed in vivo protein solubility selection that linked antibiotic resistance to the protein folding quality control mechanism of the twin-arginine translocation pathway of E. coli. After screening a human germ-line VH library, 95% of the VH proteins obtained were identified as VH3 family members; one VH protein, MG2x1, stood out among separate clones expressing individual VH variants. With further screening of combinatorial framework mutation library of MG2x1, we found a consistent bias toward substitution with tryptophan at the position of 50 and 58 in VH. Comparison of the crystal structures of the VH variants revealed that those substitutions with bulky side chain amino acids filled the cavity in the VH interface between heavy and light chains of the Fab arrangement along with the increased number of hydrogen bonds, decreased solvation energy, and increased negative charge. Accordingly, the engineered VH acquires an increased level of thermodynamic stability, reversible folding, and soluble expression. The library built with the VH variant as a scaffold was qualified as most of VH clones selected randomly were expressed as soluble form in E. coli regardless length of the combinatorial CDR. Furthermore, a non-aggregation feature of the selected VH conferred a free of humoral response in mice, even when administered together with adjuvant. As a result, this selection provides an alternative directed evolution pathway for unstable proteins, which are distinct from conventional methods based on the phage display.
Collapse
Affiliation(s)
- Dong-Sik Kim
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
| | - Hyung-Nam Song
- BioMedical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea; Department of Biotechnology and Bioinformatics, Korea University, Sejong, Republic of Korea
| | - Hyo Jung Nam
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
| | - Sung-Geun Kim
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
| | - Young-Seoub Park
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
| | - Jae-Chan Park
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
| | - Eui-Jeon Woo
- BioMedical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hyung-Kwon Lim
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
| |
Collapse
|
18
|
Portnoff AD, Stephens EA, Varner JD, DeLisa MP. Ubiquibodies, synthetic E3 ubiquitin ligases endowed with unnatural substrate specificity for targeted protein silencing. J Biol Chem 2014; 289:7844-55. [PMID: 24474696 DOI: 10.1074/jbc.m113.544825] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The ubiquitin-proteasome pathway (UPP) is the main route of protein degradation in eukaryotic cells and is a common mechanism through which numerous cellular pathways are regulated. To date, several reverse genetics techniques have been reported that harness the power of the UPP for selectively reducing the levels of otherwise stable proteins. However, each of these approaches has been narrowly developed for a single substrate and cannot be easily extended to other protein substrates of interest. To address this shortcoming, we created a generalizable protein knock-out method by engineering protein chimeras called "ubiquibodies" that combine the activity of E3 ubiquitin ligases with designer binding proteins to steer virtually any protein to the UPP for degradation. Specifically, we reprogrammed the substrate specificity of a modular human E3 ubiquitin ligase called CHIP (carboxyl terminus of Hsc70-interacting protein) by replacing its natural substrate-binding domain with a single-chain Fv (scFv) intrabody or a fibronectin type III domain monobody that target their respective antigens with high specificity and affinity. Engineered ubiquibodies reliably transferred ubiquitin to surface exposed lysines on target proteins and even catalyzed the formation of biologically relevant polyubiquitin chains. Following ectopic expression of ubiquibodies in mammalian cells, specific and systematic depletion of desired target proteins was achieved, whereas the levels of a natural substrate of CHIP were unaffected. Taken together, engineered ubiquibodies offer a simple, reproducible, and customizable means for directly removing specific cellular proteins through accelerated proteolysis.
Collapse
|
19
|
Ren C, Patel R, Robinson C. Exclusively membrane-inserted state of an uncleavable Tat precursor protein suggests lateral transfer into the bilayer from the translocon. FEBS J 2013; 280:3354-64. [PMID: 23647663 DOI: 10.1111/febs.12327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Revised: 02/28/2013] [Accepted: 04/04/2013] [Indexed: 11/26/2022]
Abstract
In bacteria, the export of proteins by the twin-arginine translocase (Tat) pathway is directed by cleavable N-terminal signal peptides. We studied the relationship between transport and maturation using a substrate, YedY, that contains an Ala > Leu substitution at the -1 position of the signal peptide. This blocks maturation and leads to the accumulation of a membrane-bound precursor form with the mature domain exposed to the periplasm. Its accumulation does not block transport of other Tat substrates, indicating that exit from the translocation channel has taken place, and the precursor protein is fir mLy integrated into the membrane bilayer. The membrane-integrated nature of the precursor, and complete absence of precursor protein in the periplasm, strongly suggest that the precursor has undergone lateral transfer into the bilayer during translocation. We propose that subsequent proteolytic processing releases the mature protein into the periplasm. A delay in processing results in an inhibition of cell growth, emphasizing a requirement for efficient maturation of Tat substrates.
Collapse
Affiliation(s)
- Chao Ren
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | | |
Collapse
|
20
|
Enough is enough: TatA demand during Tat-dependent protein transport. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:957-65. [DOI: 10.1016/j.bbamcr.2013.01.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/23/2013] [Accepted: 01/25/2013] [Indexed: 10/27/2022]
|
21
|
Sherwood LJ, Hayhurst A. Hapten mediated display and pairing of recombinant antibodies accelerates assay assembly for biothreat countermeasures. Sci Rep 2012; 2:807. [PMID: 23150778 PMCID: PMC3495282 DOI: 10.1038/srep00807] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 10/17/2012] [Indexed: 11/14/2022] Open
Abstract
A bottle-neck in recombinant antibody sandwich immunoassay development is pairing, demanding protein purification and modification to distinguish captor from tracer. We developed a simple pairing scheme using microliter amounts of E. coli osmotic shockates bearing site-specific biotinylated antibodies and demonstrated proof of principle with a single domain antibody (sdAb) that is both captor and tracer for polyvalent Marburgvirus nucleoprotein. The system could also host pairs of different sdAb specific for the 7 botulinum neurotoxin (BoNT) serotypes, enabling recognition of the cognate serotype. Inducible supE co-expression enabled sdAb populations to be propagated as either phage for more panning from repertoires or expressed as soluble sdAb for screening within a single host strain. When combined with streptavidin-g3p fusions, a novel transdisplay system was formulated to retrofit a semi-synthetic sdAb library which was mined for an anti-Ebolavirus sdAb which was immediately immunoassay ready, thereby speeding up the recombinant antibody discovery and utilization processes.
Collapse
Affiliation(s)
- Laura J. Sherwood
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Andrew Hayhurst
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, USA
| |
Collapse
|