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Santonico E. The Lambda Display Technology: A Useful Tool for the Identification of Ubiquitin-and Ubiquitin-Like-Binding Domains. Methods Mol Biol 2023; 2602:163-175. [PMID: 36446974 DOI: 10.1007/978-1-0716-2859-1_12] [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: 06/16/2023]
Abstract
Ubiquitin-binding domains (UBDs) are modular units that mediate non-covalent recognition of ubiquitin modifications. They are found in ubiquitin (Ub)-binding proteins and recognize defined surface patches of a single Ub through typically weak interactions. Although more than 200 Ub-binding proteins have been identified to date, only 29 UBD types have been reported in the human proteome, suggesting that much remains to be learned about Ub recognition. Several methods, from bioinformatics to experimental, have successfully identified Ub-binding properties in several proteins. We here report the protocol to identify Ub-binding domains by panning a human brain cDNA library whose products are displayed on the surface of lambda capsid. In parallel, we carried out a panning experiment aimed at identifying domains interacting with the Ub-like NEDD8 (neural precursor cell-expressed developmentally downregulated), which is the Ub-like protein showing the closest sequence identity (58%) to Ub. This approach proved to be very effective for the discovery of the previously unidentified UBDs CUBAN and CoCUN, and it is in principle applicable to investigate the interaction network of any other Ub-like protein.
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Affiliation(s)
- Elena Santonico
- University of Rome Tor Vergata, Via della ricerca scientifica, Rome, Italy.
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2
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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: 60] [Impact Index Per Article: 20.0] [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.
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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
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3
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Lambda bacteriophage nanoparticles displaying GP2, a HER2/neu derived peptide, induce prophylactic and therapeutic activities against TUBO tumor model in mice. Sci Rep 2019; 9:2221. [PMID: 30778090 PMCID: PMC6379380 DOI: 10.1038/s41598-018-38371-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/27/2018] [Indexed: 12/16/2022] Open
Abstract
Generating a protective and long-lasting immune response is the primary goal in the expanding field of immunotherapeutic research. In current study we designed an immunogenic bacteriophage- based vaccine to induce a cytotoxic T lymphocyte activity against a mice tumor model over-expressing HER2/neu. Bacteriophage λ displaying a HER2/neu derived peptide GP2 was constructed and used as an anti-cancer vaccine in a BALB/c mouse xenograft tumor model. The results of our study indicated that phage nanoparticles displaying GP2 as a fused peptide to the gpD phage capsid protein induced a robust CTL response. Furthermore, the chimeric phage nanoparticles protected mice against HER2/neu-positive tumor challenge in both prophylactic and therapeutic settings. In conclusion, we propose that λ phage nanoparticles decorated with GP2 peptide merit further investigation for the development of peptide-based vaccines against HER2/neu overexpressing tumors.
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4
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Catalano CE. Bacteriophage lambda: The path from biology to theranostic agent. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2018. [DOI: 10.1002/wnan.1517] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Carlos E. Catalano
- Department of Pharmaceutical Chemistry, Skaggs School of Pharmacy and Pharmaceutical ScienceUniversity of ColoradoAuroraColorado
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5
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Arab A, Nicastro J, Slavcev R, Razazan A, Barati N, Nikpoor AR, Brojeni AAM, Mosaffa F, Badiee A, Jaafari MR, Behravan J. Lambda phage nanoparticles displaying HER2-derived E75 peptide induce effective E75-CD8+ T response. Immunol Res 2017; 66:200-206. [DOI: 10.1007/s12026-017-8969-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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6
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Domina M, Lanza Cariccio V, Benfatto S, Venza M, Venza I, Borgogni E, Castellino F, Midiri A, Galbo R, Romeo L, Biondo C, Masignani V, Teti G, Felici F, Beninati C. Functional characterization of a monoclonal antibody epitope using a lambda phage display-deep sequencing platform. Sci Rep 2016; 6:31458. [PMID: 27530334 PMCID: PMC4987625 DOI: 10.1038/srep31458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/18/2016] [Indexed: 11/10/2022] Open
Abstract
We have recently described a method, named PROFILER, for the identification of antigenic regions preferentially targeted by polyclonal antibody responses after vaccination. To test the ability of the technique to provide insights into the functional properties of monoclonal antibody (mAb) epitopes, we used here a well-characterized epitope of meningococcal factor H binding protein (fHbp), which is recognized by mAb 12C1. An fHbp library, engineered on a lambda phage vector enabling surface expression of polypeptides of widely different length, was subjected to massive parallel sequencing of the phage inserts after affinity selection with the 12C1 mAb. We detected dozens of unique antibody-selected sequences, the most enriched of which (designated as FrC) could largely recapitulate the ability of fHbp to bind mAb 12C1. Computational analysis of the cumulative enrichment of single amino acids in the antibody-selected fragments identified two overrepresented stretches of residues (H248-K254 and S140-G154), whose presence was subsequently found to be required for binding of FrC to mAb 12C1. Collectively, these results suggest that the PROFILER technology can rapidly and reliably identify, in the context of complex conformational epitopes, discrete “hot spots” with a crucial role in antigen-antibody interactions, thereby providing useful clues for the functional characterization of the epitope.
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Affiliation(s)
| | | | | | - Mario Venza
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Isabella Venza
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | | | | | - Angelina Midiri
- Department of Human Pathology, University of Messina, Messina, Italy
| | - Roberta Galbo
- Department of Biological, Chemical and Environmental Sciences, University of Messina, Messina, Italy
| | - Letizia Romeo
- Department of Human Pathology, University of Messina, Messina, Italy
| | - Carmelo Biondo
- Department of Human Pathology, University of Messina, Messina, Italy
| | | | - Giuseppe Teti
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy.,Charybdis Vaccines Srl, Messina, Italy
| | - Franco Felici
- Department of Biosciences and Territory, University of Molise, Pesche, Isernia, Italy
| | - Concetta Beninati
- Scylla Biotech Srl, Messina, Italy.,Department of Human Pathology, University of Messina, Messina, Italy
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7
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Cariccio VL, Domina M, Benfatto S, Venza M, Venza I, Faleri A, Bruttini M, Bartolini E, Giuliani MM, Santini L, Brunelli B, Norais N, Borgogni E, Midiri A, Galbo R, Romeo L, Biondo C, Masignani V, Teti G, Felici F, Beninati C. Phage display revisited: Epitope mapping of a monoclonal antibody directed against Neisseria meningitidis adhesin A using the PROFILER technology. MAbs 2016; 8:741-50. [PMID: 26963435 DOI: 10.1080/19420862.2016.1158371] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
There is a strong need for rapid and reliable epitope mapping methods that can keep pace with the isolation of increasingly larger numbers of mAbs. We describe here the identification of a conformational epitope using Phage-based Representation OF ImmunoLigand Epitope Repertoire (PROFILER), a recently developed high-throughput method based on deep sequencing of antigen-specific lambda phage-displayed libraries. A novel bactericidal monoclonal antibody (mAb 9F11) raised against Neisseria meningitidis adhesin A (NadA), an important component of the Bexsero(®) anti-meningococcal vaccine, was used to evaluate the technique in comparison with other epitope mapping methods. The PROFILER technology readily identified NadA fragments that were capable of fully recapitulating the reactivity of the entire antigen against mAb 9F11. Further analysis of these fragments using mutagenesis and hydrogen-deuterium exchange mass-spectrometry allowed us to identify the binding site of mAb 9F11 (A250-D274) and an adjoining sequence (V275-H312) that was also required for the full functional reconstitution of the epitope. These data suggest that, by virtue of its ability to detect a great variety of immunoreactive antigen fragments in phage-displayed libraries, the PROFILER technology can rapidly and reliably identify epitope-containing regions and provide, in addition, useful clues for the functional characterization of conformational mAb epitopes.
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Affiliation(s)
| | | | - Salvatore Benfatto
- b Department of Human Pathology , University of Messina , Messina , Italy
| | - Mario Venza
- c Department Clinical and Experimental Medicine , University of Messina , Messina , Italy
| | - Isabella Venza
- c Department Clinical and Experimental Medicine , University of Messina , Messina , Italy
| | | | - Marco Bruttini
- d GSK Vaccines , Siena , Italy.,e Department of Life Sciences , University of Siena , Siena , Italy
| | | | | | | | | | | | | | - Angelina Midiri
- b Department of Human Pathology , University of Messina , Messina , Italy
| | - Roberta Galbo
- b Department of Human Pathology , University of Messina , Messina , Italy
| | - Letizia Romeo
- b Department of Human Pathology , University of Messina , Messina , Italy
| | - Carmelo Biondo
- b Department of Human Pathology , University of Messina , Messina , Italy
| | | | - Giuseppe Teti
- c Department Clinical and Experimental Medicine , University of Messina , Messina , Italy.,f Charybdis Vaccines Srl , Messina , Italy
| | - Franco Felici
- g Department of Biosciences and Territory , University of Molise , Pesche , Isernia , Italy
| | - Concetta Beninati
- a Scylla Biotech Srl , Messina , Italy.,b Department of Human Pathology , University of Messina , Messina , Italy
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8
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Bacteriophage lambda display systems: developments and applications. Appl Microbiol Biotechnol 2014; 98:2853-66. [PMID: 24442507 DOI: 10.1007/s00253-014-5521-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 01/03/2014] [Accepted: 01/04/2014] [Indexed: 01/01/2023]
Abstract
Bacteriophage (phage) Lambda (λ) has played a key historic role in driving our understanding of molecular genetics. The lytic nature of λ and the conformation of its major capsid protein gpD in capsid assembly offer several advantages as a phage display candidate. The unique formation of the λ capsid and the potential to exploit gpD in the design of controlled phage decoration will benefit future applications of λ display where steric hindrance and avidity are of great concern. Here, we review the recent developments in phage display technologies with phage λ and explore some key applications of this technology including vaccine delivery, gene transfer, bio-detection, and bio-control.
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9
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Krumpe LR, Mori T. Potential of phage-displayed peptide library technology to identify functional targeting peptides. Expert Opin Drug Discov 2013; 2:525. [PMID: 20150977 DOI: 10.1517/17460441.2.4.525] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Combinatorial peptide library technology is a valuable resource for drug discovery and development. Several peptide drugs developed through phage-displayed peptide library technology are presently in clinical trials and the authors envision that phage-displayed peptide library technology will assist in the discovery and development of many more. This review attempts to compile and summarize recent literature on targeting peptides developed through peptide library technology, with special emphasis on novel peptides with targeting capacity evaluated in vivo.
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Affiliation(s)
- Lauren Rh Krumpe
- SAIC-Frederick, Inc., Molecular Targets Development Program, NCI-Frederick, Frederick, Maryland 21702, USA
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10
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Pershad K, Kay BK. Generating thermal stable variants of protein domains through phage display. Methods 2012; 60:38-45. [PMID: 23276752 DOI: 10.1016/j.ymeth.2012.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 12/13/2022] Open
Abstract
Often in protein design research, one desires to generate thermally stable variants of a protein or domain. One route to identifying mutations that yield domains that remain folded and active at a higher temperature is through the use of directed evolution. A library of protein domain variants can be generated by mutagenic PCR, expressed on the surface of bacteriophage M13, and subjected to heat, such that the unfolded forms of the domain, showing reduced or no binding activity, are lost during subsequent affinity selection, whereas variants that still retain binding to their target are selected and enriched with each subsequent round of affinity selection. This approach takes advantage of the fact that bacteriophage M13 particles are heat stable and resistant to many proteases and protein denaturants. We present the application of this general approach to generating thermally stable variants of a eukaryotic peptide-binding domain. The benefits of producing such variants are that they typically express at high levels in Escherichia coli (30-60 mg/L shake flask) and remain soluble in solution at higher concentrations for longer periods of time than the wild-type form of the domain. The process of library generation and screening generally requires about one month of effort, and yields variants with >10 °C increase in thermal stability, as measured in a simple fluorescence-based thermal shift assay. It is anticipated that thermally stable variants will serve as excellent scaffolds for generating affinity reagents to a variety of targets of interest.
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Affiliation(s)
- Kritika Pershad
- Department of Biological Sciences, University of Illinois at Chicago, 845 W. Taylor St., 3240 SES-MC 066, Chicago, IL 60607-7060, USA
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11
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Li W. ORF phage display to identify cellular proteins with different functions. Methods 2012; 58:2-9. [PMID: 22836128 DOI: 10.1016/j.ymeth.2012.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 07/11/2012] [Indexed: 01/17/2023] Open
Abstract
Open reading frame (ORF) phage display is a new branch of phage display aimed at improving its efficiency to identify cellular proteins with specific binding or functional activities. Despite the success of phage display with antibody libraries and random peptide libraries, phage display with cDNA libraries of cellular proteins identifies a high percentage of non-ORF clones encoding unnatural short peptides with minimal biological implications. This is mainly because of the uncontrollable reading frames of cellular proteins in conventional cDNA libraries. ORF phage display solves this problem by eliminating non-ORF clones to generate ORF cDNA libraries. Here I summarize the procedures of ORF phage display, discuss the factors influencing its efficiency, present examples of its versatile applications, and highlight evidence of its capability of identifying biologically relevant cellular proteins. ORF phage display coupled with different selection strategies is capable of delineating diverse functions of cellular proteins with unique advantages.
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Affiliation(s)
- Wei Li
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, 1638 NW 10th Avenue, Miami, FL 33136, USA.
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12
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Eckert-Boulet N, Pedersen ML, Krogh BO, Lisby M. Optimization of ordered plasmid assembly by gap repair in Saccharomyces cerevisiae. Yeast 2012; 29:323-34. [DOI: 10.1002/yea.2912] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 06/18/2012] [Accepted: 06/18/2012] [Indexed: 11/06/2022] Open
Affiliation(s)
- Nadine Eckert-Boulet
- Department of Biology; University of Copenhagen; Ole Maaloees Vej 5; DK-2200; Copenhagen N; Denmark
| | | | - Berit Olsen Krogh
- Department of Mammalian Cell Technology, Biopharmaceutical Research Unit; Novo Nordisk A/S; Novo Nordisk Park; DK-2760; Måløv; Denmark
| | - Michael Lisby
- Department of Biology; University of Copenhagen; Ole Maaloees Vej 5; DK-2200; Copenhagen N; Denmark
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13
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Abstract
Bacteriophage λ, rediscovered in the early 1950s, has served as a model in molecular biology studies for decades. Although currently more complex organisms and more complicated biological systems can be studied, this phage is still an excellent model to investigate principles of biological processes occurring at the molecular level. In fact, very few other biological models provide possibilities to examine regulations of biological mechanisms as detailed as performed with λ. In this chapter, recent advances in our understanding of mechanisms of bacteriophage λ development are summarized and discussed. Particularly, studies on (i) phage DNA injection, (ii) molecular bases of the lysis-versus-lysogenization decision and the lysogenization process itself, (iii) prophage maintenance and induction, (iv), λ DNA replication, (v) phage-encoded recombination systems, (vi) transcription antitermination, (vii) formation of the virion structure, and (viii) lysis of the host cell, as published during several past years, will be presented.
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14
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Derda R, Tang SKY, Li SC, Ng S, Matochko W, Jafari MR. Diversity of phage-displayed libraries of peptides during panning and amplification. Molecules 2011; 16:1776-803. [PMID: 21339712 PMCID: PMC6259649 DOI: 10.3390/molecules16021776] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 02/10/2011] [Accepted: 02/17/2011] [Indexed: 01/15/2023] Open
Abstract
The amplification of phage-displayed libraries is an essential step in the selection of ligands from these libraries. The amplification of libraries, however, decreases their diversity and limits the number of binding clones that a screen can identify. While this decrease might not be a problem for screens against targets with a single binding site (e.g., proteins), it can severely hinder the identification of useful ligands for targets with multiple binding sites (e.g., cells). This review aims to characterize the loss in the diversity of libraries during amplification. Analysis of the peptide sequences obtained in several hundred screens of peptide libraries shows explicitly that there is a significant decrease in library diversity that occurs during the amplification of phage in bacteria. This loss during amplification is not unique to specific libraries: it is observed in many of the phage display systems we have surveyed. The loss in library diversity originates from competition among phage clones in a common pool of bacteria. Based on growth data from the literature and models of phage growth, we show that this competition originates from growth rate differences of only a few percent for different phage clones. We summarize the findings using a simple two-dimensional "phage phase diagram", which describes how the collapse of libraries, due to panning and amplification, leads to the identification of only a subset of the available ligands. This review also highlights techniques that allow elimination of amplification-induced losses of diversity, and how these techniques can be used to improve phage-display selection and enable the identification of novel ligands.
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Affiliation(s)
- Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, AB T6G2G2, Canada.
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15
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Lindner T, Kolmar H, Haberkorn U, Mier W. DNA libraries for the construction of phage libraries: statistical and structural requirements and synthetic methods. Molecules 2011; 16:1625-41. [PMID: 21326140 PMCID: PMC6259622 DOI: 10.3390/molecules16021625] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 01/26/2011] [Accepted: 02/11/2011] [Indexed: 01/19/2023] Open
Abstract
Peptide-based molecular probes identified by bacteriophage (phage) display technology expand the peptide repertoire for in vivo diagnosis and therapy of cancer. Numerous peptides that bind cancer-associated antigens have been discovered by panning phage libraries. However, until now only few of the peptides selected by phage display have entered clinical applications. The success of phage derived peptides essentially depends on the quality of the library screened. This review summarizes the methods to achieve highly homogenous libraries that cover a maximal sequence space. Biochemical and chemical strategies for the synthesis of DNA libraries and the techniques for their integration into the viral genome are discussed in detail. A focus is set on the methods that enable the exclusion of disturbing sequences. In addition, the parameters that define the variability, the minimal numbers of copies per library and the use of alternating panning cycles to avoid the loss of selected hits are evaluated.
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Affiliation(s)
- Thomas Lindner
- Department of Nuclear Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 400, D-69120 Heidelberg, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Darmstadt University of Technology, Petersenstrase 22, 64287 Darmstadt, Germany
| | - Uwe Haberkorn
- Department of Nuclear Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 400, D-69120 Heidelberg, Germany
| | - Walter Mier
- Department of Nuclear Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 400, D-69120 Heidelberg, Germany
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +49-6221-56-7720; Fax: +49-6221-56-33629
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16
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Hayes S, Gamage LNA, Hayes C. Dual expression system for assembling phage lambda display particle (LDP) vaccine to porcine Circovirus 2 (PCV2). Vaccine 2010; 28:6789-99. [PMID: 20674873 DOI: 10.1016/j.vaccine.2010.07.047] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 07/07/2010] [Accepted: 07/15/2010] [Indexed: 11/16/2022]
Abstract
The bacteriophage lambda small capsid protein D forms trimers on the phage head. D-fusion polypeptides can be expressed from plasmids in E. coli and remain soluble without aggregation. We report a dual expression system for the display of four immunodominant regions of porcine Circovirus 2 (PCV2) capsid protein (CAP) as D-CAP fusions on lambda display particles (LDP). The LDP-D-CAP preparation proved an effective vaccine in pigs, eliciting both cellular and humoral immune responses and PCV2 neutralizing antibodies. In our dual system wild type D expression was encoded by a heteroimmune infecting phage. The D-fusion protein expression in the infected cells was from an inducible plasmid, enabling the deferral of D-fusion expression until needed. The effective vaccine preparation depended upon the gradient purification of very high concentration, essentially tail-less display particles, not previously described.
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Affiliation(s)
- Sidney Hayes
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada.
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17
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Caberoy NB, Zhou Y, Jiang X, Alvarado G, Li W. Efficient identification of tubby-binding proteins by an improved system of T7 phage display. J Mol Recognit 2010; 23:74-83. [PMID: 19718693 DOI: 10.1002/jmr.983] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mutation in the tubby gene causes adult-onset obesity, progressive retinal, and cochlear degeneration with unknown mechanism. In contrast, mutations in tubby-like protein 1 (Tulp1), whose C-terminus is highly homologous to tubby, only lead to retinal degeneration. We speculate that their diverse N-terminus may define their distinct disease profile. To elucidate the binding partners of tubby, we used tubby N-terminus (tubby-N) as bait to identify unknown binding proteins with open-reading-frame (ORF) phage display. T7 phage display was engineered with three improvements: high-quality ORF phage display cDNA library, specific phage elution by protease cleavage, and dual phage display for sensitive high throughput screening. The new system is capable of identifying unknown bait-binding proteins in as fast as approximately 4-7 days. While phage display with conventional cDNA libraries identifies high percentage of out-of-frame unnatural short peptides, all 28 tubby-N-binding clones identified by ORF phage display were ORFs. They encode 16 proteins, including 8 nuclear proteins. Fourteen proteins were analyzed by yeast two-hybrid assay and protein pull-down assay with ten of them independently verified. Comparative binding analyses revealed several proteins binding to both tubby and Tulp1 as well as one tubby-specific binding protein. These data suggest that tubby-N is capable of interacting with multiple nuclear and cytoplasmic protein binding partners. These results demonstrated that the newly-engineered ORF phage display is a powerful technology to identify unknown protein-protein interactions.
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Affiliation(s)
- Nora B Caberoy
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
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18
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Functional viral metagenomics and the next generation of molecular tools. Trends Microbiol 2009; 18:20-9. [PMID: 19896852 DOI: 10.1016/j.tim.2009.10.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Revised: 10/14/2009] [Accepted: 10/19/2009] [Indexed: 12/13/2022]
Abstract
The enzymes of bacteriophages and other viruses have been essential research tools since the first days of molecular biology. However, the current repertoire of viral enzymes only hints at their overall potential. The most commonly used enzymes are derived from a surprisingly small number of cultivated viruses, which is remarkable considering the extreme abundance and diversity of viruses revealed over the past decade by metagenomic analysis. To access the treasure trove of enzymes hidden in the global virosphere and develop them for research, therapeutic and diagnostic uses, improvements are needed in our ability to rapidly and efficiently discover, express and characterize viral genes to produce useful proteins. In this paper, we discuss improvements to sampling and cloning methods, functional and genomics-based screens, and expression systems, which should accelerate discovery of new enzymes and other viral proteins for use in research and medicine.
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Gamage LN, Ellis J, Hayes S. Immunogenicity of bacteriophage lambda particles displaying porcine Circovirus 2 (PCV2) capsid protein epitopes. Vaccine 2009; 27:6595-604. [DOI: 10.1016/j.vaccine.2009.08.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2009] [Revised: 07/30/2009] [Accepted: 08/06/2009] [Indexed: 11/27/2022]
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New perspective for phage display as an efficient and versatile technology of functional proteomics. Appl Microbiol Biotechnol 2009; 85:909-19. [PMID: 19885657 DOI: 10.1007/s00253-009-2277-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 09/23/2009] [Accepted: 09/23/2009] [Indexed: 10/20/2022]
Abstract
Phage display with antibody libraries has been widely used with versatile applications. However, phage display with cDNA libraries is rare and inefficient. Because of uncontrollable reading frames and stop codons in cDNA repertoires, high percentage of phage clones identified from conventional cDNA libraries are non-open reading frames (non-ORFs) encoding unnatural short peptides with minimal implications in protein networks. Consequently, phage display has not been used as a technology of functional proteomics to elucidate protein-protein interactions like yeast two-hybrid system and mass spectrometry-based technologies. Several strategies, including C-terminal display and ORF cDNA libraries, have been explored to circumvent the technical problem. The accumulative endeavors eventually led to the efficient elucidation of a large number of tubby- and phosphatidylserine-binding proteins in recent studies by ORF phage display with minimal reading frame issue. ORF phage display inherits all the versatile applications of antibody phage display, but enables efficient identification of real endogenous proteins with efficiency, sensitivity, and accuracy comparable to other technologies of functional proteomics. Its ELISA-like procedure can be conveniently adapted by individual laboratories or fully automated for high-throughput screening. Thus, ORF phage display is an efficient, sensitive, versatile, and convenient technology of functional proteomics for elucidation of global and pathway-specific protein-protein interactions, disease mechanisms, or therapeutic targets.
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Efficient identification of phosphatidylserine-binding proteins by ORF phage display. Biochem Biophys Res Commun 2009; 386:197-201. [PMID: 19520055 DOI: 10.1016/j.bbrc.2009.06.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 06/05/2009] [Indexed: 12/28/2022]
Abstract
To efficiently elucidate the biological roles of phosphatidylserine (PS), we developed open-reading-frame (ORF) phage display to identify PS-binding proteins. The procedure of phage panning was optimized with a phage clone expressing MFG-E8, a well-known PS-binding protein. Three rounds of phage panning with ORF phage display cDNA library resulted in approximately 300-fold enrichment in PS-binding activity. A total of 17 PS-binding phage clones were identified. Unlike phage display with conventional cDNA libraries, all 17 PS-binding clones were ORFs encoding 13 real proteins. Sequence analysis revealed that all identified PS-specific phage clones had dimeric basic amino acid residues. GST fusion proteins were expressed for 3 PS-binding proteins and verified for their binding activity to PS liposomes, but not phosphatidylcholine liposomes. These results elucidated previously unknown PS-binding proteins and demonstrated that ORF phage display is a versatile technology capable of efficiently identifying binding proteins for non-protein molecules like PS.
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Abstract
This review focusses on the isolation of proteins from genomic or cDNA expression products libraries displayed on phage. The use of phage display is highlighted for the characterization of binding proteins with diverse biological functions. Phage display is compared with another strategy, the yeast two-hybrid method. The combination of both strategies is especially powerful to eliminate false positives and to get information on the biochemical functions of proteins.
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Affiliation(s)
- Jean-Luc Jestin
- URA CNRS 2128, Département de Biologie Structurale et Chimie, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris 15, France.
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Dahan S, Chevet E, Liu JF, Dominguez M. Antibody-based Proteomics: From bench to bedside. Proteomics Clin Appl 2007; 1:922-33. [PMID: 21136747 DOI: 10.1002/prca.200700153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Indexed: 01/09/2023]
Abstract
Over the past 75 years, antibodies have gone from being recognized as disease biomarkers to being used as very powerful therapeutic tools. This evolution has been accelerated by the identification of mAb and the extensive use of immunological tools both at fundamental and clinical levels. In this review, we evaluate how antibodies can be used to assess the proteome of cells or tissues and their relevance for clinical applications. These antibody-based proteomics approaches also require analytical and technological pipelines as well as specific enabling tools which are described. Our first objective was to establish how large-scale datasets (provided by high-throughput studies such as proteomics and transcriptomics) can be integrated with literature searches and clinical data to identify potentially relevant markers against which antibodies should be raised. Then based on an extensive literature review and our experience, we compare the methodologies developed to produce specific antibodies either in vivo or in vitro. This is followed by the description of the validation tools currently available and it also includes the use of antibody-based approaches in the establishment of molecular signatures utilized at the bench and soon available for bedside use.
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Matsubara T, Sato T. Identification of Oligosaccharide-Recognition Molecules by Phage-Display Technology. TRENDS GLYCOSCI GLYC 2007. [DOI: 10.4052/tigg.19.133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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