Display of expression products of cDNA libraries on phage surfaces. A versatile screening system for selective isolation of genes by specific gene-product/ligand interaction

In vitro alpha-complementation of beta-galactosidase on a bacteriophage surface

Surface display of large multimeric non-secreted proteins is advantageous on the bacteriophage lambda compared with the widely used filamentous phage systems. A model system, the alpha-complementation of beta-galactosidase, was used for both further general characterization of protein-protein interactions on the lambda tail tube surface and for specifically probing the structure of the phage-displayed beta-galactosidase tetramer. In this complementation system, dimeric enzymatically inactive N-terminal deletion mutants of beta-galactosidase (alpha-acceptors) interact with peptides whose sequences span the region of the deletion (alpha-peptides) with the subsequent formation of tetramers and restoration of activity. The lambda phage could tolerate incorporation into their tail tubes of a limited number of copies of V protein (gpV) subunits C-terminally modified with an active alpha-peptide. Purified alpha-peptide phage showed specific in vitro alpha-complementation with an alpha-acceptor extract; the features of this reaction suggested that each complemented monomer can directly associate with an alpha-peptide displayed within the same tail tube structure. In contrast to the alpha-peptide, attempts to surface display an alpha-acceptor protein in a similar manner were unsuccessful. The implications of this work for surface-display cDNA libraries are discussed.

Purification of storage granule protein-23. A novel protein identified by phage display technology and interaction with type I plasminogen activator inhibitor

Type 1 plasminogen activator inhibitor (PAI-1) is a key regulator of the fibrinolytic cascade that is stored in a rapidly releasable form within platelet alpha-granules. To identify proteins that may participate in the targeting or storage of this potent inhibitor, this report investigates the applicability of utilizing filamentous bacteriophages to display proteins expressed by cells containing a regulated secretory pathway and their enrichment based upon an interaction with PAI-1. For this purpose, RNA was extracted from AtT-20 cells (i.e. a classical model cell system for intracellular protein sorting), reverse transcribed, amplified using polymerase chain reaction primers containing internal restriction sites, and cloned into the phagemid pCOMB3H for expression as fusion constructs with the bacteriophage gene III protein. Escherichia coli was transformed with the phagemids and infected with VCSM13 helper phage, and the resulting AtT-20 cDNA-bacteriophage library was enriched by panning against solid- and solution-phase PAI-1. The enriched cDNA library was subcloned into a prokaryotic expression vector system that replaces the gene III protein with a decapeptide tag for immunologic quantitation. One novel cDNA clone (i.e. A-61), which preferentially recognized solution-phase PAI-1 and reacted positively with antibodies derived from a rabbit immunized with alpha-granules, was subcloned into the prokaryotic expression vector pTrcHis to create a construct containing an N-terminal six-histidine purification tag. This construct was expressed in E. coli, purified by nickel-chelate chromatography followed by preparative SDS-polyacrylamide gel electrophoresis, and utilized for the generation of polyclonal antibodies. Immunoblotting analysis employing antibodies against the purified A-61 construct revealed a 23-kDa protein present in the regulated secretory pathway of AtT-20 cells. The 23-kDa molecule was purified from media conditioned by AtT-20 cells by ion exchange chromatography on DEAE-Sephacel, molecular sieve chromatography on Sephacryl S-100, chromatofocusing on Polybuffer exchanger 94, and affinity chromatography on PAI-1-Sepharose. N-terminal amino acid sequencing of a 16-kDa Lys-C proteolytic fragment of the 23-kDa storage granule protein was employed to confirm its identity with the cDNA sequence of clone A-61. These data indicate that phage display of cDNA libraries fused to the C-terminal region of the gene III protein and their enrichment via an interaction with a target molecule can be utilized to define other proteins present within a particular cellular pathway.

Expression cloning of cDNA by phage display selection

Expression cloning of a mouse kappa chain fragment has been achieved from a cDNA library by display of expressed proteins on filamentous phage and affinity selection for binding to anti-mouse Fab antibodies. Expressed proteins were anchored to the phage coat by a synthetic, anti-parallel leucine zipper, which had been selected from a semi-randomized zipper library for the ability to connect a test protein to phage. From a library of 4 x 10(6) transformants, two separate clones displaying different size cDNA inserts were recovered after four selection rounds. These results further demonstrate the utility of phage display for cDNA expression cloning.

Phage display of proteins

Phage display of proteins continues to be an important technology with a variety of applications. In the past year, advances have been made in coupling rational protein design with the power of the display selection process. In addition to the widely used filamentous phage, other bacteriophage surface expression systems have now been developed, some of which may be of particular use for the selection of surface-display cDNA clones.

Selection of proteins and peptides from libraries displayed on filamentous bacteriophage

This article attempts to review recent developments in the rapidly developing field of phage display libraries. The current state of peptide, antibody, and cDNA libraries, as well as current and future applications of phage display libraries are discussed. The main focus of the article is on the methods for selecting binding ligands against targets in a variety of different formats. These include solid phase and in-solution selection methods, and the strategies used to select for higher affinity, and binding ligands against impure and cellular target proteins.

Humoral and cell-mediated autoimmunity in allergy to Aspergillus fumigatus

A cDNA encoding an allergenic protein was isolated from an Aspergillus fumigatus (A. fumigatus) cDNA library displayed on the surface of filamentous phage. Serum immunoglobulin E (IgE) from A. fumigatus-sensitized individuals was used to enrich phage-expressing gene products binding to IgE. One of the cDNAs encoded a 26.7-kD protein that was identified as a manganese superoxide dismutase (MnSOD) sharing 51.5% identity and 67.2% homology to the corresponding human enzyme. Both human and A. fumigatus MnSOD coding sequences were expressed in Escherichia coli as [His]6-tagged fusion proteins and purified by Ni(2+)-chelate affinity chromatography. The two recombinant MnSODs were both recognized by IgE antibodies from subjects allergic to the A. fumigatus MnSOD and elicited specific immediate type allergic skin reactions in these individuals. Moreover, both human and A. fumigatus MnSOD induced proliferation in peripheral blood mononuclear cells of A. fumigatus-allergic subjects who showed specific IgE responses and reacted in skin tests to MnSOD. These observations provide evidence for autoreactivity to the human MnSOD in allergic persons sensitized to an environmental allergen from A. fumigatus who share a high degree of sequence homology to the corresponding human enzyme.

Phage presentation

There has recently been great interest in the use of the filamentous bacteriophage fd as a vehicle for the display of peptides and proteins. Phage libraries displaying random peptides up to 38 amino acids in length can be used (i) to select for ligands able to bind specific target molecules; (ii) to mimic non-proteinaceous ligands; and (iii) as a tool to map epitopes recognized by antibodies. The display of proteins or their functional domains provides a system for the analysis of structure-function relationships, and the potential to generate proteins with altered binding characteristics or novel catalytic properties. The display of short immunogenic determinants on fusion phage may provide a basis for the development of novel peptide vaccines, whilst the expression of libraries of antibody fragments may provide a method to by-pass hybridoma technology in the generation of monoclonal antibodies.

Modifying the specificity and activity of the Enterobacter cloacae P99 beta-lactamase by mutagenesis within an M13 phage vector

A library of Enterobacter cloacae P99 beta-lactamase mutants was produced to investigate the importance of residues 286-290 for substrate binding and catalysis and to characterize mutants with altered specificities and activities for various 3'-substituted cephalosporins. This region of the enzyme is a component of the active site that has not been implicated as participating in the catalytic mechanism but, based on molecular modeling, should contact the 3' substituents of cephalosporins. Random mutagenesis was carried out within an M13 phage vector by hybridization mutagenesis, and the phage library could be highly enriched for active beta-lactamase genes by incubation of infected bacteria with beta-lactam antibiotics. The mutants were characterized by Michaelis-Menten kinetic analyses with several cephalosporin substrates and spanned a 25-fold range of k(cat), 24-fold range of K(m), and 6-fold range of k(cat)/K(m) values. All five amino acid positions were found to be permissive to substitution, but the active mutant proteins carried substitutions that likely maintained the structure of the region. Serine 287 was the least permissive to change, requiring small, uncharged residues for retention of catalytic activity. The variation of Michaelis-Menten kinetic parameters observed in these enzymes was shown to be significant in the context of in vitro cytotoxicity assays with the cephalosporin-doxorubicin prodrug C-Dox and is suitable for experiments to probe the relationship between enzyme kinetics and efficacy in enzyme-prodrug approaches to targeted therapy.

Automated serology with recombinant allergens. A feasibility study

Diagnosis of allergic conditions is based on skin prick- and/or intradermal tests and on serology. Both methods make use of allergenic preparations and the results mainly depend on the quality of the substances applied and on the reactivity of the subjects. Recombinant allergens can be produced as highly pure proteins. They may contribute to a significant improvement of the diagnosis of allergic diseases provided that the allergens became available in a pure, fully antigenic form suitable for routine assessments. We have studied the diagnostic properties of recombinant Aspergillus fumigatus allergen I (rAsp f I/a), a major allergen recognised by about 60% of the A. fumigatus allergic individuals, to test the feasibility of using recombinant allergens for automated serology in the Pharmacia CAP System, a new solid-phase immunoassay. ImmunoCAPs carrying immobilised rAsp f I/a were produced and evaluated using sera from well characterised patients with allergic bronchopulmonary aspergillosis (ABPA), allergic asthmatics with or without A. fumigatus sensitisation, and healthy control persons. The clinical parameters used for the diagnosis of allergy to A. fumigatus were RAST and skin test reactivity to commercial A. fumigatus extracts. IgE antibodies recognising rAsp f I/a were determined by a direct antigen-specific ELISA and with the newly developed rAsp f I/a ImmunoCAPs. Quantitative results from the two rAsp f I/a detection systems correlated closely, indicating that this recombinant allergen can be incorporated in the Pharmacia CAP System with unaltered antigenic activity. The behaviour of a panel of recombinant A. fumigatus allergens in the Pharmacia CAP System will be evaluated in the near future to assess the potential of recombinant allergens for the automated diagnosis of allergic conditions.

Finding prospective partners in the library: the two-hybrid system and phage display find a match

The two-hybrid system uses the efficacy of yeast genetic assays to identify protein-protein interactions. It permits the rapid cloning of genes encoding products that interact with a given protein of interest. Also being developed are phage display methods that allow direct physical selection of binding proteins. These methods have significantly altered strategies for analysing signaling and regulatory pathways.

Phage display

Phage display is a powerful method for the selection and evolution of proteins and peptides. Applications include the generation of potent and novel antibodies, the in vitro improvement of protein affinity and function, epitope discovery, the development of leads for vaccine research and the identification of interacting proteins using cDNA libraries.

Phage display: protein engineering by directed evolution

Phage display of proteins has become an important tool for protein engineering. Over the past year, the versatility of the technology has expanded to include the development of DNA-binding proteins with novel specificities, energetics of protein folding and directed evolution of antibodies. In addition, display of expressed cDNA libraries opens an exciting opportunity for studying protein-protein interactions.

Surface expression and ligand-based selection of cDNAs fused to filamentous phage gene VI

We describe a novel phage display system that affords the surface expression and hence affinity selection of cDNAs. The strategy is based on a new approach to functionally display proteins on filamentous phage through the attachment to the C-terminus of the minor coat protein VI. The utility of the method was evaluated using a cDNA library derived from the parasite Ancylostoma caninum. cDNA sequences were fused in each of the three reading frames to the 3'-end of the M13 gene VI expressed by a phagemid vector. Phages rescued from this cDNA expression library were subjected to biopanning against two serine proteases, trypsin and the human coagulation factor Xa. This led to the identification of cDNAs encoding novel members of two different families of serine protease inhibitors. The authenticity of the cDNA selected with trypsin as the target was demonstrated by purifying the encoded potent Kunitz-type inhibitor from an Ancylostoma caninum extract. The rapid isolation of specific cDNAs with the protein VI monovalent display system should facilitate the search for novel biologically important ligands.