Phage Technology Research Articles

Size of the ligand complex between the N-terminal domain of the gene III coat protein and the non-infectious phage strongly influences the usefulness of in vitro selective infective phage technology

Size of the ligand complex between the N-terminal domain of the gene III coat protein and the non-infectious phage strongly influences the usefulness of in vitro selective infective phage technology

Size of the ligand complex between the N-terminal domain of the gene III coat protein and the non-infectious phage strongly influences the usefulness of in vitro selective infective phage technology

The selective infective phage (SIP) technology allows a rapid positive selection of interacting pairs of biological molecules that restore to non-infectious phages their ability to infect the bacterial host. After a successful infection, the phage is amplified and the DNA encoding the interacting ligand is isolated from the phage genome and sequenced. In our studies we have evaluated the usefulness of SIP for the identification and cloning of proteins interacting with a biotinylated target binding to a newly designed adapter molecule consisting of streptavidin fused to the C-terminus of the extracellular domain of the phage minor coat protein III. The new adapter was expressed in Escherichia coli and refolded from inclusion bodies. The two different domains joined within the chimaera were found to be biologically functional. We also demonstrated that non-covalent interactions between a non-infectious phage displaying a short peptide, which specifically binds the streptavidin, and the adapter molecule restore phage infectivity. To evaluate the potential of SIP as a general and generic tool for the screening of cDNA libraries that encode the ligands displayed at the surface of the phage and binding to biotinylated targets, we have increased both the size of the displayed ligand on the phage and the size of the biotinylated target bound to the streptavidin domain of the adapter molecule. In our model systems we show that the size of either the ligand or the target is a limiting factor for the technology.

CAT's phage technology patent upheld

CAT's phage technology patent upheld

22] Selectively infective phage technology

Publisher Summary This chapter describes a selection technology related to phage display, the selectively infective phage (SIP) technology. In both SIP and phage display, libraries of proteins or peptides of interest are displayed on the tip of a filamentous phage fused to the gene 3 protein (g3p). However, in contrast to the conventional phage display in which separation of binders with an immobilized ligand is required, in SIP technology the selection step is carried out in solution and directly coupled to the infection event. Therefore, no elution of binders is ever necessary, and incomplete elution of the most tightly binding molecules is not a limitation. This is achieved by taking an advantage of the modular structure of g3p, which occurs probably in five copies on the tip of the filamentous phage and consists of the N-terminal domains N1 [68 amino acid (aa)], N2 (131 aa), and the C-terminal domain CT (150 aa), connected by the glycine-rich linkers G1 (18 aa) and G2 (39 aa). However, this system, which is more powerful but also less controllable, can be used only with proteins and peptides for both partners. This chapter provides several general protocols that apply for in vitro and in vivo SIP and compares in more detail the use of both methods by the means of a few examples. Two other names, direct rescue interaction (DIRE) and selection and amplification of phage (SAP), have also been used for the SIP technology.

Exploiting recombination in single bacteria to make large phage antibody libraries.

The creation of large phage antibody libraries has become an important goal in selecting antibodies against any antigen. Here we describe a method for making libraries so large that the complete diversity cannot be accessed using traditional phage technology. This involves the creation of a primary phage scFv library in a phagemid vector containing two nonhomologous lox sites. Contrary to the current dogma, we found that infecting Cre recombinase-expressing bacteria by such a primary library at a high multiplicity of infection results in the entry of many different phagemid into the cell. Exchange of Vh and Vl genes between such phagemids creates many new V h/Vl combinations, all of which are functional. On the basis of the observed recombination, the library is calculated to have a diversity of 3x1011. A library created using this method was validated by the selection of high affinity antibodies against a large number of different protein antigens.

Selectively infective phage (SIP) technology: scope and limitations

We review here the selectively infective phage (SIP) technology, a powerful tool for the rapid selection of protein–ligand and peptide–ligand pairs with very high affinities. SIP is highly suitable for discriminating between molecules with subtle stability and folding differences. We discuss the preferred types of applications for this technology and some pitfalls inherent in the in vivo SIP method that have become apparent in its application with highly randomized libraries, as well as some precautions that should be taken in successfully applying this technology.

Phage display of a cellulose binding domain from Clostridium thermocellum and its application as a tool for antibody engineering

Phage display of antibody fragments has proved to be a powerful tool for the isolation and in vitro evolution of these biologically important molecules. However, the general usefulness of this technology is still limited by some technical difficulties. One of the most debilitating obstacles to the widespread application of the technology is the accumulation of “insert loss” clones in the libraries; phagemid clones from which the DNA encoding part or all of the cloned antibody fragment had been deleted. Another difficulty arises when phage technology is applied for cloning hybridoma-derived antibody genes, where myeloma derived light chains, irrelevant to the hybridoma's antibody specificity may be fortuitously cloned. Here, we report the construction of a novel phage-display system designed to address these problems. In our system a single-chain Fv (scFv) is expressed as an in-frame fusion protein with a cellulose-binding domain (CBD) derived from the Clostridium thermocellum cellulosome. The CBD domain serves as an affinity tag allowing rapid phage capture and concentration from crude culture supernatants, and immunological detection of both displaying phage and soluble scFv produced thereof. We demonstrate the utility of our system in solving the technical difficulties described above, and in speeding up the process of scFv isolation from combinatorial antibody repertoires.

Reproducing the natural evolution of protein structural features with the selectively infective phage (SIP) technology. the kink in the first strand of antibody kappa domains

The β-sandwich structure of immunoglobulin variable domains is characterized by a typical kink in the first strand, which allows the first part of the strand to hydrogen bond to the outer β-sheet (away from the VH-VL interface) and the second part to the inner β-sheet. This kink differs in length and sequence between the Vκ, Vλ and VH domains and yet is involved in several almost perfectly conserved interactions with framework residues. We have used the selectively infective phage (SIP) system to select the optimal kink region from several defined libraries, using an anti-hemagglutinin single-chain Fv (scFv) fragment as a model system. Both for the kink with the Vκ domain length and that with the Vλ length, a sequence distribution was selected that coincides remarkably well with the sequence distribution of natural antibodies. The selected scFv fragments were purified and characterized, and thermodynamic stability was found to be the prime factor responsible for selection. These data show that the SIP technology can be used for optimizing protein structural features by evolutionary approaches.

Non-repetitive single-chain Fv linkers selected by selectively infective phage (SIP) technology.

By using the selectively infective phage (SIP) technology, we selected non-repetitive linkers for a single-chain Fv fragment to have genes more robust against deletions in PCR-based gene assembly and directed evolution experiments than is the case for the classical (Gly4Ser)3 linker. We designed linkers encoding turns at both ends and random positions in the middle where glycines and polar and charged residues were allowed to occur. After only a single round of SIP, all clones obtained were fully functional. Properties such as antigen binding constants, urea denaturation curves and expression of soluble scFv fragments were identical with those of the parental fragment with the (Gly4Ser)3 linker. This demonstrates that SIP is a very fast and powerful technique to remove rapidly sequences of poor functionality, exclusively yielding sequences of the desired overall property in a single round.

High affinity human antibodies by phage display

The development of phage display has now made it possible to consider the isolation of human antibodies directly without immunization. Recent advances in the field of human immunogenetics and in phage technology have led to the assembly of 'naive' human repertoires in vitro whose complexity approach that of the natural immune system. Screening of these libraries has allowed the isolation in one step of antibodies with affinities in the nanomolar range.

Inhibition of murine leukaemia virus retrotranscription by the intracellular expression of a phage-derived anti-reverse transcriptase antibody fragment.

The intracellular targeting of recombinant antibodies is an experimental strategy to interfere with the function of selected molecules that is being utilized in a variety of different systems for research and medical applications. Since recombinant antibodies are increasingly being derived from phage display libraries, we have exploited phage technology to isolate, from a large combinatorial library, human antibody fragments directed against human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT). We describe in this paper the in vitro and in vivo properties of a neutralizing anti-RT antibody fragment. We demonstrate that the heavy chain domain (VH-CH1) of the phage-derived antibody is able to inhibit the retroviral enzyme, in that it neutralizes the RNA-dependent DNA polymerase activity of HIV-1 RT. The VH-CH1 antibody fragment also neutralizes the activity of RT of drug-resistant HIV-1 mutants as well as that of murine retrovirus RT. To confirm the broad reactivity of the synthetic antibody fragment, we have assessed the ability of the intracellularly expressed VH-CH1 protein to interfere with murine retroviral infection. To this end, we developed an in vivo selection procedure based on the antibody-mediated resistance to a cytotoxic retrovirus and used this selection procedure to rescue, from a heterogeneous population, cells expressing the VH-CH1 antibody fragment. We finally demonstrate that the intracellular expression of the recombinant heavy chain antibody fragment leads to an efficient inhibition of viral retrotranscription by murine-based retrovirus.

Selectively infective phage (SIP) technology: a novel method for in vivo selection of interacting protein-ligand pairs.

Selectively infective phage (SIP) technology: A novel method for in vivo selection of interacting protein–ligand pairs

Selectively infective phages (SIP).

We review here advances in the selectively infective phage (SIP) technology, a novel method for the in vivo selection of interacting protein-ligand pairs. A 'selectively infective phage' consists of two components, a filamentous phage particle made non-infective by replacing its N-terminal domains of gene3 protein (g3p) with a ligand-binding protein, and an 'adapter' molecule in which the ligand is linked to those N-terminal domains of g3p which are missing from the phage particle. Infectivity is restored when the displayed protein binds the ligand and thereby attaches the missing N-terminal domains of g3p to the phage particle. Phage propagation becomes strictly dependent on the protein-ligand interaction. This method shows promise both in the area of library screening and in the optimization of peptides or proteins.

Strategies to identify sequences or antigens unique to multiple sclerosis.

Chronic inflammatory and infectious diseases of the central nervous system (CNS) are characterized by increased IgG and oligoclonal bands (OGBs) in the brain and cerebrospinal fluid (CSF). The OGBs in CNS infectious diseases of known cause have been shown to be directed against the pathogenic agent. In multiple sclerosis (MS), the antigenic specificity of the OGBs is unknown, but could be directed against an infectious agent, an autoantigen, or both. In a molecular approach to identify antigens specific for MS, we constructed directional cDNA expression libraries with mRNA extracted from chronic and acute MS plaques and periplaque white matter. The libraries were: (1) screened to identify clones whose expression products react with MS CSF, but not with CSF from other infectious and inflammatory diseases of the CNS; (2) subtracted by hybridization to mRNA from normal human brain white matter and differentially screened to detect unique MS transcripts; and (3) used as template in polymerase chain reactions to amplify, clone, and sequence IgG heavy and light chain variable regions (VH and VL, respectively) expressed in MS plaques. Analysis of the VH and VL IgG repertoire in MS brain may identify disease-relevant IgG sequences that can be assembled into functional antibodies using recombinant phage technology. Such recombinant antibodies will be useful to probe brain tissue to identify antigens unique to MS.

Human recombinant antibodies specific for hepatitis C virus core and envelope E2 peptides from an immune phage display library.

Hepatitis C virus (HCV) is the aetiological agent responsible for most cases of non-A non-B hepatitis. Hepatitis C is a disease of clinical importance because of its high infection rate in blood donors and its persistence as chronic infections which may lead to cirrhosis and hepatocellular carcinoma in the long term. The variability of the HCV genome has posed difficulties in serological detection and vaccine design. The recent advance in phage technology offers a means of cloning human anti-HCV antibodies of a defined specificity that may have potential therapeutic use. We now report the generation of a phage display library using the V(H) genes of a HCV-infected patient and the V(L) genes of two non-immune individuals. From this library we were able to obtain specific IgG single-chain Fvs (scFvs) that recognize viral core and envelope proteins by selection on synthetic peptides derived from the core sequence PKARRPEGRTWAQPG and the envelope E2 sequence RPIDDFDQGWGPITY. The specificity of the scFvs was demonstrated by their specific reactions with homologous peptides in ELISA and the specific blocking of scFv binding by homologous peptides, in a dose-dependent manner, in inhibition ELISA. The binding of the anticore 4c2 to homologous peptide was blocked by HCV-positive human sera in an antibody-concentration-dependent manner, suggesting that the scFv recognizes a similar if not identical epitope to those of one or more of the polyclonal antibodies present in the sera.

Selective Screening of a Large Phage Display Library of Plasminogen Activator Inhibitor 1 Mutants to Localize Interaction Sites with Either Thrombin or the Variable Region 1 of Tissue-type Plasminogen Activator

Phage display technology has been exploited to study in detail the interaction between plasminogen activator inhibitor 1 (PAI-1) and either thrombin or an essential positively charged "loop" of tissue-type plasminogen activator (t-PA), denoted variable region 1 (VR1). For this purpose, a PAI-1 mutant phage library was used that served as a reservoir of PAI-1 proteins potentially deficient in the interaction with either VR1 or thrombin. A stringent two-step selection procedure was developed. (i) A negative selection was performed by incubating the pComb3/PAI-1 mutant library with an excess of a thrombin mutant with its VR1 domain substituted with that of t-PA (thrombin-VR1). (ii) The remaining phages were complexed with t-PA (positive selection) and selected by panning with an immobilized anti-t-PA monoclonal antibody. Four consecutive panning rounds yielded an enrichment of pComb3/PAI-1 mutant phages of approximately 50-fold. Sequence analysis of 16 different cDNAs, encoding PAI-1 mutants that are hampered in the binding to thrombin-VR1, revealed the following mutations. Four independent variants share a mutation of the P4' residue (Glu350 --> Lys). Nine independent PAI-1 variants share a substitution of P1' (Met347 --> Lys), whereas three others share a P2 substitution (Ala345 --> Asp). Kinetic analysis of representative PAI-1 mutants provides evidence that the P4' residue is essential for the interaction with the VR1 domain, consistent with the data of Madison et al. (Madison, E.L., Goldsmith, E.J., Gething, M.J., Sambrook, J.F., and Gerard, R.D. (1990) J. Biol. Chem. 265, 21423-21426), whereas the P1' and P2 residues confer thrombin specificity. Concordant with the design of the selection procedure, mutants were obtained that inhibit thrombin-VR1 at least 100-fold slower than wild-type PAI-1, identifying residues that are central to the interaction with either thrombin or VR1. This study demonstrates that phage technology can be used to analyze large numbers of mutants defective in their interaction with other (domains of) proteins, provided an adequate selection scheme is devised.

Construction of D29 shuttle phasmids and luciferase reporter phages for detection of mycobacteria

Diseases caused by Mycobacterium tuberculosis, M. leprae and M. avium, cause significant morbidity and mortality worldwide. Effective treatments require that the organisms be speciated and that drug susceptibilities for the causative organisms be characterized. Reporter phage technology has been developed as a rapid and convenient method for identifying mycobacterial species and evaluating drug resistance. In this report we describe the construction of luciferase reporter phages from mycobacteriophage D29 DNA. Shuttle phasmids were first constructed with D29 in order to identify non-essential regions of the D29 genomes and to introduce unique cloning sites within that region. Using this approach, we observed that all of the D29 shuttle phasmids had the cosmid vector localized to one area of the phage genome near one cohesive end. These shuttle phasmids had been constructed with a cosmid that could be readily excised from the D29 genome with different sets of restriction enzymes. Luciferase reporter phages were made by substituting the luciferase cassette for the cosmid vector. Recombinant phages with the luciferase cassette fall into two groups. One group produced light and had the expression cassette oriented with the promoter directing transcription away from the cohesive end. In contrast, the other group had the expression cassette in the opposite orientation and failed to produce light during lytic infection, but did produce light in L5 lysogens which are known to repress D29 promoters. These results suggest that a phage promoter of the D29 phage can occlude the expression of a promoter introduced into this region. D29 luciferase reporter phages are capable of detecting low numbers of L5 lysogens like L5 luciferase phages. However, unlike L5 luciferase phages, D29 luciferase phages can readily infect M. tuberculosis and M. bovis BCG, demonstrating that these phages can be used to evaluate drug susceptibilities of many types of mycobacteria.

Making monoclonal antibodies by repertoire cloning

In this review we will focus on the applications of the basic knowledge gained by analysing immunoglobulin gene sequences and their transcription and translation. This knowledge allowed the isolation of immunoglobulin genes from a polyclonal source of lymophocytes by the polymerase chain reaction. In parallel, filamentous bacterial phage technology was adapted to express immunoglobulin genes in Escherichia coli in order to produce phage libraries containing 107–11different immunoglobulin genes. The possibility of cloning such a huge repertoire allowed to immunize animals with a mixture of antigens followed by the isolation of the desired monoclonal antibody from the phage library. Future work will aim at in vitro manipulating genes encoding immunoglobulins to obtain antibodies with desired specificity and biological function.

Identification of biologically active peptides using random libraries displayed on phage

The construction of new and increasingly diverse libraries, as well as the implementation of more powerful selection schemes, has led to the identification of linear peptides that mimic complex epitopes. Phage display techniques are allowing the selection of disease-related peptides, which reproduce the antigenic and immunogenic properties of natural antigens, using whole sera from patients. The range of applications of phage technology has been extended to include the search for peptides binding to molecules other than antibodies, such as cell receptors and enzymes.

Bacterial surface presentation of proteins and peptides: an alternative to phage technology?

Bacterial surface presentation of proteins and peptides: an alternative to phage technology?