# Patent

## Title
Recombinant bacteriophage and methods for their use

## Abstract

Recombinant P4 bacteriophage containing modified tail fibers having a base plate attachment region (BPAR) from a P2 bacteriophage gene H product and a heterologous receptor binding domain (RBD) are disclosed. Methods for the use of the recombinant P4 bacteriophage, such as to detect the presence of a target bacterium in a sample, are also described.

## Background
RELATED APPLICATIONS
This application is a continuation-in-part application of U.S. application Ser. No. 12/701,431, filed Feb. 5, 2010, which is a divisional application U.S. application Ser. No. 11/929,867, filed Oct. 30, 2007, now U.S. Pat. No. 7,700,729, which is a continuation-in-part application of U.S. application Ser. No. 11/748,432, filed May 14, 2007, now U.S. Pat. No. 7,732,586, which claims benefit to U.S. Provisional Application Ser. No. 60/747,299, filed May 15, 2006, all of which are incorporated by reference as if fully set forth.


SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jan. 3, 2013, is named CA1944-2nd_revised_SL.txt and is 273,551 bytes in size.
FIELD OF THE DISCLOSURE
This disclosure relates to modified forms of naturally occurring high molecular weight (hmw) bacteriocins, such as the R-type pyocins of Pseudomonas aeruginosa. The bacteriocins are modified at the ends of their tail fibers in a region responsible for binding specificity and affinity to their cognate binding partners, or receptors, such as those on the surface of bacteria. Methods for the use of the modified bacteriocins, such as to bind receptors, including virulence or fitness factors, on the surfaces of bacteria, are also described. This disclosure also relates to R-type pyocins wherein the tail fibers are modified to include globular proteins, which proteins can bind and degrade cell surface structures, such as polysaccharides. Unnatural systems for production of R-type pyocins by bacterial cells generally regarded as safe (“GRAS”) by regulatory authorities are described as are R-type pyocins produced by such GRAS bacteria.
BACKGROUND OF THE DISCLOSURE
Currently far more global attention is focused on threats from viral pathogens than from bacterial diseases. However, omnipresent antibiotic-resistant bacteria continue to wreak havoc on patient care and cost containment in hospitals and other medical care facilities. At the same time, there is a retreat from antibiotic development in favor of drugs for chronic diseases and life style improvements. In the last twenty years only two new classes of antibiotics (oxazolidinones and lipopeptides) have been introduced into the U.S. market (Wenzel, 2004).
In the United States alone, there are over 2 million cases of hospital acquired bacterial infections every year. Of these, approximately 90,000 people will die. The most alarming statistic is that over 70% of these bacterial culprits are resistant to at least one antibacterial drug (Bad Bugs, No Drugs, 2004). This number continues to increase at an alarming rate. The annual cost to the U.S. economy of these antibiotic-resistant nosocomial infections exceeds $5 billion. The reality of this threatening global situation will force a new approach to the development and use of antibacterial agents (Talbot et al., 2006). Where extensive use (and abuse) of antibiotics in human and animal medicine flourished, so has the emergence of antibiotic-resistant bacterial pathogens to the point that many antibiotics that were once “wonder drugs” are now clinically ineffective (Microbial Threats to Health, 2003).
As one example, Pseudomonas aeruginosa is a ubiquitous pathogen for plants and animals that is exhibiting a rapidly rising incidence of resistance to multiple antibiotic drugs (Microbial Threats to Health, 2003; Bad Bugs, No Drugs, 2004). P. aeruginosa is an aerobic, motile, gram-negative, rod. P. aeruginosa normally inhabits soil, water, and vegetation. Although it seldom causes disease in healthy people, it is an opportunistic pathogen which accounts for about 10% of all nosocomial infections (National Nosocomial Infection Survey report-Data Summary from October 1986-April 1996). P. aeruginosa is the most common pathogen affecting Cystic Fibrosis (CF) patients with 61% of the specimens culturing positive (Govan, J. R. W. and V. Deretic, 1996, Microbiol. Reviews, 60(3):530-574) as well as one of the two most common pathogens observed in intensive care units (Jarvis, W. R. et al., 1992, J. Antimicrob. Chemother., 29(a supp.):19-24).
Mortality from some P. aeruginosa infections can be as high as 50%. Presently, P. aeruginosa infection can still be effectively controlled by antibiotics, particularly by using a combination of drugs. However, resistance to several of the common antibiotics has been shown and is particularly problematic in intensive care units (Archibald, L. et al., 1997, Clin. Infectious Dis., 24(2):211-215; Fish, D. N., et al., 1995, Pharmacotherapy, 15(3):279-291). Additionally, P. aeruginosa has already demonstrated mechanisms for acquiring plasmids containing multiple antibiotic resistance genes (Jakoby, G. A. (1986), The bacteria, Vol. X, The biology of Pseudomonas, pp. 265-294, J. R. Sokach (ed.) Academic Press, London) and at present there are no approved vaccines for Pseudomonas infection.
Like many other bacterial species, strain variability in P. aeruginosa is quite significant. Variability has been shown to occur by a number of different mechanisms, these include, but are not limited to, the integration of prophages into a bacterial genome (Zierdt, C. H. and P. J. Schmidt, 1964, J. Bacteriol. 87:1003-1010), the addition of the cytotoxin gene from bacteriophages (Hayashi, T., et al., 1994, FEMS Microbiol. Lett. 122:239-244) and via transposons (Sinclair, M. I. and B. W. Holloway, 1982, J. Bacteriol. 151:569-579). Through this type of diversity, new pathogenic mechanisms have been incorporated into P. aeruginosa. These and other transitions such as the conversion to the mucoid phenotype, commonly seen in CF, clearly illustrate the need for continued vigilance.
These concerns point to the need for diagnostic tools and therapeutics aimed at proper identification of drug-resistant strains and eradication of virulence.
Many bacteria produce bacteriocins, which are bactericidal substances. Bacteriocins are composed of polypeptides and vary in molecular weight. While bacteriocins have been used for their antibacterial properties, some have more limited bactericidal spectra than many clinically used antibiotics. For example some bacteriocins have been reported as recognizing, and so acting on members of the same or closely related species by binding receptor sites on sensitive, or susceptible, organisms.
As a broad classification, bacteriocins have been divided into three types. The first are small molecules which are thermal stable. Examples of this first type include Colicin V (where colicins are specific to coliform bacteria). The second type, S-type pyocins produced by P. aeruginosa, are higher molecular weight protein molecules. The third type includes bacteriocins that genetically and morphologically resemble the tail portions of bacteriophages. Examples of this latter type include the F-type and the R-type pyocins of P. aeruginosa as well as enterocoliticin of Yersinia. These pyocins have been reported as being derived from ancestral bacteriophages. The F-pyocins have structural similarities to the lambda phage family, and the latter two R-type pyocins are related to the P2 phage family.
R-type pyocins are similar to the non-flexible and contractile tail portions of bacteriophages of the myoviridae family and are encoded in a single cluster of genes in the Pseudomonas genome (Shinomiya et al., 1983). See FIG. 1. After binding specifically to a target bacterium these pyocins form a pore in the bacterial cell, compromising the integrity of its cytoplasmic membrane and causing membrane depolarization. F-type pyocins are also similar to a bacteriophage tail, but they have a flexible and non-contractile rod-like structure. Pyocins are produced by the majority of P. aeruginosa strains, and some strains synthesize more than one pyocin.
R-type pyocins are complex high molecular weight bacteriocins produced by some Pseudomonas aeruginosa strains, and have bactericidal activity against certain other P. aeruginosa strains (for a review see Michel-Briand and Baysse, 2002). Five R-type pyocins have been identified to date and, based on their target spectra (see below), are termed R1 through R5. Strain PAO1 produces R2 pyocin, which is encoded in a gene cluster consisting of 16 open reading frames (ORFs), 12 of which show significant sequence similarity to ORFs of bacteriophages P2, PS17, ΦCTX, and other P2-like phages (Nakayama et al., 2000). Pyocin production is induced by DNA damage (Matsui et al., 1993) and is regulated by RecA, which degrades PrtR, the repressor of PrtN, a positive transcription regulator of the cluster. Induction of pyocin genes results in synthesis of approximately 200 pyocin particles per bacterial cell followed by lysis of the cell by mechanisms similar to those of bacteriophage lysis. Pyocins rapidly and specifically kill target cells by first binding to the lipopolysaccharide (LPS) via their tail fibers, followed by sheath contraction and core penetration through the bacterial outer membrane, cell wall and cytoplasmic membrane. This penetration compromises the integrity of the cytoplasmic membrane and depolarization of the membrane potential (Uratani and Hoshino, 1984). In many respects pyocins can be viewed as defective prophages adapted by the host to produce protease- and acid-resistant, noninfectious antibacterial particles consisting only of the adapted tail apparatus, that is, without capsids or DNA. The replication of the pyocin genes requires the replication of the bacterial genome in which they are embedded.
The five different pyocin receptor specificities are related linearly to one another with two branches. (Ito et al, 1970; Meadow and Wells, 1978; Kageyama, 1975). R5 pyocin has the broadest spectrum and includes the specificities of the other four. The receptors for the other four R-types form two branches, or families of specificities, that diverge from R5. One branch includes the receptors for R3, R4, and R2, in that order where the receptor specificity for R3 pyocin is the most distal from the cell surface. The second branch contains the R1 receptor, which seems to have a specificity determinant unrelated to those for R2, R3, and R4. The two branches seem to be attached to the receptor for R5 since all P. aeruginosa strains that are sensitive to any of R1-R4 pyocins are sensitive also to R5, while some strains are sensitive only to R5 pyocin. Some P. aeruginosa strains are resistant to all 5 naturally occurring R-type pyocins.
P. aeruginosa pyocins specifically kill mainly strains of P. aeruginosa but have also been shown to kill some strains of Hemophilius, Neisseria and Campylobacter species (Filiatrault et al., 2001; Morse et al, 1976; Morse et al, 1980; Blackwell et al., 1981, 1982).
The specificity of R-type pyocins is conferred by the tail fiber encoded by the gene: prf15. PRF15 protein is very closely related to the tail fibers of phages of the Myoviridae family, particularly P2-like phages (Nakayama et al., 2000). These tail fibers are homotrimers arranged symmetrically on a base plate structure with six copies per particle, as shown in FIG. 1. The N-terminal region of the tail fiber binds to the baseplate, and the C-terminal portion, probably near the tip, binds to the bacterial receptor and thereby confers killing specificity. A cognate chaperone, PRF16 protein, encoded by prf16 gene (in the case of R-type pyocins) is located immediately downstream of prf15, and is needed for proper folding of the tail fiber and/or assembly of the tail fibers on the pyocin structure. R-type pyocin particles have been described as immuno chemically and genetically similar to the tails of certain P. aeruginosa bacteriophages (Kageyama 1975, Kageyama et al. 1979, Shinomiya et al. 1989, and Shinomiya et al. 1983b). It has been proposed that R-type pyocins and Pseudomonas bacteriophages, such as PS-17 and ΦCTX, are related through a common ancestral lysogenic bacteriophage from which genes encoding head proteins and replication functions were lost and the residual phage genes adapted for their function as components of the defensive R-type pyocins (Shinomiya et al. 1989).
Similar R-type high molecular weight bacteriocins have been described in other bacteria including Yersinia enterocolitica (Strauch et al., 2001), Listeria monocytogenes (Zink et al, 1995), Staphylococcus aureus (Birmingham & Pattee, 1981) and Erwinia amylovora (Jabrane et al., 2002). Classification and nomenclature of bacteriocins have undergone changes over time, particularly given expanding evidence of their origin, chemistry and activities. Typically, the naming of bacteriocins is based on the producing species. For example, E. coli produces bacteriocins termed colicins; Pseudomonas aeruginosa produces pyocins; Listeria monocytogenes produces monocins; Yersinia enterociliticus produces enterocoliticins; and so forth. Historically, the classification began with the identification of about 20 colicins which were classified as A-V. In most cases, each bacteriocin appears to be specific in action to the same, or to taxonomically related, species of organisms. Pyocin-producing strains typically are resistant to their own pyocin. A general assay for the concentration of bacteriocin is described in U.S. Pat. No. 4,142,939.
Certain pathogenic E. coli strains, such as E. coli O157:H7, are food-borne pathogens. Outbreaks of illnesses from E. coli O157:H7-contaminated meats, raw vegetables, dairy products, juices, and the like, have caused considerable morbidity and mortality. Agents and methods are needed to effectively and safely sterilize or sanitize food products that could be contaminated with these pathogenic bacteria.
Citation of the above documents is not intended as an admission that any of the foregoing is pertinent prior art. All statements as to the date or representation as to the contents of these documents is based on the information available to the applicant and does not constitute any admission as to the correctness of the dates or contents of these documents.
SUMMARY OF THE DISCLOSURE
This disclosure relates to engineered forms of the class of bacteriocins that resemble, but are distinct from, bacteriophage tails. These bacteriocins include R-type pyocins, tail-like bacteriocins, R-type bacteriocins, or other high molecular weight (hmw) bacteriocins related to the tail structures of bacteriophages. For ease of reference, the term “hmw bacteriocin” will be used herein to refer to the bacteriocins of the disclosure, including, but not limited to, R-type bacteriocins, R-type pyocins, monocins, enterocoliticins, meningocins and competence factor of Staphylococcus aureus (Thompson and Pattee, 1981).
Natural hmw bacteriocins are typically thermolabile, trypsin resistant, and can be induced by agents, which activate the SOS system. For example, they also have been identified in many enterobacteria, Pseudomonas species, Rhizobium lupin, Listeria monocytogenes, Bacillus species, Yersinia species, Erwinia species, and Flavobacterium species.
An engineered hmw bacteriocin is composed of multiple copies of a number of different polypeptide subunits and possesses one or more, usually six, tail fibers made up of tail fiber proteins. Each tail fiber contains a receptor binding domain (RBD) which binds to, or interacts with, a receptor to form a binding pair. The RBD is the portion of a tail fiber that comprises the bacteria binding property that makes it the first member of the binding pair. An RBD as disclosed herein comprises modification of a protein in the tail fiber to form a modified tail fiber. The modified tail fiber with the other polypeptide subunits forms an engineered (or modified) hmw bacteriocin. The receptor to which the RBD binds is the second member of the binding pair, and may be the same as, or different from, the receptor for a bacteriocin without the modified tail fiber. In some embodiments of the disclosure, the second member of a binding pair is a virulence or fitness factor of a pathogenic bacterium. In other embodiments, the second member is a component of the outermost layer(s) of a bacterial cell, such as a cell membrane or, in the case of gram-positive bacteria, cell wall component.
In comparison to an hmw bacteriocin lacking the modified tail fiber, an engineered hmw bacteriocin may differ in the number, manner, and binding strength of its interactions with a receptor. Thus an engineered hmw bacteriocin may have different or additional binding properties (e.g. binding specificities, affinities, and/or avidities) in comparison to a bacteriocin without the modification. An engineered hmw bacteriocin is not a naturally occurring molecule but may be a modified version of a naturally occurring molecule. Alternatively, an engineered hmw bacteriocin may be a modified version of another non-naturally occurring bacteriocin. In most embodiments, an engineered hmw bacteriocin remains a lethal agent for bacterial cells expressing a receptor bound by the bacteriocin.
In a first aspect, the disclosure includes an hmw bacteriocin comprising a tail fiber protein with a modified RBD. Non-limiting examples of hmw bacteriocins include R-type pyocins. In some embodiments, the modified RBD comprises a change in the amino acid sequence of the domain relative to a naturally occurring bacteriocin. Non-limiting examples of a change in amino acid sequence include substitution, insertion (addition), or deletion of one or more amino acids. Of course combinations of one or more substitutions, insertions (additions), and deletions may also be used.
In other embodiments, the tail fiber comprises a heterologous, or non-bacteriocin, sequence in one or more of the three tail fiber protein monomers that make up a single trimeric tail fiber. And while the tail fibers in a native, or naturally occurring, bacteriocin may be homotrimeric to form an RBD, the tail fiber of an engineered hmw bacteriocin is either heterotrimeric, where one or two of the protein monomers is different from the other(s), or homotrimeric where all three protein monomers are identically non-native (non-naturally occurring). The presence of heterologous (or non-native) sequence, in one or more protein monomers allows the trimer to form a tail fiber with a modified RBD.
The heterologous sequence is thus in a part of the monomer(s) such that at least the RBD of the tail fiber is altered in an assembled trimer. The altered RBD changes the binding characteristics and properties of the tail fiber and thereby the binding activity of a hmw bacteriocin containing the tail fiber. In some embodiments, the heterologous RBD is derived from another bacteriocin or a tail protein from a bacteriophage or prophage. In many cases, the heterologous RBD is a polypeptide including at least part of the C-terminal portion of a tail fiber protein of a bacteriocin, a bacteriophage tail fiber protein, or a presumptive tail fiber protein, the sequence of which has been derived from a gene of a viable or even defective lysogenic bacteriophage found within the genome of a bacterium.
The heterologous RBD can be derived from a bacteriophage that encodes a tail protein or a tail spike-like protein, which protein is globular and preferably, polysaccharide specific. Tail spikes are tail components, usually homotrimeric in structure, such as those found in bacteriophages P22 and epsilon 15. They perform similarly to tail fiber proteins and can be engineered. Therefore, for the purposes of this disclosure, tail spikes or portions thereof are considered RBDs. These proteins can bind and degrade cell surface polysaccharide structures. The same motif of the tail spike protein structure that binds the enzyme substrate can provide the RBD function, since the substrate for the enzyme may also serve as the receptor on the surface of the target bacteria. For example, phiV10 is a bacteriophage belonging to the podoviridae group, and can infect E. coli O157:H7 strains. (Waddell & Poppe 2000; Genbank NC—007804). The phiV10 tail spike (SEQ ID NO: 60) specifically recognizes, binds to, and degrades the O157 antigen on the surface of pathogenic E. coli O157:H7. Other globular proteins with polymer binding and degrading activities, such as but not limited to, SEQ. ID NO.: 61, 62, 63, 64, and 65 can serve as RBD structures in engineered hmw bacteriocins.
The tail spike of the CUS3 prophage of K1 strain of E. coli RS218, SEQ. ID. NO.:61 is an endosialidase very similar to that of the tail proteins of phages K1E, and K1F that recognize and degrade the capsule of K1 strains of E. coli. The CUS3 tail spike has a head binding domain similar to the P22 tail spike protein and a C-terminus related to the other phage endosialidases. Fusing this tail spike or a portion thereof to the R2 tail fiber base plate attachment region (BPAR) will create a pyocin that can kill K1 strains of E. coli. 
The tail spike of bacteriophage HK620, SEQ. ID. NO.:62, is the tail spike of HK620, a P22-like phage. It is specific for the O-antigen of E. coli H. Fusing this tail spike or a portion thereof to the R2 tail fiber BPAR will create a pyocin that can kill H strains of E. coli. 
The tail spike of phage Sf6, SEQ. ID. NO.:63, is also P22-like and recognizes and degrades the Shigella flexneri O-antigen. Fusing this tail spike or a portion thereof to the R2 tail fiber BPAR will create a pyocin that can kill Shigella flexneri strains.
The tail spike of phage ST64T, SEQ. ID. NO.:64, is P22-like, and recognizes the O-antigen of Salmonella typhimurium DT64. Fusing this tail spike or a portion thereof to the R2 tail fiber BPAR will create a pyocin that can kill Salmonella typhimurium strains such as DT64.
Phage epsilon 15 tail spike, SEQ. ID. NO.:65, is similar to the phiV10 tail spike and specific for group E1 Salmonella enterica. Fusing this tail spike or a portion thereof to the R2 tail fiber BPAR will create a pyocin that can kill group E1 Salmonella enterica strains.
Tail spike proteins and portions thereof may fold properly without the facilitation by a specific chaperone. Thus, the generation of fusions between an R-type pyocin tail fiber and a heterologous tail spike protein as an RBD may not require an RBD-specific chaperone as usually does the fusion between an R-type pyocin tail fiber and a heterologous tail fiber protein from another R-type pyocin or a myoviridae such as P2, L-413c, AB17 or PS17.
The heterologous RBD is fused to a polypeptide containing a BPAR of a hmw bacteriocin or a myoviridae phage tail fiber protein. The BPAR containing polypeptide may contain all or part of the N-terminal portion of an hmw bacteriocin tail fiber, where the N-terminal portion can consist of any part of the tail fiber except the very C-terminus.
In other embodiments, the heterologous RBD is derived from the major tropism determinant (MTD) of Bordetella bacteriophage. Non-limiting examples include a heterologous RBD comprising a modified or diversified tropism determinant, optionally with all or part of the RBD of a tail fiber of a bacteriophage. In some embodiments, the bacteriophage tail fiber is that of the Vibrio harveyi myovirus-like (VHML) bacteriophage or its diversified derivatives or those of another prophage or bacteriophage that comprises a Diversity Generating Retroelement (DGR) structure.
The disclosure further includes a portion of an engineered hmw bacteriocin where the portion retains the bacteriocin's activity of binding a receptor on a bacterial cell surface and then promoting the penetration of the cell membrane. Thus the portion may be any that retains the binding (recognition) and membrane penetration activities of an engineered hmw bacteriocin. In some embodiments, the portion comprises one or more bacteriocin polypeptides that are truncated.
In a related aspect, the disclosure includes modified tail fibers that may be part of an hmw bacteriocin of the disclosure. The trimeric tail fiber may comprise one or more tail fiber proteins with a modified RBD or a heterologous RBD. In some embodiments, the modified monomeric tail fiber protein is derived from an R-type bacteriocin while in other embodiments, the tail fiber protein is derived from a bacteriophage tail fiber or a bacteriophage tail spike protein.
The disclosure also includes native, isolated, or recombinant nucleic acid sequences encoding a modified tail fiber protein, as well as vectors and/or (host) cells containing the coding sequences. The vectors and/or host cells may be used to express the coding sequences to produce native, isolated, or modified tail fiber proteins which form tail fibers and are incorporated into an engineered hmw bacteriocin of the disclosure. A sequence encoding a modified tail fiber protein may also be introduced into a bacterial cell which produces, or is capable of producing, an hmw bacteriocin in the presence of the modified tail fiber protein.
In some instances the bacterium for production will be those designated as “generally recognized as safe,” or “GRAS,” under the U.S. Federal Food, Drug, and Cosmetic Act, such as for food additives or food ingredients. Typically any substance that is intentionally added to food is a food additive that is subject to review and approval by the U.S. Food and Drug Administration (FDA) unless the substance is generally recognized by experts as having been adequately shown to be safe under the conditions of its intended use. A GRAS substance can be utilized without pre-approval.
Expression of the modified tail fiber protein results in the production of a modified hmw bacteriocin by the cell. If natural bacteriocin tail fiber protein sequence(s) or the nucleic acid(s) encoding such protein is/are inactivated or removed, then only modified hmw bacteriocins will be produced. If natural bacteriocin tail fiber protein sequence(s) or the nucleic acid(s) encoding such protein are retained, then modified hmw bacteriocins will be produced along with the natural bacteriocin tail fibers, and the modified pyocins generated may be mixtures of both modified pyocins and natural pyocins. In addition, the pyocins generated from such production host bacteria may contain bivalent (multivalent) pyocins, that is, contain single pyocin particles with a mixture of two types of tail fibers, each with its specific binding properties. Such multivalent pyocins have multiple, that is, two or more, binding and killing specificities within the same pyocin particle or molecule. The transfected bacteria may be propagated to produce hmw bacteriocins that prevent or inhibit the growth of other bacteria that express a receptor bound by the modified hmw bacteriocin or by one of the hmw bacteriocins from the mixture of natural plus modified hmw bacteriocins.
In some embodiments, the receptor is a virulence or fitness factor of a virulent or pathogenic bacterial strain such that exposure to the modified hmw bacteriocin prevents or inhibits growth of the virulent or pathogenic strain. Non-limiting examples of virulence factors targeted by an engineered hmw bacteriocin include those encoded by the sequences disclosed in U.S. Pat. No. 6,355,411 and published patent application WO 99/27129 (Ausubel et al.).
The exposure is optionally via contact, or co-culturing, with transfected bacteria expressing the hmw bacteriocin. The disclosure includes allowing propagation of the transfected bacteria in vivo, on or within an animal or plant subject. The in vivo application of the transfected bacteria provides a state of protection against bacteria expressing a surface receptor targeted by the engineered hmw bacteriocin. The state of protection is analogous to a state of immunity, where the transfected bacteria essentially augment or supplement the animal or plant organism's immune or other defense system.
In other embodiments, the nucleic acid sequence coding an RBD of a modified monomeric tail fiber protein is part of a genetic system which permits the identification, physical isolation and/or selection of the coding sequence. As non-limiting examples, the genetic system may comprise the coding sequence in a phage, lysogenic phage, transducing particle, cosmid, or phage genome allowing its identification, isolation, and/or selection. In some embodiments, the sequence is fused with a portion of a fiber gene and expressed to produce a modified tail fiber trimer that will cause the modified hmw bacteriocin to bind to the surface of and kill the host organism harboring the lysogenic phage from which the RBD coding sequence was identified or isolated. Detection of a phenotype in the modified tail fiber trimer permits the sequence to be selected and/or screened, identified, and isolated. In some embodiments, the phenotype may be a desired, and possibly rare, receptor-binding property.
The disclosure includes a library of phages, transducing particles, cosmids, or phage genomes, containing a plurality of DNA and/or RNA sequences, each encoding a modified tail fiber protein. This coupling of binding phenotype to encoding genotype of the RBD allows the expression of a plurality of modified RBDs such that the sequences encoding them are represented within the library. In some embodiments, the members of a library each contain a sequence encoding one modified tail fiber protein such that homotrimeric tail fibers are expressed and available for screening or selection to determine the respective binding phenotype of a library member. In other embodiments, the members of a library include those with more than one sequence encoding a modified tail fiber protein such that heterotrimeric tail fibers disclosed herein may be expressed and screened or selected for their binding phenotypes. The binding phenotype of a member of the library is thus coupled to the respective coding sequence(s). Once the genotype encoding the desired or advantageous RBD has been so identified, it can be used to create the tail fiber for a modified hmw bacteriocin. By deploying the cognate chaperone function of a tail fiber, such as that of VHML, that naturally diversifies its RBD, one can be assured of proper folding of a tail fiber containing a diversified RBD derived from VHML.
Vectors, host cells, phages, transducing particles, cosmids, phage genomes, and libraries as disclosed herein may be considered compositions comprising a tail fiber protein encoding nucleic acid molecule.
Compositions of the disclosure also comprise fusion proteins resulting from the fusion of the RBD protein to the BPAR protein. For example, all or part of the phiV10 tail spike is fused to the BPAR of the R-type pyocin tail fiber PRF15. In some instances, these fusion proteins can be provided in the context of other proteins, or phage or cellular components. Alternatively, they may be isolated or separated. The fusion proteins can be part of a library and available for screening or selection, and/or may be associated with a carrier or excipient for administration. They can be prepared via recombinant methods or synthesized chemically.
Additional compositions of the disclosure comprise an engineered hmw bacteriocin or an anti-bacterial portion thereof. The compositions are anti-bacterial by virtue of the hmw bacteriocin, and may comprise a carrier or excipient. Of course the carrier or excipient is one that is suitable for use in combination with a multisubunit complex protein like an hmw bacteriocin. In some embodiments, the carrier or excipient is pharmaceutically acceptable such that the composition may be used clinically or agriculturally. In other embodiments, the carrier or excipient is suitable for topical, pulmonary, gastrointestinal, or systemic administration, such as to a human or a non-human animal. In additional embodiments, the carrier or excipient is suitable for administration to a surface or to a non-animal organism such as a plant or fresh produce from a plant as non-limiting examples.
A composition as disclosed herein may comprise more than one fusion protein or engineered hmw bacteriocin or comprise one or more additional agents, including but not limited to, a naturally occurring hmw bacteriocin desired for use with the engineered hmw bacteriocin. Non-limiting examples of an additional agent include an enzyme, an antibiotic, an anti-fungal agent, a bactericide, an analgesic, and an anti-inflammatory agent.
In a further aspect, the disclosure provides methods of using an hmw bacteriocin related product described herein. Embodiments of the disclosure include methods of inhibiting bacterial cell growth or inducing bacterial cell death. Such methods comprise contacting a susceptible bacterial cell or cells with an effective amount of an engineered hmw bacteriocin, or with an anti-bacterial portion thereof, such as a fusion protein. Alternatively a composition containing the hmw bacteriocin, or anti-bacterial portion thereof, may be used. In some cases, an effective amount may be equivalent to as few as one, on average, hmw bacteriocin per bacterial cell. Higher amounts also may be used.
In other embodiments, a method of compromising the integrity of the cytoplasmic membrane of a bacterium is provided. The compromise may result in the loss of membrane potential and/or loss of some cellular contents. Such methods comprise contacting the membrane with a fusion protein, or an engineered hmw bacteriocin, or anti-bacterial portion thereof. In many cases, the membrane will be that of virulent or pathogenic bacteria.
In some embodiments, the methods of the disclosure may comprise in vivo application (or administration) of a fusion protein or an engineered hmw bacteriocin, or an anti-bacterial portion thereof, within a subject. Alternatively, the methods may comprise in vitro or ex vivo contacting.
In a yet additional aspect, the disclosure provides a method of forming non-virulent bacteria from virulent progenitor bacteria. The method comprises contacting virulent bacteria with an engineered hmw bacteriocin, or an anti-bacterial portion thereof, which binds a virulence or fitness factor of the virulent bacteria. The contacting may be under conditions wherein not all of the bacteria are killed, or wholly inhibited in cell growth, by the used amount of hmw bacteriocin, or anti-bacterial portion thereof. The contacting provides a selective pressure that allows the targeted bacterium to survive the engineered hmw bacteriocin or anti-bacterial portion thereof and to propagate only if it has become a non-virulent mutant or modified bacteria progeny that is not susceptible (and so resistant) to the engineered hmw bacteriocin or anti-bacterial portion thereof. In some embodiments, the resistance is due to the lack of expression of the virulence or fitness factor or receptor for the engineered hmw bacteriocin, or anti-bacterial portion thereof, thereby avoiding attack by the engineered hmw bacteriocin. In another embodiment the resistance may be due to an alteration in the virulence or fitness factor such that it no longer serves as an effective receptor for the RBD of the modified pyocin and in the altered form also compromises its virulence or fitness function. The acquisition of resistance by the surviving progeny, and the resultant change in virulence or fitness of a formerly virulent bacterium, can be determined in vivo or in vitro to demonstrate its compromised pathogenicity.
In a related aspect, the disclosure provides a method of maintaining a population of non-virulent bacteria by contact with an engineered hmw bacteriocin, or an anti-bacterial portion thereof, which binds to and mediates its bactericidal effect via a virulence or fitness factor of the virulent bacteria. The presence of the hmw bacteriocin prevents growth (or generation or propagation) of virulent bacteria and so maintains the population as non-virulent. In some embodiments, the contacting may be by use of a bacterial cell, as described herein, which expresses the engineered hmw bacteriocin or anti-bacterial portion thereof.
The details of one or more embodiments of the disclosure are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the disclosure will be apparent from the drawings and detailed description, and from the claims.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 provides the electron micrograph of an R-type pyocin particle revealing 4 of the 6 tail fibers in Panel A, and a schematic of the major components of an R-type pyocin particle in Panel B.
FIG. 2 provides spot serial (5×) dilution assays of wild type pyocins (R2), pyocin particles produced from the tail fiber deletion strain (PA01Δprf15), and pyocins complemented with the R2-P2 tail fiber fusion. Target bacteria are P. aeruginosa 13s and E. coli C1a. Wild type R2 pyocin particles can kill Pseudomonas but not E. coli. The tail fiber deletion strain produces no active pyocin particles, but when complemented in trans with the R2-P2 tail fiber fusion, it now can kill E. coli C1a.
FIG. 3 is complementing the R2 pyocin structure with an R2-P2 tail fiber fusion. The C-terminal (RBD) portion of the P2 tail fiber gene was fused to the N-terminal (BPAR) portion of the R2 tail fiber, as shown in part A.
Part B of FIG. 3 shows a schematic of the wild type R2 pyocin (left). The R2 pyocin is complemented with the R2 (BPAR)-P2 (RBD) fusion construct to produce particles (right) that have the chimeric tail fibers incorporated into the structure. The R2-P2 particles have an altered killing spectrum and now target certain E. coli strains.
FIG. 4 provides a multiple R2-P2 fusions and their bactericidal activities. The N-terminus, 1-164 amino acids, of R2 (Base-Plate Binding Region, “BPAR”) was fused to various C-terminal portions of P2 (RBD). The numbers represent the amino acid reside numbers of the respective proteins. The bactericidal activity of the modified pyocins (against E. coli C) containing each of the constructed tail fibers are indicated as present (+) or absent (−).
FIG. 5 shows various portions of the N-terminus of the R2 tail fiber (BPAR) fused to the C-terminal 158-669 portion (RBD) of the P2 tail fiber. The numbers represent the amino acid reside numbers of the respective proteins. The bactericidal activity of the modified pyocins (against E. coli C) containing each of the constructed tail fibers are indicated as present (+) or absent (−).
FIG. 6 shows multiple R2-P2 fusions and their bactericidal activities. N-terminus, 1-240 amino acids, of R2 (BPAR) was fused to various C-terminal portions of P2 (RBD). The numbers represent the amino acid reside numbers of the respective proteins. The bactericidal activity of the modified pyocins (against E. coli C) containing each of the constructed tail fibers are indicated as present (+) or absent (−).
FIG. 7 provides various portions of the N-terminus of the R2 tail fiber (BPAR) fused to the C-terminal 322-669 portion (RBD) of the P2 tail fiber. The numbers represent the amino acid reside numbers of the respective proteins. The bactericidal activity of the modified pyocins (against E. coli C) containing each of the constructed tail fibers are indicated as present (+) or absent (−).
FIG. 8 shows the trans complementation of the PA01Δprf15 R2 pyocin structure with various R-type pyocin tail fibers, tail fiber fusions and chaperones. Activities of the R1 through R5 complemented pyocins were assessed by spotting onto indicator strain Pseudomonas aeruginosa 13s, which is sensitive to all pyocin types. The R2-P2 complemented pyocins were tested for activity using E. coli C as the indicator, and the R2-L-413c complemented pyocin was tested on Yersinia pestis strain KIM.
The R2, R3, and R4 PRF15 tail fibers could be complemented by the endogenous PRF16 of the PA01Δprf15 R2 pyocin. R1 and R5 PRF15 tail fibers, which differ at the C-terminus compared to R2, required, for maximal activity, their own cognate PRF16 (which itself differs from the R2 counterpart). Both the R2-P2 and R2-L-413c fusions, which contain the C-terminus (RBD) of the phage P2 and L-413c tail fibers, respectively, require their cognate tail fiber assembly chaperones encoded by gene G of the phage.
FIG. 9 shows the pyocin tail fiber and chaperone expression vector pUCP30T. The genes, prf15 and prf16, are expressed using a Pseudomonas/E. coli shuttle vector (Schweitzer) with replication origins (ori pRO1600, rep, and oriT) for both species. Cloning sites are shown by the indicated restriction enzyme sites of cleavage. The plasmid confers gentamicin resistance (Gm R) and is maintained by adding gentamicin to the culture media. Transcription of both genes is driven by the tac promoter which is negatively regulated by lacIQ. When transformed into Pseudomonas aeruginosa strain PAO1Δprf15, the genes, e.g. prf15 and prf16, incorporated into the plasmid are expressed in trans after being induced with IPTG simultaneously with the mitomycin C induction of those pyocin genes remaining in the PAO1 Δprf15 host production bacteria.
FIG. 10 provides the construction of Yersinia pestis specific pyocin tail fiber. Similar to the strategy that was used to construct R2-P2, the C-terminal (RBD) encoding portion of the L-413c tail fiber gene was fused to an N-terminal portion (BPAR) of the R2 tail fiber. When expressed in trans to complement the R2 tail fiber deletion strain PA01Δprf15, modified pyocin particles are produced containing the chimeric R2-L-413c tail fibers that can efficiently kill Y. pestis but not Pseudomonas. 
FIG. 11A shows representative tail fiber fusions of the bacteriophages P2 and phiV10 tail fiber receptor binding domains (RBD) to the R2 pyocin tail fiber base plate attachment region (BPAR).
FIG. 11B provides bactericidal activities of pyocins that have incorporated either the R2-P2 tail fiber fusion or the R2-V10 tail fiber fusion into their structures. Pyocins were produced by expressing the tail fiber fusions in trans in PAO1Δprf15 while simultaneously inducing the pyocin genes. Pyocin activity was assessed by the spot method on lawns of E. coli EDL933 and TEA026. EDL933 is a wild type strain that produces the O157 antigen. TEA026 is a mutant of EDL933 defective in O-antigen production (Ho and Waldor, 2007). EDL933 is sensitive to R2-V10 but not R2-P2. TEA026 is sensitive to pyocin R2-P2 but not R2-V10. This indicates that the O157-antigen is the receptor for the V10 RBD and that the P2 RBD recognizes the lipopolysaccharide.
FIG. 12 is a cartoon of the P4 plasmid, pDG218, containing the genes for gentamicin resistance (aacC1) and a fusion tail fiber such as P2 H-V10 inserted in the non-essential region of the P4 satellite phage and driven by the left early promoter, PLE. The other indicated genes and functions are from P4sid1 (Shore et al., 1977).
FIG. 13 provides the amino acid sequences or nucleic acid sequences for SEQ ID NOS:1-71, provided on pages 13A-13N.
FIG. 14 provides a schematic of a recombinant P4/P2 genome construct, in which the P4 genome modified so as to include a gentamicin-resistance gene (acc1) and the P2 tail fiber gene P2-H. The other indicated genes are those of the wild type P4 phage.
FIG. 15 provides a photograph of the growth of E. coli O157:H7 (EDL933) on agar plates containing gentimicin, when a mixture of E. coli C1a and E. coli O157:H7, at the proportions shown, is contacted with recombinant P4/P2 bacteriophage containing the construct in FIG. 14.
FIG. 16 provides a photograph of the growth of E. coli C1a or E. coli O157:H7 (EDL933) on agar plates containing gentimicin, when a mixture recombinant P4 bacteriophage particles, at the proportions shown, is contacted with either E. coli C1a or E. coli O157:H7.



DEFINITIONS
As used herein, an hmw bacteriocin includes an R-type pyocin, tail-like bacteriocin, R-type bacteriocin, and R-type pyocins, monocins, enterocoliticins, meningocins, or other high molecular weight (hmw) bacteriocins. An hmw bacteriocin includes modified versions of R-type pyocins, enterocoliticins, monocins, and meningocins (see Kingsbury “Bacteriocin production by strains of Neisseria meningitidis.” J Bacteriol. 91(5):1696-9, 1966). A modified or engineered hmw bacteriocin may be a modified R-type pyocin selected from the R1, R2, R3, R4, or R5 pyocin of P. aeruginosa. The modified or engineered bacteriocins may include the tail spikes of a bacteriophage, such as phiV10.
A bacteriocin of the disclosure may be thermolabile, mild acid resistant, trypsin resistant, sedimentable by centrifugation at about 65,000×g, and resolvable by electron microscope (see Jabrane et al. Appl. Environ. Microbiol. 68:5704-5710, 2002; Daw et al. Micron 27:467-479, 1996; Bradley Bacteriol. Revs. 31:230-314, 1967; and Kageyama et al. Life Sciences 9:471-476, 1962. In many cases, an engineered hmw bacteriocin disclosed herein has one or more, in any combination, of these properties. An additional property common to bacteriocins and engineered hmw bacteriocins disclosed herein is that they do not contain nucleic acid and thus are replication deficient such that they cannot reproduce themselves after or during the killing of a target bacterium as can many bacteriophages.
R-type pyocins, and other hmw bacteriocins disclosed herein, are complex molecules comprising multiple protein, or polypeptide, subunits and resemble the tail structures of bacteriophages of the myoviridae family. In naturally occurring R-type pyocins, the subunit structures are encoded by the bacterial genome such as that of P. aeruginosa and form pyocins to serve as natural defenses against other bacteria (Kageyama, 1975). A sensitive, target bacterium can be killed by a single R-type pyocin molecule (Kageyama, 1964; Shinomiya & Shiga, 1979; Morse et al., 1980; Strauch et al., 2001).
A “target bacterium” or “target bacteria” refer to a bacterium or bacteria that are bound by an engineered hmw bacteriocin of the disclosure and/or whose growth, survival, or replication is inhibited thereby. The term “growth inhibition” or variations thereof refers to the slowing or stopping of the rate of a bacteria cell's division or cessation of bacterial cell division, or to death of the bacteria.
As used herein, a “nucleic acid” typically refers to deoxyribonucleotide or ribonucleotides polymers (pure or mixed) in single- or double-stranded form. The term may encompass nucleic acids containing nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding, structural, or functional properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Non-limiting examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-0-methyl ribonucleotides, and peptide-nucleic acids (PNAs). The term nucleic acid may, in some contexts, be used interchangeably with gene, cDNA, mRNA, oligonucleotide, and polynucleotide.
A particular nucleic acid sequence also encompasses conservatively modified variants thereof (such as degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third (“wobble”) position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues. Thus a nucleic acid sequence encoding a protein sequence disclosed herein also encompasses modified variants thereof as described herein.
The terms “polypeptide”, “peptide”, and “protein” are typically used interchangeably herein to refer to a polymer of amino acid residues. Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission.
Virulence factors are those molecules that contribute to the pathogenicity of an organism but not its general viability. Upon the loss of a virulence factor the organism is less pathogenic but not necessarily less viable. Virulence factors may have any one of numerous functions, for example, regulating gene expression, providing adhesion or mobility, pumping out antibiotic agents, or forming protective coatings including biofilms.
Fitness factors are those molecules that contribute to the organism's general viability, growth rate or competitiveness in its environment. Upon the loss of a fitness factor, the organism is less viable or competitive and because of this compromise, indirectly less pathogenic. Fitness factors may also possess any one of numerous functions, for example, acquiring nutrients, ions or water, forming components or protectants of cell membranes or cell walls, replicating, repairing or mutagenizing nucleic acids, providing defense from or offense towards environmental or competitive insults.
Some virulence and fitness factors are present on the surface of the bacterium and thereby accessible to an hmw bacteriocin disclosed herein. By binding to some surface virulence or fitness factors, an hmw bacteriocin can mediate killing by puncturing the cell membranes, compromising the integrity of the cytoplasmic membrane and/or dissipating the membrane potential of the cell. Those surface accessible molecules most likely to support hmw bacteriocin binding and killing are proteins, polysaccharides, and lipopolysaccharides of the outer membrane. Accordingly, potential targets for engineered hmw bacteriocins are virulence factors and fitness factors that are proteins, polysaccharides and lipopolysaccharides of the outer membrane. Some non-limiting examples of virulence factor targets for engineered pyocins include intramembrane cleaving protease (iCLIP) metalloproteases; IL and IIL galactose- and fucose-binding lectins; microbial surface components recognizing adhesive matrix molecule (MSCRAMM) proteins; and adhesin, such as ACE.
The ultimate success of targeting a specific virulence factor depends on its topography on the bacterial surface, its density on the surface, perhaps its two-dimensional mobility within the outer membrane, and its prevalence in clinical or field isolates of the pathogen. For example, OprM is a porin-like outer membrane protein involved in multiple efflux pumps, e.g. the MexAB system, and prevalent in many gram-negative bacteria (Wong and Hancock, 2000). TolC, similar to OprM, is a required accessory protein for many efflux pumps of gram-negative pathogens (Koronakis et al., 2004; Piddock, 2006). In addition, several members of the YcrC family of secretins are outer membrane proteins necessary for the translocation of pathogenic effector proteins by the type three secretion system (“T3SS”), on which many gram-negative pathogens such as P. aeruginosa and Yersinia pestis are dependent for intoxicating their mammalian host (Galan and Collmer. 1999; Koster et al., 1997; Cornelis, 2006). In addition, the YscW family members are lipoproteins also anchored in the outer membrane to assist the insertion of the secretins into the membrane (Burghout et al., 2004).
Additional non-limiting examples of virulence and fitness factors include an aquaporin, such as the E. coli aquaporin-Z water channel (see Calamita, 2000); RetS (see Goodman et al., 2004; and Zolfaghar et al., 2005); members of the 7TMR-DISM family (see Anantharaman et al., 2003); OprM (see Wong et al., 2000; and SEQ ID NO:11); bacterial proteins such as OprJ (SEQ ID NO:12), OprN (SEQ ID NO:13), AprF (SEQ ID NO:14), OpmM (SEQ ID NO:15), OpmA (SEQ ID NO:16), OpmD (SEQ ID NO:17), OpmE (SEQ ID NO:18), OpmQ (SE ID NO:35), OpmB (SEQ ID NO:36), OpmJ (SEQ ID NO:37), OpmG (SEQ ID NO:38), OpmI (SEQ ID NO:39), OpmH (SEQ ID NO:40), OpmK (SEQ ID NO:41), OpmN (SEQ ID NO:42), OpmF (SEQ ID NO:43), or OpmL (SEQ ID NO:44); OprD family of porins (see Tamber et al., 2006); ACE, or the E. faecalis OG1RF encoded ACE gene (see Sreedhar et al., 2000; and Rich, et al., 1999); PA-IL and PA-IIL galactose- and fucose-binding lectins (see Mitchell et al., 2002); plant and animal virulence genes described by He et al., 2004; extracellular pyrophosphate moieties (see Bonev et al., 2004); metalloproteases (see Rudner et al., 1999); and transposon encoded surface molecules (see Jacobs et al., 2003).
Other non-limiting examples of virulence factors targeted by a disclosed engineered hmw bacteriocin include those encoded by the open reading frames (ORFs) disclosed in U.S. Pat. No. 6,355,411 and WO 99/27129. In some embodiments, a factor targeted by a bacteriocin disclosed herein is one encoded by the following ORFs from the U.S. Patent:











ORF number
Encoding
















5
Unknown


9
Unknown


21
Possibly receptor


23
Possibly ABC transporter


33
Unknown


41
Possibly mucin like


43
Unknown


51
Unknown


53
Possibly mucin like


85
Unknown


89
Possibly lipoprotein receptor


91
Unknown


95
Possibly proteophosphoglycan, cell surface


107
Possibly ABC


110
Possibly membrane glycosyltransferase


113
Possibly multidrug resistance protein MexA


132
Possibly muc d


134
Possibly 6-UDP mannose dehydrogenase


149
Possibly MDR transporter potential target


150
Possibly multidrug resistance protein MexA


203
Possibly ABC transporter ATPase component


204
Possibly ATPase component of ABC transport


205
Possibly ATPase component of ABC transport


206
Possibly ATPase component of ABC transport


207
Possibly ATPase component of ABC transport


208
Possibly ATPase component of ABC transport


209
Possibly ABC


213
Possibly NhaP-type Na+/H+ and K+/H+



antiporters


215
Unknown


227
Possibly receptor


239
Possibly deoxycytidine triphosphate deaminase


241
Possibly UTPase


249
Unknown


255
Unknown


261
Possibly 6-phosphoglyconate dehydrogenase


263
Possibly ABC transporter


273
Unknown


277
Possibly PE-PGRS family member


289
Possibly 6-phosphogluconate dehydrogenase


291
Possibly Glycosyl transferase


297
Possibly ligA


301
Possibly glycosyltransferase


309
Possibly cation/multidrug efflux pump


323
Unknown


327
Unknown


331
Possibly sensor with putative PilR kinase


333
Possibly Tonb protein transport


341
Possibly Pil R


349
Possibly Pil A or R


363
Possibly orfz


365
Possibly ABC transporter


375
Possibly mucin


377
Possibly fimT pilus


381
Possibly H1 immobilization antigen


383
Possibly fimU


387
Possibly PilV pilus


393
Possibly pilW et


401
Possibly pil X


403
Possibly antigen cd3


411
Unknown


413
Unknown


419
Possibly pil E


421
Possibly pyl y2


427
Possibly PE-PGRS outer membrane antigen


437
Possibly ABC ligA









DETAILED DESCRIPTION OF MODES OF PRACTICING THE DISCLOSURE
General
Hmw bacteriocins have the ability to quickly kill bacteria. A few early reports of in vivo studies have shown that they can be effective in mice for this application (Haas et al., 1974; Merrikin and Terry, 1972). This invention provides that when administered preferably either intraperitonealy or intravenously, wild type R2 pyocin can rescue mice from acute, lethal peritonitis caused by antibiotic-resistant Pseudomonas aeruginosa and that R2 pyocins can act at very low doses, such as 109 pyocins or less than 1 μg total protein in a single dose (data not shown).
For hmw bacteriocins to be clinically useful as antibacterial agents, however; the problem of their narrow bactericidal spectra must be addressed. While this can be viewed as an advantage in that it is possible to specifically target a particular species or strain without affecting the normal flora and thereby causing minimal collateral damage, the types of species/strains that are sensitive to known bacteriocins are limited. For example, R-type pyocins currently are known to be produced by some Pseudomonas aeruginosa strains, and have activity against a narrow range of other Pseudomonas strains and a few other gram negative species. R-type bacteriocins from other species have been reported (such as Erwinia, see Jabrane 2002, and Yersinia enterocolitica, see Strauch) but the occurrence appears to be limited. Myoviridae phages, on the other hand, are quite widespread and common and are found throughout both the gram negative and gram positive bacterial classes.
This disclosure demonstrates that it is possible to change the spectrum of a hmw bacteriocin. A major spectrum determinant among both pyocins and their related phages lies in the tail fiber, which binds to the bacterial surface specifically, interacting through its C-terminal portion (RBD) with a component of the LPS or other cell surface structure. The LPS can be highly variable between different species and strains of bacteria, and bacteriophage tail fibers are themselves highly variable, particularly in this C-terminal region that interacts with the cell surface (Tetart, Desplats). This variability apparently reflects phages' constant adaptations to changing host surfaces. It has been observed that different phage types that infect the same host (E. coli phages P2, Mu, and P1) have sequence similarity in the C-terminal portion of the tail fiber (Haggard-Ljungquist E, Halling C, Calendar R.), indicating that horizontal transfer in these genetic regions likely plays a role in host specificity. For example, R2 pyocin has a very high degree of sequence similarity to Pseudomonas phage phiCTX, a phage that is also very closely related to E. coli phage P2. Comparing the tail fiber sequences of the R2 pyocin and P2, more sequence similarity is seen at the N-terminus (BPAR) than with the C-terminus (RBD), suggesting that the C-terminus plays the role in host specificity.
As disclosed herein, it is possible to alter the target spectrum of a pyocin or other hmw bacteriocin by engineering the C-terminal portion of the tail fiber gene. It is notable that this spectrum change can occur across species and genus barriers, demonstrating that natural R-type pyocins and other natural hmw bacteriocins can be modified as disclosed herein and developed into antimicrobials with broader spectra.
Modified hmw Bacteriocins
The disclosure provides engineered hmw bacteriocins with altered binding specificities and/or affinities. In some embodiments, an hmw bacteriocin of the disclosure specifically binds to exposed surface molecules that act as virulence factors or fitness factors of pathogenic bacteria. The term “specifically (or selectively) binds” refers to a binding reaction that is determinative of the presence of the bound ligand, often in a heterogeneous population of proteins and other biological matter. As a result, the engineered hmw bacteriocin once bound specifically can generically kill the pathogenic bacteria. Furthermore, in order to become resistant to the engineered hmw bacteriocin, the targeted pathogenic bacteria must lose its recognition or binding site for the hmw bacteriocin. Stated differently, if the modified hmw bacteriocin specifically and exclusively uses the virulence or fitness factor as its receptor, the bacteria would be forced to compromise or even completely lose its virulence or fitness in order to escape killing by the engineered hmw bacteriocin.
A modified hmw bacteriocin of the disclosure resembles a bacteriophage tail but comprises a binding capability, or receptor binding domain (RBD), that has been changed relative to an unmodified, naturally occurring, or native bacteriocin. The RBD may be changed in amino acid sequence by use of recombinant DNA techniques as described herein. The term “recombinant”, typically used with reference to a cell, or nucleic acid, protein, or vector, indicates that the cell, nucleic acid, protein or vector, has been modified by the introduction of a heterologous nucleic acid or protein or the alteration of a native nucleic acid or protein, or that the cell is derived from a cell so modified. So a recombinant cell expresses genes that are not found within the native (non-recombinant) form of the cell or expresses native genes that are abnormally expressed, under expressed, or not expressed at all.
In many embodiments, the RBD may be modified to be that of a tail fiber or tail spike from another bacteriocin or a bacteriophage. As one non-limiting example disclosed herein, the RBD of R2 pyocin is modified by fusing the C-terminal portion of the tail fiber protein (RBD) of a phage (that infects a different host) to the N-terminal portion (BPAR) of the R2 tail fiber protein. By fusing the C-terminus of the P2 tail fiber to the R2 PRF15 and co-expressing the P2 cognate chaperone, the target bacteria spectrum of the R2 was changed to kill E. coli C. See FIG. 2.
In additional embodiments, hmw bacteriocins are engineered otherwise. The disclosure includes an hmw bacteriocin designed or selected to recognize, or target, a surface molecule of a bacterium (such as a pathogenic bacterium). The surface molecule may be considered a receptor on a bacterium recognized, or bound, by the hmw bacteriocin.
The disclosure is based on the properties of an hmw bacteriocin tail fiber to bind to, or interact with, a receptor to form a binding pair. The binding or interaction occurs through the RBD of the tail fiber, which is the first member of the binding pair, with the receptor being the second member of the pair. In many embodiments, the receptor is a bacterial cell surface molecule or portion thereof. In other embodiments, the receptor is a molecule with properties of a virulence or fitness factor of a pathogenic bacterium.
A modified or engineered hmw bacteriocin disclosed herein comprises a tail fiber having both a base plate attachment region (BPAR) and a modified, or heterologous, RBD. As described herein, the tail fiber is a trimeric structure of three tail fiber protein subunits, each of which also comprises a first domain corresponding to, and forming, the BPAR in a tail fiber and a second domain corresponding to, and forming, a modified or heterologous RBD in a tail fiber.
Typically, “heterologous” when used with reference to portions of a protein or nucleic acid sequence indicates that the sequence comprises two or more subsequences that are not usually found in the same relationship to each other in nature. For instance, a heterologous protein indicates that the protein comprises two or more subsequences that are not found in the same relationship to each other in nature. “Heterologous” also means that the amino acid or nucleic acid sequence is not normally found in conjunction with the other sequences or is not normally contained in the selected plasmid, vector, or host. In other words, it is not native to the system for which it is now utilized. For example, proteins produced by an organism that is not the wild type source of those proteins.
So in many embodiments, the disclosure includes an hmw bacteriocin tail fiber protein comprising a BPAR of the protein and a modified, or heterologous, RBD. The BPAR is typically at the N-terminal region of a tail fiber protein, while the RBD is typically at the C-terminal region. Other than the modified, or heterologous, RBD, the tail fiber protein may be that of any naturally occurring hmw bacteriocin, with a pyocin, monocin, enterocoliticin, or meningocin being non-limiting examples. In some embodiments, the tail fiber protein of R1-pyocin, R2-pyocin, R3-pyocin, R4-pyocin, and R5-pyocin, as represented by SEQ ID NO:1, 3, 5, 7, 9, respectively, may be used as described herein. In additional embodiments, the tail fiber protein may be that or those of the ΦCTX phage SEQ ID NO:45, or that of phage PS17 SEQ ID NO:19 or that of the VHML bacteriophage SEQ ID NO:21 and 22.
Embodiments of the disclosure include combinations of an hmw bacteriocin tail fiber protein BPAR and a RBD from a bacteriophage tail fiber protein, as shown in FIG. 3. In some cases, a combination may include the N-terminal amino acids from position 1 to about position 164 or position 240 of a bacteriocin tail fiber protein. This polypeptide fragment may be fused to a region of a bacteriophage tail fiber protein including its C-terminal portion containing an RBD. The region may be a polypeptide fragment lacking the N-terminal region from position 1 to about position 150, about position 170, about position 190, about position 290, about position 300, or about position 320.
Using the R2 pyocin and the P2 phage tail fiber protein as non-limiting examples, the BPAR containing fragment may include the N-terminal amino acids from position 1 to position 164 or 240. See FIGS. 4-7. The RBD containing fragment may include the C-terminal, and from about 347 to about 755 amino acids in length of the P2 or related phage tail fiber proteins. The fusion may be readily prepared by recombinant DNA techniques with nucleic acid sequences encoding the R2 tail fiber protein, such as prf15, and the P2 phage gene H encoding its tail fiber protein. When the RBD is derived from the tail fiber of another hmw bacteriocin or myoviridae, the cognate chaperone of the RBD needs to be co-expressed with the fusion tail fiber genes in order to ensure the assembly of the modified tail fibers into a functioning pyocin structure. See FIG. 8.
Another non-limiting example is the use of the R2 pyocin and the phiV10 phage. The BPAR containing fragment may include the N-terminal amino acids from position 1 to position 161 or 164 of the PRF15 protein. The RBD containing fragment may include the c-terminal amino acids from position 204, 211, or 217 to position 875 of the V10 tail spike protein. See FIG. 11A, and SEQ ID NOs: 67, 68, 69.
In other embodiments, a modified RBD comprises a change in the amino acid sequence of the RBD relative to a naturally occurring RBD or relative to the BPAR present in the tail fiber protein. Non-limiting examples of a change in amino acid sequence include substitution, insertion (or addition), or deletion of one or more amino acids.
In embodiments comprising the substitution of RBD amino acid residues, about 1%, about 2%, about 3%, about 4%, about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, about 15%, about 16%, about 17%, about 18%, about 19%, about 20%, about 22%, about 24%, about 26%, about 28%, about 30%, about 35%, about 40%, about 45%, or about 50%, or more, of the C-terminal in a tail fiber protein are substituted. In some embodiments, the substitutions are within about 245, about 260, about 275, or about 290, or more, residues from the C-terminal.
The positions for substitution maybe any one or more, in any combination, within that region. Exemplary positions include, but are not limited to, 448, 449, 452, 453, 454, 455, 459, 460, 462, 463, 464, 469, 472, 473, 474, 475, 478, 480, 484, 485, 486, 491, 494, 496, 497, 498, 499, 505, 506, 507, 508, 510, 512, 514, 517, 518, 519, 520, 521, 523, 527, 528, 530, 531, 533, 535, 537, 538, 541, 543, 546, 548, 561, 603, 604, 605, 606, 610, 618, 621, 624, 626, 627, 628, 629, 631, 632, 633, 638, 641, 642, 645, 646, 647, 648, 649, 650, 651, 652, 653, 654, 655, 657, 659, 663, 664, 665, 666, 667, 668, 669, 670, 671, 672, 673, 674, 675, 676, 677, 678, 679, 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, and 691, as well as any combination thereof, in SEQ ID NO:1, 3, 5, 7, or 9. In some embodiments, the substitution is conservative as described herein. In other embodiments, the substitution is with a non-conservative substitution.
In further embodiments, insertions and deletions of amino acid residues within the same region at the C-terminal of a tail fiber protein may be made.
Other sources of RBDs include, but are not limited to, T-4 and other T-even or pseudoT-even phages, phages T-3 and T-7, T-7 super-group of phages, phage Mu, phage P22, phage L-413c, podophages, lambdoid phages and even polysaccharide binding or specific protein binding enzymes or ligands, the binding properties of which can serve RBD functions as did the tail spike protein of phiV10.
RBD from Diversification
In further embodiments, a tail fiber protein comprises a substitution with, or insertion of, an RBD derived from an organism that diversifies the structure by deploying a Diversity Generating Retroelement (DGR), as described in published Patent Application US 2006-0121450, published Jun. 8, 2006 (incorporated herein by reference as if fully set forth). The major tropism determinant (MTD) of Bordetella bacteriophage BPP-1 is one such structure. The sequence of MTD is represented by SEQ ID NO:24 as disclosed herein. In other embodiments, the substitution is with part of the MTD sequence, such as, but not limited to, the region from residue 49 to 381, from residue 171 to 381, or from residues 306 to 381, of SEQ ID NO:24. The insertion of the MTD sequence, or any fragment thereof (such as those listed above), to the end of a tail fiber protein, such as after position 691 of SEQ ID NO:3, is within the embodiments disclosed herein. The substitution of the MTD sequence, or any fragment thereof (such as those listed above), may be for any non-BPAR region of a tail fiber protein. Non-limiting examples include the region of SEQ ID NO:1, 3, 5, 7, or 9 beginning at about position 643, 625, 562, 448, 428, 231, and 163 through to the C-terminus of the sequence (see FIGS. 4-7 for exemplifications of these substitutions).
As described herein, the tropism determinant sequence in a tail fiber may be diversified to produce a plurality of modified or heterologous RBDs. The nucleic acid sequence encoding the tropism determinant comprises a variable region (VR) which may be operatively linked, in cis or in trans, to a template region (TR) such that the TR is a template sequence that directs site-specific mutagenesis of the VR. The operative linkage of the VR and TR regions also includes an operative linkage to sequences encoding a reverse transcriptase (RT) activity, which may be present in trans relative to the VR. Sites of variability in the VR of the tropism determinant correspond to adenine residues in the generally homologous template region, TR, which itself is invariant and essential for sequence alterations in the VR. So while an initial molecule may contain a TR that is identical to the VR, the adenine residues present in the TR will result in the mutagenesis or diversification of the corresponding positions in the VR sequence. So if the TR sequence is a perfect direct repeat of the sequence in the VR, diversification of the VR region results in one or more adenine residues in the VR, also found in the TR, being mutated to another nucleotide, that is cytosine, thymine or guanine, without change in the TR sequence. This system may be used to alter the VR region, and thus the RBD, of a modified tail fiber protein as described herein.
Upon diversification, the tail fiber protein may be varied such that the resultant RBD has at least 80%, at least 85%, at least 90%, or at least 95% homology to the major tropism determinant (MTD) of Bordetella bacteriophage BPP-1, as represented by SEQ ID NO:24. As described herein, the tail fiber protein and tropism determinant combination may be a substitution, or an insertion, of a tropism determinant sequence or portion thereof into the tail fiber protein sequence. Thus the resultant tail fiber protein may be viewed as comprising a substitution or insertion with a binding domain with at least 80%, at least 85%, at least 90%, or at least 95% homology as recited above.
A nucleic acid molecule encoding a tail fiber and a tropism determinant combination may be used for diversification and sequence variation. Thus nucleic acid combinations of sequences encoding all or part of a tail fiber protein, and all or part of a tropism determinant, are within the disclosed embodiments. Other embodiments include nucleic acid molecules encoding any tail fiber protein with a modified or heterologous RBD as disclosed herein. In some embodiments, the encoded modified or heterologous RBD comprises a change in the amino acid sequence of the RBD relative to a naturally occurring RBD or relative to the BPAR present in the tail fiber protein as described above.
In additional embodiments, a tail fiber protein encoding nucleic acid molecule may be made available for diversification to form a modified tail fiber protein disclosed herein. The nucleic acid molecule, under control of a suitable promoter, is operatively placed 5′ to an atd-TR-brt region. The TR sequence may be referred to as TR′ and prepared based upon the VR sequence as discussed below. The resulting nucleic acid construct may carry a deletion of the transcription terminator structure upstream of the atd.
A region of the nucleic acid molecule encoding the C-terminal end of the tail fiber protein as described above, is selected to be the VR and then operatively linked to a TR′ sequence containing adenine residues at positions, that when varied, direct amino acid changes in the sequence encoded by the VR. Such adenine residues may be deliberately designed to be the first or second position of codons within the VR. The TR′ sequence can initially be identical to the selected VR followed by site directed mutagenesis or de novo nucleic acid synthesis to prepare a TR′ sequence that contains adenine residues only at the corresponding positions to direct mutagenesis and diversification in the encoded tail fiber protein.
Preparation and Use of hmw Bacteriocins
The nucleic acid molecules described herein may be used to express and prepare tail fiber proteins, including modified or engineered proteins, by any means known to the skilled person. In some embodiments, the expression is via the use of a vector containing the nucleic acid molecule operably linked to a heterologous promoter that can direct the expression of the encoded tail fiber protein. The promoter can be controlled by an exogenous molecule that acts as an inducer or co-repressor to express or not express the tail fiber proteins.
In many embodiments, the expression may occur with expression of an accessory gene, such as a tail fiber “chaperone” encoding sequence reported for various bacteriophages. The presence of a cognate chaperone for the RBD portion when derived from a tail fiber of a hmw bacteriocin or myoviridae facilitates assembly of an hmw bacteriocin of the disclosure without necessarily becoming a part of the bacteriocin, as shown in FIG. 8. One non-limiting example of a chaperone is encoded by R2 prf16 (SEQ ID NO:4), and it corresponds to (or is the cognate chaperone for) the R2 pyocin tail fiber protein encoded by prf15 (SEQ ID NO:3). Other examples include gene G in the P2 (SEQ ID NO:26), gene G on L-413c (SEQ ID NO:29), the cognate chaperone, SEQ ID NO: 20, for the PS17 tail fiber, and the Orf 38 (SEQ ID NO:23) in VHML bacteriophages, each of which is the cognate chaperone to the respective tail fiber gene in each of these myoviridae phages. These genes are homologues to the phage T4 gp38 (SEQ ID NO:32), which is known to be responsible for proper folding of the T4 tail fiber (SEQ ID NO:31) into trimers (Burda, Qu, Hashemolhosseni).
The use of a cognate chaperone is advantageous because a non-cognate chaperone may be insufficient to correctly fold a given tail fiber protein and/or assemble it into an hmw bacteriocin, as shown in FIG. 8. As a non-limiting example, the R2 prf16 gene product has been observed to be insufficient to complement the folding of a modified tail fiber compromising an R2 BPAR fused to a P2 RBD portion of a tail fiber. Without being bound by theory, and offered to improve the understanding of the present disclosure, it is believed that a chaperone may act specifically on the C-terminal portion of its cognate tail fiber protein and that the tail fibers and their chaperones have co-evolved. However, Qu et al. isolated a T4 gp37 tail fiber mutant that suppresses the requirement for gp38, its cognate chaperone. This mutant had in gp37 a duplication of a coiled-coil motif, which may itself play a role in folding. Therefore, it is further believed that a tail fiber protein may be designed to contain such a change so that it folds properly without the need to co-express a cognate chaperone.
Therefore, embodiments of the disclosure include a bacterial cell transfected with a nucleic acid molecule encoding a modified or engineered tail fiber protein, optionally co-expressed with a chaperone, as described herein. Expression of the nucleic acid molecule, optionally with an accessory (chaperone) protein, results in the production of modified or engineered tail fibers of the disclosure. The disclosure also includes expression of more than one modified or engineered tail fiber protein through the use of more than one nucleic acid molecule to result in mixed homotrimeric tail fibers or even heterotrimeric tail fibers. Additionally, sequences encoding the tail fiber protein and chaperone may be contained within a single nucleic acid molecule, such as a plasmid or other vector, or by separate molecules. Where a single nucleic acid molecule is used, the sequences optionally may be under the control of the same regulatory sequence(s). Alternatively, the coding sequences may be under separate regulatory control.
In some embodiments, the bacterial cell is also capable of expressing the additional subunits to form an hmw bacteriocin comprising a modified or engineered tail fiber. In one group of embodiments, the endogenous tail fiber protein coding sequence of the bacterial cell is inactivated or deleted. Optionally, the other subunits may be encoded by sequences on a nucleic acid molecule, such as a plasmid or other vector, separate from that which contains a sequence encoding a tail fiber protein and/or chaperone. Thus the tail fiber protein and/or chaperone may be provided one or more nucleic acid molecules in trans relative to the other subunits.
The nucleic acids, vectors, and bacterial cells may be used in a method of producing a modified or engineered hmw bacteriocin as disclosed herein. Such a method may comprise culturing bacterial cells containing nucleic acid molecules as described above under conditions resulting in the expression and production of the tail fiber and hmw bacteriocin. In some embodiments of the disclosure the conditions are in vivo within an animal.
In one group of embodiments, a method of preparing an hmw bacteriocin comprises expressing the bacteriocin subunits, including the modified or engineered tail fiber protein, in a host bacterium, and harvesting the hmw bacteriocin from the bacterial culture. The host bacterium is a complementary host production bacterium that encodes and expresses the other subunits necessary for the production of the bacteriocin. The term “host bacterium” or “host bacteria” refers to a bacterium or bacteria used to produce an hmw bacteriocin disclosed herein. Host bacteria or bacterium may also be referred to as “host production bacterium”, “host production bacteria”, “production bacterium” or “production bacteria”. The “harvesting of an hmw bacteriocin from a bacterial culture” generally comprises removing the bacteriocin from the host bacterial culture.
In an alternative group of embodiments, a method of preparing an hmw bacteriocin with a modified tail fiber as described herein is provided. The method may comprise preparing a nucleic acid molecule encoding a modified tail fiber protein by any means disclosed herein and expressing the nucleic acid molecule in a cell under conditions wherein an hmw bacteriocin is produced.
Embodiments of the disclosure include an hmw bacteriocin comprising a tail fiber protein as described herein. In one group of embodiments, the bacteriocin comprises a tail fiber protein comprised in part of the amino acid sequence represented by SEQ ID NO:1, 3, 5, 7, 9. In other embodiments, the bacteriocin is a modified or engineered pyocin, monocin, enterocoliticin, or meningocin comprising a tail fiber with a heterologous modified RBD. In many embodiments, the heterologous modified RBD binds a bacterial virulence or fitness factor.
In further embodiments, engineered hmw bacteriocins with multivalent tail fibers are disclosed. MTD of Bordetella bronchiseptica bacteriophage BPP-1 has been found by X-ray crystallographic analysis to be a highly intertwined pyramidal homotrimer with the three sets of twelve non-contiguous variable amino acid residues forming three rather flat receptor-binding sites at the tetrahedron's base and located in a convergently evolved C-type lectin (“CTL”) domain. Comparison of the structures of five MTD variants at 1.5 Å resolution showed that the main chain conformation of variable residues is structurally invariant, with inserts in the CTL and trimeric assembly both contributing to formation of a static scaffold for combinatorial display of variable residues, thereby minimizing the incidence of protein misfolding (McMahon et al., 2005). Thus a single tail fiber may be generated to contain three properly folded mixed monomers, since the structures of the variant tropism determinant fibers are identical except for the non-interacting, solvent-exposed twelve amino acid residues.
The structure of the dominant MTD-P1 variant bound to its receptor, the Bordetella virulence factor pertactin, also has been solved by crystallography and characterized. One of the monomers of MTD binds to one structural domain on pertactin; a second identical monomer of the same MTD binds a different, non-symmetrical structural domain of the same (monomeric) pertactin molecule; a third MTD monomer remains unbound.
The above variant MTD structures and the binding interaction between MTD and its target, pertactin, may be applied to the design and selection of multivalent tail fibers. For example, it is evident that an MTD monomer can exhibit affinities for two different structural domains and yet in multimeric format possess sufficient avidity to effect functional phage binding and infection. Furthermore, not all monomers of a fiber need be bound to a receptor to provide adequate avidity for phage binding and infection. These data and conclusions along with the knowledge that for at least T4 bacteriophages, also a member of the myoviridae family, only three (homotrimeric) tail fibers need be bound to receptors to trigger tail sheath contraction and core penetration of bacterial membranes, indicates several means of generating a multivalent hmw bacteriocin.
Such engineered multivalent hmw bacteriocins have broader host ranges and are capable of binding to more than a single virulence or fitness factor even on the same bacterial organism, thereby making it more difficult for targeted bacteria to develop resistance by mutational loss of expression of all targeted, relevant receptors. An R-type bacteriocin can be engineered to possess two independent sets of three identical tail fibers. The fibers of one set comprised of the same three non-identical monomers, and the fibers of the other set comprised of three different non-identical monomers. Each monomer can possess binding affinities for two different epitopes (e.g. two different receptors), just as does the tropism determinant. Thereby any bacterium expressing any one or more of the 12 different targeted receptor molecules (2 “epitopes”/monomer times 3 monomers/tail fiber times 2 sets of different tail fibers/R-type bacteriocin equals 12 targeted receptors) would bind the engineered multivalent hmw bacteriocin and trigger its penetration of the membrane. Such engineered hmw bacteriocins have an unnaturally broad host range and, in addition, make it highly unlikely that a bacterium expressing more than a single targeted receptor could become resistant to the engineered hmw bacteriocins.
In other aspects, methods for the use of an hmw bacteriocin of the disclosure are provided. In some embodiments, a method of compromising the integrity of the cytoplasmic membrane of a bacterium is disclosed. The method may comprise contacting a target bacterium with a fusion peptide or an hmw bacteriocin, or portion thereof, as disclosed herein. Alternatively, the contact may be with an hmw bacteriocin containing composition disclosed herein.
In one group of embodiments, the contacting occurs in vivo within a subject. Thus a method of compromising the membrane integrity of a bacterium in a subject is disclosed. The method may comprise administering a fusion peptide or an hmw bacteriocin or a portion thereof as described herein to the subject. In another group of embodiments, the contacting occurs ex vivo or in vitro.
The methods can be used as a stand-alone therapy or as an adjunctive therapy, such as for the treatment of bacterial populations. Numerous antimicrobial agents (including antibiotics and chemotherapeutic agents) are known which would be useful in combination with these methods to treating bacteria-based conditions.
In yet additional embodiments, a method of forming non-virulent or unfit bacteria progeny from virulent progenitor bacteria is provided. The method may comprise contacting virulent bacteria with an hmw bacteriocin which binds a virulence or fitness factor of said virulent progenitor bacteria as disclosed herein. The method then may continue by allowing selection of non-virulent bacteria progeny that no longer express the virulence or fitness factor.
In an alternative embodiment, a method of maintaining a population of non-virulent bacteria is provided. The method may comprise contacting the population with an hmw bacteriocin which binds a virulence or fitness factor of virulent bacteria. The method then continues and prevents propagation of virulent bacteria. Without being bound by theory, and offered to improve the understanding of the disclosure, an emergence of bacterial resistance to an engineered hmw bacteriocin will be accompanied by a compromised virulence or fitness of the pathogenic bacteria.
The methods of the disclosure also may be applied in an environment where bacterial growth is not desired or is considered to be harmful. Non-limiting examples include the sterilizing of environments, including medical settings and operating room facilities; as well as food or food preparation surfaces or areas, including where raw meat or fish are handled or discarded. The methods may also be used to sterilize heat sensitive objects, medical devices, and tissue implants, including transplant organs.
In particular, food or food products are affected by pathogenic or undersirable bacteria, such as certain strains of E. coli. However, in some instances, only certain species or groups of bacteria are pathogenic, so specific bacteriocin can be designed to target these groups or species. For example, one may choose to kill or mitigate an E. coli strain, such as O157:H7, but leave other natural, non-harmful E. coli unaffected. Therefore, selective or whole, santization or sterilization of bacteria is possible depending upon the use of one or more bacteriocins.
In another embodiment, methods of diagnostic screening or selection are provided. A sample of a suspected or known bacteria can be screened against one or more engineered bacteriocins to identify their potential therapeutic effects against the bacteria.
Furthermore, the engineered bacteriocins can be utilized to selectively or generally detect the presence of the pathogenic bacteria. In some instances, the bacteriocins would be labeled with a detectable marker, such that in the presence of the targeted bacteria, the label would be detected or identified.
Target Bacteria
The engineered hmw bacteriocins of the disclosure may be modified to target a receptor on a variety of bacterial species and strains, including pathogenic bacteria, such as nosocomial or pyogenic bacteria, as non-limiting examples. In addition to targeting the virulence factors of select bacteria as described herein, bacteria that are already susceptible to bacteriophages are one non-limiting group of bacteria that may be inhibited by an hmw bacteriocin, such as an engineered pyocin, of the disclosure. These bacteria include the gram negative bacteria that are susceptible, as well as not susceptible, to naturally occurring pyocins. Additional non-limiting examples include gram negative bacteria as a group as well as gram positive bacteria. There are reports of hmw bacteriocin-like entities in gram positive bacteria that target other gram positive bacteria (Thompson & Pattee, 1981; Birmingham & Pattee, 1981; Zink et al., 1995). In some embodiments, the target bacterium is identified or diagnosed. Non-limiting examples of such bacteria include those of the genus Escherichia, Staphylococcus, Clostridium, Acinetobacter, Pseudomonas, or Streptococcus. 
As a non-limiting example of targeting a virulence factor, the disclosure includes the use of a phage tail fiber protein RBD like that of the tail spike protein from the podoviridae phage phiV10 that infects E. coli O157:H7 but does not infect a mutant strain TEA026 derived therefrom that has lost the O157 antigen (Ho and Waldor, 2007). The binding of this phage requires the presence of the O157 antigen, a virulence factor, involved in gut colonization by the pathogenic E. coli O157:H7 organism (Ho and Waldor, 2007). Therefore, an hmw bacteriocin of the disclosure may contain a modified tail fiber protein containing the globular RBD from the tail spike protein (SEQ ID NO:60) of the above described phage phiV10 such that the modified hmw bacteriocin targets a virulence factor, the O157 antigen, of E. coli O157:H7. The globular tail spike protein does not have a cognate chaperone as it apparently folds without such, and thus a chaperone is not required for the assembly of its fusion with the BPAR of R2 Prf15.
An “infection” refers to growth of bacteria, such as in a subject or tissue or non-bacterial cell, wherein the bacteria actually or potentially could cause disease or a symptom in the subject, tissue or non-bacterial cell. Treatment of an infection may include prophylactic treatment of substances or materials. Non-limiting examples include donated organs, tissues, and cells; medical equipment, like a respirator or dialysis machine; or wounds, such as those during or after surgery. Other uses include the removal of target bacteria which may cause problems upon further growth. In additional embodiments, an hmw bacteriocin is used to treat food, plants or harvested parts of plants with bacterial infections or contaminations, or to treat environmental occurrences of the target bacteria, such as in a hospital or commercial setting.
The disclosure provides for the treatment, by administration or contact with an hmw bacteriocin disclosed herein to target the bacteria, of such infections in tissues and subjects as follows. The infections include the common infections of the cornea (“keratitis” and corneal ulcers), at least two-thirds of which are caused by P. aeruginosa. Approximately 30% of these pathogens are reported to be resistant to multiple antibiotics (Mah-Sadorra et al., 2005). Bacterial infection of the cornea is considered a relatively uncommon, but serious condition, requiring urgent medical attention, because of the potential for reduced vision or even vision loss in the affected eye(s). Other common infections which may be treated, and are caused by antibiotic-resistant P. aeruginosa, include ear infections, e.g. “swimmer's ear” (Roland & Stroman, 2002), those secondary to severe burns and wounds (Holder, 1993), and cystic fibrosis. Cystic fibrosis is consistently aggravated by chronic, antibiotic-resistant infections caused by P. aeruginosa and its close relative, Burkholderia cepacia (Govan & Deretic, 1996), and these pathogens in cystic fibrosis may be treated by use of an engineered hmw bacteriocin. Because bacteriocins like pyocins will tolerate freeze-drying (Higerd et al., 1969), the disclosure includes a freeze-dried formulation of a bacteriocin for administration to enhance the likelihood of successful delivery to the upper and/or lower airway of the respiratory tract.
As described herein, the treatment of a subject is typically of “a subject in need of treatment”. The determination, or diagnosis, of the need for treatment may be made by a skilled person, such as a clinician, by use of art recognized means. In some embodiments, the subject is an animal or plant with a bacterial infection that is potentially life-threatening or that impairs health or shortens the lifespan of the organism.
In additional embodiments, a method to kill or inhibit the growth of bacteria in a biofilm is provided. Such a method may comprise contacting a biofilm with an hmw bacteriocin disclosed herein which targets bacteria in the biofilm.
As described herein, an anti-bacterial hmw bacteriocin is used to inhibit growth, survival, or replication of a particular bacterium. The bacterium may be a pathogenic or environmentally deleterious strain, or may be treated in a prophylactic manner. A pathogenic microorganism generally causes disease, sometimes only in particular circumstances.
The bacteria may also be that of a nosocomial (hospital derived) infection, environmental bacteria, and pyogenic (pus forming) bacteria. The methods and compositions of the disclosure can be used to inhibit growth of nosocomial bacteria, including bacteria that populate a typical hospital environment, or bacteria that are present on human skin or nose or in the human gastrointestinal tract, or bacteria that infect and form pus in wounds. Nosocomial infections are infections which become evident during a hospital stay or are related to a procedure performed in a hospital. These procedure-related infections often become evident after patients are discharged from the hospital. The most common nosocomial bacterial infections are urinary tract infections, surgical-site infections, pneumonia, C. difficile associated diarrhea and pseudomembrane colitis, and serious systemic infections in which bacteria can be grown from blood.
The methods and compositions of the disclosure may be used to inhibit growth of gram negative or gram positive bacteria. Non-limiting examples of gram positive bacteria include Staphylococcus (pyogenic), Enterococcus (opportunistic), Streptococcus, Enterococcus, Bacillus, Micrococcus, Mycobacterium, Corynebacterium, and Clostridium. Non-limiting examples of gram negative bacteria include Pseudomonas (pyogenic), E. coli (opportunistic), Salmonella (opportunistic), Campylobacter (opportunistic), Proteus (pyogenic), Klebsiella (opportunistic), Enterobacter (pyogenic), Citrobacter (pyogenic), gram negative non-fermenter rods (such as Acinetobacter), and Shigella. The pyogenic cocci are spherical bacteria that cause various suppurative (pus-producing) infections in animals. Included are the gram-positive cocci Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae, and the gram-negative cocci, Neisseria gonorrhoeae, and N. meningitidis. 
In additional embodiments, the disclosed methods and compositions of the disclosure are used to inhibit growth, particularly of antibiotic resistant bacteria. Non-limiting examples include numerous bacterial pathogens that have become multi-drug resistant (MDR).
Engineering Pyocins
Francois Jacob discovered and first described pyocins as high molecular weight bacteriocins (Jacob, 1954). Similar bacteriocin-like entities have been described in multiple other gram negative bacteria (Coetzee et al., 1968) as well as in Listeria moncytogenes (Zink et al. 1995) and Staphylococcus aureus (Thompson and Pattee, 1981), both of which are gram positive organisms. While pyocins morphologically resemble the tails of contractile (myoviridae) bacteriophages, they are not simple defective phages; there are meaningful differences. For example, differences exist in physical and chemical stability between pyocins and phage tails (Kageyama & Egami, 1962; Nakayama et al., 2000). While the host ranges of pyocins are relatively narrow and usually restricted to strains of the same species, there are exceptions (Morse et al, 1976; Blackwell et al., 1982). On the other hand, myoviridae bacteriophages can exhibit broad host ranges, and their host ranges, like those of R-type pyocins, are determined by the binding specificities of the tips of their tail fibers (Tetart et al., 2001).
For numerous phage tail fibers, the distal (3′-terminal) third of the gene varies in mutants or variants with altered phage host ranges, or “tropisms” (Ackermann, 2003). As a non-limiting example, the major tropism determinant (MTD), the receptor binding protein of Bordetella bacteriophage BPP-1, varies greatly in sequence (Liu et al., 2004; Doulatov et al. 2004). Variation in tropism determinants depends on a phage-encoded retroelement (Diversity Generating Retroelement, or DGR) that belongs to a family of DGRs implicated in generating sequence variation in various phage and bacterial genomes. The Bordetella DGR can produce more than 1013 different sequence variants of MTD, rivaling the 1014-1016 possible sequences of antibodies. Tropism determinant variants are produced by a unique adenine-specific mutagenesis process involving DGR-encoded reverse transcriptase (bRT) and a stable template region (TR). Variability in MTD is focused to 12 adenine-encoded amino acids that are scattered across its C-terminal variable region (VR) (Doulatov et al. 2004). The 3-dimensional crystal structures of numerous Bordetella MTD variants have been solved and confirm, as described below, that the tip of the structure determines the binding specificity and thereby the major tropism (host range) of the phage (McMahon et al., 2005). Thus, as further described below, the tropism determinant and its related DGR system may be used in the practice of the disclosure.
Many Pseudomonas species possess the genes for the R-type pyocins (Takeya et al., 1969; Kageyama, 1975). The R-type pyocin locus consists of about 16 complementation groups including about 10 structural genes plus regulatory and chaperone genes (Shinomiya et al. 1983a; Shinomiya et al., 1983b). Morphologically and genetically the R-type pyocins resemble the tails of myoviridae bacteriophages but have no head structure and thus no nucleic acid content (Kageyama, 1964; Ishii et al., 1965; Shimizu et al., 1982). They are thought to have evolved from the phage tail structure of a P2-related ancestor, but they are not simple defective phages, having been further adapted for their role as defensive bactericidal agents (Nakayama et al, 2000). Similar to bacteriophages, however, pyocins do bind to specific molecular “receptors” on target bacteria and penetrate their membranes with a “core” or needle-like structure (Uratani & Hoshino, 1984). As an immediate consequence of the core penetration of the membranes, the bacterium is killed by compromise of the integrity of its cytoplasmic membrane and dissipation of its membrane potential, a bactericidal event that can result from an attack by a single pyocin (Iijima, 1978; Uratani & Hoshino, 1984; Strauch et al., 2001).
The RBD, or Receptor Binding Determinant of R-pyocin binding, of a typical R-type pyocin binds to a bacterial surface molecule. In the case of an R2 pyocin isolate, the RBD resides in the carboxy-terminal portion of its tail fiber. The tail fiber is a homotrimer of the product of the prf15 gene (Nakayama et al., 2000). Modification of the RBD in the prf15 gene and recombination of the modified prf15 gene into a system that produces R-type pyocins allows production of an engineered pyocin with modified binding specificity.
The major tropism determinant (MTD) of Bordetella bacteriophage possesses several unique and useful properties as a binding domain. The functional form of MTD in Bordetella bacteriophage is a homotrimer that binds the virulence factor protein, pertactin, in Bordetella. Thus, the MTD gene may be fused to the distal end of the prf15 gene to take advantage of the MTD properties. So as described herein, an aspect of the disclosure includes construction of a fusion protein between the P. aeruginosa R-type pyocin tail fiber protein (PRF15) and the major tropism determinant (MTD) of Bordetella phage, BPP-1. A PRF15-MTD fusion may be used to complement in trans a P. aeruginosa PA01Δprf15 to bind and kill pertactin-expressing Bordetella bronchiseptica or pertactin-expressing E. coli. 
Additionally, the P2 or P4 bacteriophage may be used as a surrogate to harbor the prf15-MTD or other tail fiber fusion genes such that the genotype is coupled to the binding phenotype of the tail fiber. This permits efficient transduction, selection, and isolation of the tail fiber gene encoding the desired RBD.
Modes of Administration
An engineered hmw bacteriocin of the disclosure may be administered by any suitable means. Non-limiting examples include topical or localized administration as well as pulmonary (inhalation), gastrointestinal, by catheter or drip tube, or systemic administration to a subject. Representative, and non-limiting, examples of systemic administration include intraperitoneal and intravenous administration. The protective effects of intraperitoneally and intravenously administered pyocins have been demonstrated in mice infected systemically with lethal doses P. aeruginosa strains sensitive in vitro to the administered pyocins (Merrikin & Terry, 1972; Haas et al., 1974). In some embodiments, contact between an hmw bacteriocin disclosed herein and a target bacterial population results in a decrease in the population of at least 10, at least 100, at least 1000, or at least 10,000, or more, fold decrease relative to the absence of the bacteriocin. In other embodiments, the contact may result in a decrease in detectability of the bacteria by at least 5, at least 10, at least 20, at least 30, at least 40, or at least 50, or more, fold relative to the absence of the bacteriocin.
An engineered hmw bacteriocin of the disclosure may be administered to any subject afflicted with, diagnosed as afflicted with, or suspected of being afflicted with, an infection or contamination by bacteria susceptible to the hmw bacteriocin. Non-limiting examples of such a subject include animal (mammalian, reptilian, amphibian, avian, and fish) species as well as insects, plants and fungi. Representative, and non-limiting, examples of mammalian species include humans; non-human primates; agriculturally relevant species such as cattle, pigs, goats, and sheep; rodents, such as mice and rats; mammals for companionship, display, or show, such as dogs, cats, guinea pigs, rabbits, and horses; and mammals for work, such as dogs and horses. Representative, and non-limiting, examples of avian species include chickens, ducks, geese, and birds for companionship or show, such as parrots and parakeets. An animal subject treated with an engineered bacteriocin of the disclosure may also be a quadruped, a biped, an aquatic animal, a vertebrate, or an invertebrate, including insects.
In some embodiments, the subject to be treated is a human child or other young animal which has yet to reach maturity. Thus the disclosure includes the treatment of pediatric conditions comprising infection with bacteria or other microorganism susceptible to an hmw bacteriocin of the disclosure.
The disclosure also provides for the treatment or prevention of an opportunistic infection, such as that resulting from an undesirable growth of bacteria that are present in the microbial flora of a human subject or a non-human animal. An opportunistic infection may be the result of an immunosuppressed condition in a subject or the result of antibiotic treatment that alter the commensal flora of the genitourinary (GU) or gastrointestinal (GI) tract. Thus the disclosure also provides for the treatment or prophylaxis of immunosuppressed subjects and subjects exposed to other pharmaceutical agents. An hmw bacteriocin with its anti-bacterial activity may be used in combination with another anti-bacterial or anti-microbial agent, such as an antibiotic or anti-fungal agent as non-limiting examples. An “anti-microbial agent” is an agent or compound that can be used to inhibit the growth of, or to kill, single celled organisms. Anti-microbial agents include antibiotics, chemotherapeutic agents, antibodies (with or without complement), chemical inhibitors of DNA, RNA, protein, lipid, or cell wall synthesis or functions.
In some embodiments, an hmw bacteriocin or fusion protein is formulated with a “pharmaceutically acceptable” excipient or carrier. Such a component is one that is suitable for use with humans, animals, and/or plants without undue adverse side effects. Non-limiting examples of adverse side effects include toxicity, irritation, and/or allergic response. The excipient or carrier is typically one that is commensurate with a reasonable benefit/risk ratio. In many embodiments, the carrier or excipient is suitable for topical or systemic administration. Non-limiting pharmaceutically suitable carriers include sterile aqueous or non-aqueous solutions, suspensions, and emulsions. Examples include, but are not limited to, standard pharmaceutical excipients such as a phosphate buffered saline solution, water, emulsions such as oil/water emulsion, and various types of wetting agents. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyloleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like.
Additional formulations and pharmaceutical compositions disclosed herein comprise an isolated hmw bacteriocin specific for a bacterial host; a mixture of two, three, five, ten, or twenty or more bacteriocins that target the same bacterial hosts; and a mixture of two, three, five, ten, or twenty or more bacteriocins that target different bacterial hosts or different strains of the same bacterial host.
Optionally, a composition comprising an hmw bacteriocin of the disclosure may also be lyophilized using means well known in the art. Subsequent reconstitution and use may be practiced as known in the field.
Also provided are formulations comprising microencapsulated hmw bacteriocin. In some embodiments, these may provide sustained release kinetics or allow oral ingestion to pass through the stomach and into the small or large intestine. In general, the pharmaceutical compositions can be prepared in various forms, such as granules, tablets, pills, suppositories, capsules (e. g. adapted for oral delivery), microbeads, microspheres, liposomes, suspensions, salves, pastes, lotions, and the like. Pharmaceutical grade organic or inorganic carriers and/or diluents suitable for oral and topical use can be used to make up compositions comprising the therapeutically-active compounds. Stabilizing agents, wetting and emulsifying agents, salts for varying the osmotic pressure, or buffers for securing an adequate pH value may be included.
An hmw bacteriocin is typically used in an amount or concentration that is “safe and effective”, which refers to a quantity that is sufficient to produce a desired therapeutic response without undue adverse side effects like those described above. An hmw bacteriocin may also be used in an amount or concentration that is “therapeutically effective”, which refers to an amount effective to yield a desired therapeutic response, such as, but not limited to, an amount effective to slow the rate of bacterial cell division, or to cause cessation of bacterial cell division, or to cause death or decrease rate of population growth of the bacteria. The safe and effective amount or therapeutically effective amount will vary with various factors but may be readily determined by the skilled practitioner without undue experimentation. Non-limiting examples of factors include the particular condition being treated, the physical condition of the subject, the type of subject being treated, the duration of the treatment, the nature of concurrent therapy (if any), and the specific formulations employed.
Additionally, and in anticipation of a possible emergence of bacterial resistance to an engineered hmw bacteriocin, there can be a concomitant compromise of the organisms' virulence or fitness where the bacteriocin targets the virulence or fitness factor of the targeted bacteria. Because a major, but non-limiting, mechanism by which a bacterium may become resistant to an hmw bacteriocin is the loss of its receptor for the bacteriocin, the targeting of a virulence or fitness factor as disclosed herein provides many advantages over traditional antibiotics and bacteriophages. The resistance to traditional antibiotics and bacteriophages can result from many different mechanisms other than loss of the receptor or target molecule of the antibacterial agent. As non-limiting examples, an hmw bacteriocin of the disclosure would not be subject to a bacterial efflux pump to remove the bacteriocin from the cellular environment and would not be subject to a bacterial nucleic acid deactivation mechanism.
Having now generally described the inventive subject matter, the same will be more readily understood through reference to the following examples which are provided by way of illustration, and are not intended to be limiting of the disclosure, unless specified.
EXAMPLES
The following examples are offered to illustrate, but not to limit the claimed subject matter.
Example 1
Modified hmw Bacteriocins Containing a Fusion Protein
a) Complementation System
To facilitate the preparation of a modified hmw bacteriocin as described herein, construction of a system to complement tail fibers in trans was established. Using the R2 pyocin as a representative model, creation of a deletion of the R2 prf15 coding sequence in the P. aeruginosa PAO1 genome was used to create a platform in which a complementing tail fiber protein, such as a modified prf15 gene product, was expressed in trans.
Generally, the deletion was made by the method of Hoang et al. to create P. aeruginosa strain PAO1Δprf15. The prf16 coding region, SEQ ID NO:4, for the R2 chaperone overlaps the end of the R2 prf15 gene by 8 nucleotides and the ribosome binding site lies within the prf15 coding region, SEQ ID NO:3. The PRF16 protein, which is not necessarily incorporated into the pyocin structure, has been reported to be required for assembly of the trimeric tail fiber and thus for maximum bactericidal activity (FIG. 8 and Nakayama et al., 2000). Therefore, both the transcription start site for prf16 and its ribosome binding site were left intact such that the chaperone would be produced upon induction of the modified pyocin construct encoding a “tail-less,” defective pyocin.
Briefly, an in-frame deletion of codons 11-301 of prf15 was made in PAO1 as follows. A 1.1 kb KpnI-AgeI fragment upstream of the desired deletion was amplified by PCR from PA01 genomic DNA using primers AV085 (5′-GCTTCAATGTGCAGCGTTTGC) (SEQ ID NO:46), and AV088 (5′-GCCACACCGGTAGCGGAAAGGCCACCGTATTTCGGAGTAT) (SEQ ID NO:47), and a 2.2 kb AgeI-EcoRI fragment was amplified using primers AV087 (5′-ATACTCCGAAATACGGTGGCCTTTCCGCTACCGGTGTGGC) (SEQ ID NO:48) and AV086 (5′-TCCTTGAATTCCGCTTGCTGCCGAAGTTCTT) (SEQ ID NO:49). The resulting restriction fragments were cloned into the KpnI and EcoRI sites of pEX18Gm (Hoang et al) to make pEXGm-Δprf15. The finished construct was transformed into strain PAO1 by electroporation (Chuanchuen et al). Integrants were selected with 100 μg/ml gentamicin, and segregants were then selected in media containing 5 μg/ml sucrose and lacking NaCl and gentamicin. Deletion candidates were confirmed by PCR analysis, pyocin induction, and sequencing of a PCR-amplified fragment.
Strain PAO1Δprf15 grows similarly to its parent strain, PAO1, and the pyocin encoding genes remain inducible through the SOS response, leading to lysis of the cell. While there appears to be some production of pyocin gene products, stable “tail-less” pyocin particles were not produced from PAO1Δprf15.
R2 pyocin prf15 was expressed in trans by first cloning the coding sequence into the broad host range Pseudomonas/E. coli shuttle vector, pUCP30T. See FIG. 9. In some initial constructs, transcription was driven constitutively or under lacI control from the tac promoter. But in other constructs, transcription was modified to be regulated with an endogenous prf15 promoter such that expression would be regulated through the SOS response. This permitted the expression of the modified prf15 gene to be induced synchronously with the expression of the other pyocin genes residing in the PAO1Δprf15 genome.
Briefly, the broad host-range vector pUCP30T (Schweizer, H. P et al) was modified by filling in the unique BspHI site to form pUCP30TΔBsp. A tac promoter was amplified by PCR from an MTD expression vector (a gift from Jeffery F. Miller, UCLA) using primers AV110 (5′-TTTATTAGCGGAAGAGCCGACTGCACGGTGCACCAATG) (SEQ ID NO:50) and AV114 (5′-CCCTCGAATTCATGAATACTGTTTCCTGTGTGAAATTG) (SEQ ID NO:51), then cloned into pUCP30TΔBsp to create pUCP-tac.
The R2 PRF15 coding region was amplified from a subclone using primers AV118 (5′-CTTCCTTTCATGACGACCAATACTCCGAA) (SEQ ID NO:52) and AV116 (5′-ACCACGAATTCTTCATCGTCCAAATGCCTC) (SEQ ID NO:53), while R2 prf15 and prf16 were amplified using primers AV118 and AV086 (5′-TCCTTGAATTCCGCTTGCTGCCGAAGTTCTT) (SEQ ID NO:49). The amplified fragments of prf15 and prf15/16 were cloned into pUCPtac digested with BspHI and EcoRI to yield pUCP-tac-prf15 and PUCP-tac-prf15/16.
For expression using the endogenous prf15 promoter, prf15 and prf16 were amplified together with the 1088 bp sequence upstream of prf15 from a subclone using primers AV107 (5′-CACCATCTAGACAATACGAGAGCGACAAGTC) (SEQ ID NO:54) and AV091 (5′-TCCTCAAGCTTACGTTGGTTACCGTAACGCCGTG) (SEQ ID NO:55) and cloned into pUCP30T digested with XbaI and HindIII to create pUCP-R2p-prf15/16.
Bacteria in log phase suspension growth and containing the expression plasmids were treated with 3 μg mitomycin C/ml to induce pyocin production. Stable pyocins were produced upon induction with yields similar to that of wild type PAO1. The pyocins had the same bactericidal spectrum and level of activity as R2 pyocin produced from PAO1. Thus, production of a stable pyocin complex required the expression of a tail fiber protein in addition to expression of the other pyocin encoding genes, and expression of the tail fiber gene in trans was sufficient.
When prf15 was expressed constitutively from the tac promoter, cell growth was markedly slower than when it was regulated by lad or the endogenous promoter. Although it appears that production of PRF15 alone in the cell is detrimental, yields of pyocins generated from both promoters are comparable.
A plasmid construct was prepared from which R2 prf16 was co-expressed with R2 prf15 to insure proper temporal expression prf16 for folding of PRF15 expressed in trans.
b) Recombinant hmw Bacteriocins
As described herein, five different R-type pyocins, based on spectra and termed R1-5, have been recognized. Because gene sequences encoding the tail fiber proteins were known only for R1 (SEQ ID NO:1) and R2 (SEQ ID NO:3), PCR was used to isolate and sequence the R3 (SEQ ID NO:5), R4 (SEQ ID NO:7), and R5 (SEQ ID NO:9) pyocin tail fiber genes along with their cognate chaperone encoding sequences present in their producer strains, SEQ ID NO:6, 8, and 10, respectively. The chaperone genes of pyocins R1 and R2 were also cloned and sequenced, SEQ ID NO:2 and 4, respectively. To confirm the hypothesis that the tail fiber dictates spectra, the sequences encoding R1, R3, R4, and R5 pyocin tail fiber proteins were obtained and expressed in trans in PAO1Δprf15 such that they would be incorporated into the R2 pyocin structure. Each of the resulting recombinant strains was then induced to produce pyocins and the spectrum of each was determined by spot assays, as shown in FIGS. 2 and 8.
c) Fusion Proteins as Functional Tail Fibers on Pyocins: R2-P2
A fusion of the R2 tail fiber prf15 gene and bacteriophage P2 gene H sequences was created, expressed and used to produce additional modified hmw bacteriocins of the disclosure. Bacteriophage P2, which infects many E. coli strains, has a tail fiber encoding gene H, (SEQ ID NO:25) that has significant sequence similarity to R2 prf15 (SEQ ID NO:3), particularly at the N-terminus-encoding portion. The portion of gene H encoding the C-terminal 551 amino acid residues of the P2 tail fiber protein, which is the putative region conferring target specificity (RBD), was fused to the portion of prf15 encoding the 164 amino acid N-terminal baseplate-binding (BPAR) portion of R2 PRF15 to encode a modified tail fiber protein (SEQ ID NO:27).
Bacteriophage P2 also encodes a putative tail fiber chaperone, encoded by gene G (SEQ ID NO:26), similar to that encoded by R2 pyocin prf16 (SEQ ID NO:4), and the chaperones of many of the other myoviridae phages. Because it is likely that the gene G encoded chaperone is important for folding the C-terminal portion of the P2 tail fiber protein in the fusion, constructs were made to co-express P2 gene G.
The portion of R2 prf15 encoding amino acids 1-164 was amplified from a subclone using primers AV118 and AV127 (5′-TTCTTTAAGCTTTTCCTTCACCCAGTCCTG) (SEQ ID NO:56) and was digested with BspHI and HindIII. The protion of P2 gene H encoding amino acids from position 158-669 was amplified from a P2 phage stock (Richard Calendar) using primers AV124 (5′-CCTCCTGAATTCTTATTGCGGCATTTCCG) (SEQ ID NO:57) and AV126 (5′-TCCTTCGAATTCTTACACCTGCGCAACGT) (SEQ ID NO:58). P2 gene H 158-669 plus gene G was amplified using primers AV124 and AV125 (5′-CCTCCTGAATTCTTATTGCGGCATTTCCG) (SEQ ID NO: 59). Each of the PCR products from P2 were digested with HindIII and EcoRI. pUCP-tac-R2-P2H was created by cloning the prf15 fragment encoding the 1-164 amino acid fragment together with the P2 gene H fragment encoding the 158-669 amino acid fragment into pUCP-tac digested with BspHI and EcoRI. pUCP-tac-R2-P2HG was generated by cloning the prf15 fragment encoding the 1-164 amino acid fragment together with the P2 gene H fragment encoding the 158-669 amino acid fragment plus gene G into pUCP-tac digested with BspHI and EcoRI.
Briefly, PA01Δprf15 was transformed with the prf15-P2 gene H fusion constructs and pyocin production was induced with mitomycin C. Pyocin particles were purified and tested for activity by spot tests and by the bacterial survival assay (see FIG. 2). The purified pyocin particles containing the R2-P2 fusion tail fiber had bactericidal activity against E. coli strain C1a but were incapable of killing P. aeruginosa strain 13s. Furthermore, the expression of P2 gene G was needed to produce active pyocin. This supports the hypothesis that the chaperone is required for proper folding of the C-terminal portion of the tail fiber, as shown in FIG. 8.
The abilities of a range of different R2-P2 tail fiber protein fusions to form functional pyocins that kill E. coli C1a were explored by a series of different R2-P2 fusions. Representative examples of these fusions are shown in FIGS. 4-7, along with the indication of their resulting bactericidal activities against E. coli C1a.
d) Additional Fusion Proteins as Functional Tail Fibers on Pyocins: R2-L-413c,
An additional modified hmw bacteriocin has been produced to target Y. pestis. L-413c is a yersiniophage that infects most strains of Y. pestis (Richard Calendar, personal communication). Most of the L-413c genome is highly similar to P2 with the notable exception of its tail fiber gene H, SEQ ID NO:28, which has diverged considerably from that of P2. Without being bound by theory, and offered to improve the understanding of the disclosure, variation in the tail fiber gene H, and thus the encoded protein, is the feature that most likely accounts for its differing host range.
The N-terminus of L-413c gene H (SEQ ID NO:28), however, shares considerably sequence similarity to its P2 counterpart (SEQ ID NO:25), likely due to its function of baseplate binding. A fusion was constructed to create a fusion tail fiber with the N-terminal 1-164 amino acids from R2 PRF15 fused to the C terminal (positions 158-913) portion of the L-413c tail fiber to create a modified tail fiber, as shown in FIG. 10 (SEQ ID NO:30). The fusion was expressed in PAO1Δprf15 along with the L-413c tail fiber cognate chaperone, gene G (SEQ ID NO:29), as described above. After induction, the produced pyocin particles killed Y. pestis KIM as well as E. coli C and thus had a killing spectrum analogous to the host range of yersiniophage L-413c. The modified pyocins did not kill any of the tested Pseudomonas strains.
e) Additional Fusion Proteins as Tail Fibers on Pyocins: R2-VHML
A further modified hmw pyocin particle has been made with a novel fusion tail fiber created between the P. aeruginosa R2 pyocin tail fiber BPAR (encoded by prf15) and one of the two tail fiber genes (SEQ ID NO:21 AND 22) of Vibrio harveyi Myovirus-Like (VHML) bacteriophage. We fused the diversifiable portion of the tail fiber (Oakey and Owens, 2000; Oakey et al., 2002; Doulatov et al. 2004) to the R2 pyocin tail fiber. The orf35 gene [SEQ ID NO:22] and that of its presumed cognate chaperone, orf38 [SEQ ID NO:23], were synthesized based on new DNA sequence data obtained from Dr. Oakey's VHML phage provided to the Australian National Genome Center in Brisbane. A series of fusions was generated between R2 prf15 and the orf35 gene, and the fusions were co-expressed with orf38 in PA01Δprf15. For example, the fusion between BPAR R2 1-164 and VHML Orf35 26-410 formed robust R-type pyocin particles that could be purified and revealed the R-type pyocin proteins including fusion tail fibers of the expected size when analyzed by SDS PAGE.
Data generated in our laboratory has shown that with one exception, the only chimeric R-type pyocin tail fiber structures forming R-type pyocin particles that can be purified and reveal appropriate proteins on SDS PAGE were those that exhibit bactericidal activity on the expected target bacteria. The one exception has been this one chimeric R2 prf15-VHML orf35 fusion. This chimeric R-type pyocin preparation was not bactericidal for any of the Vibrio species tested, but the strain of V. harveyi from which the lysogenic VHML bacteriophage was isolated for DNA sequencing cannot be imported to the U.S. because of its pathogenicity to crustacean and oysters. We conclude that we have generated an “orphan” chimeric R2 prf15-VHML orf35 pyocin and that the resulting modified hmw bacteriocin with the VHML-derived RBD can be subjected to diversification by the natural DGR of VHML.
f) Additional Fusion Proteins as Functional Tail Fibers on Pyocins: R2-V10
Bacteriophage phiV10 belongs to the podoviridae group and can infect most common E. coli O157:H7 strains (Waddell and Poppe, 2000; Genbank NC—007804). Phage phiV10 does not encode a tail fiber like that of phage P2 or R-type pyocins but instead encodes a tail spike-like protein similar to that of bacteriophages P22 and epsilon15. These tail spikes are globular proteins that typically are polysaccharide-specific and degrade the surface polysaccharide structures to which they bind. It is likely that the phiV10 tail spike specifically recognizes, binds to and degrades the O157 antigen on the surface of the pathogenic E. coli O157:H7.
We deployed as RBD various C-terminal portions, such as aa 204-875, 211-875, and 217-875, of the phiV10 tail spike protein (SEQ ID NO.:60) by genetically fusing them individually to N-terminal BPAR encoding portions, such as aa 1-161 and 1-164, of the R2 pyocin tail fiber. When three of these recombinant fusion genes (R2 Prf15 1-164:V10 tail spike 204-875[SEQ ID NO.: 67]; R2 Prf15 1-164:V10 tail spike 217-875 [SEQ ID NO.: 68]; and R2 Prf15 1-161:V10 tail spike 211-875 [SEQ ID NO.: 69]) were expressed individually in the appropriate Pseudomonas strain (PAO1Δprf15), those pyocin particles produced and released had incorporated into their structure functional R2-V10 tail fusions. These chimeric pyocin particles had bactericidal activity against all eight E. coli O157:H7 strains in our laboratory but did not kill any other E. coli strains, including mutants of EDL933 that have a defective O157 antigen. Furthermore, the chimeric R2-V10 pyocin digested the O157 antigen as evidenced by SDS PAGE of LPS extracted from E. coli EDL933. We have therefore created a recombinant R-type pyocin that specifically recognized and digested the O157 antigen, a known virulence factor of E. coli O157:H7, and killed specifically E. coli O157:H7 strains.
To determine whether mutants resistant to R2-V10 pyocin that might emerge from E. coli O157:H7 treated with R2-V10 pyocin would loose their O157 virulence factor, we selected, with and without prior chemical mutagenesis, EDL933 E. coli mutants resistant to R2-V10 pyocins. The LPS structures of seven independent mutants were analyzed by SDS PAGE to determine whether they had altered O-antigen structures. Each of the seven had different qualitatively or profoundly quantitatively altered O157 antigens demonstrating that resistance to R2-V10 did result in loss of the virulence factor, O157, from the E. coli O157:H7 pathogen.
When modeling the phiV10 tail spike protein with the Quickfire software (Imperial College, London), which utilizes a suite of protein structure analysis programs, we found that it predicted in the C-terminal 422 amino acids [SEQ ID NO: 60] structural homology with a galacturonase [SEQ ID NO: 66]. This explained the ability of portions of the V10 tail spike when fused to the N-terminal portion of pyocin Prf15 [such as SEQ ID NO:67, 68, 69] to enable the recombinant R-type pyocin to kill E. coli O157 by binding to the O157 antigen, which contained alpha-D-Gal2NAc, but not to kill the TEA026 mutant known to lack alpha-D-Gal2NAc in its O-antigen or the other 7 classes of EDL933 mutants described above. Quickfire also showed that the phiV10 tail spike has structural homology to the endorhamnosidase of phage P22 tail spike [SEQ ID NO: 70], a phage tail protein known to bind and degrade the Salmonella O-antigen. Thus, the fusion of protein with such a catalytic function to the N-terminal BPAR of the tail fiber of an R-type pyocin conveyed to the recombinant R-type pyocin the ability to utilize the enzyme's substrate binding property to target and kill bacteria expressing the enzyme's substrate on its surface.
Thus, R-type pyocins have been engineered to have different specificities using tail proteins from phages with tail structures naturally dissimilar to R-type pyocins, thus creating unnatural R-type pyocins.
g) Additional fusion proteins as functional tail fibers on pyocins: R2-PS17 Pseudomonas aeruginosa phage PS17 was obtained from the Félix d'Hérelle Reference Center for Bacterial Viruses, Universtie Laval, Canada. PS17 plaques were produced by infection of Pseudomonas aeruginosa strain PML14. PML14 cells lysogenic for phage PS17 were isolated by streaking cells from a plaque onto fresh tryptic soy agar plates. Lysogeny was verified by colony PCR amplification with primers AV168 and AV167, which were designed from Genbank sequence BPSFIFII. An overnight culture of the lysogenic cells was diluted 1:100 in 200 ml tryptic soy broth and shaken (225 rpm) at 37° C. until the optical density at 600 nm was approximately 0.2. Mitomycin C was added to a final concentration of μg/ml, and the culture was shaken a further 5 hours, at which time lysis was apparent. Deoxyribonuclease (Invitrogen, 1 unit/40 ml) was added, and the lysate was incubated at 37° C. for 30 minutes to reduce viscosity. The debris was then removed by centrifugation at 12,000 rpm for 30 minutes in a Beckman JA-25.50 rotor. The lysate was titered on strain PML14 and determined to be approximately 8×109 pfu/ml. Phage DNA was isolated from 40 ml of the cleared lysate using a Qiagen Lambda miniprep kit, following the manufacturer's instructions and using 3 columns from the kit. The DNA was resuspended in a total of 40 μl.







Primer sequences (listed 5' to 3'):


AV168


(SEQ ID NO: 72)


TCACGGTAACGAATGTGGACG


 


AV167


(SEQ ID NO: 73)


TTTCAGCCAGTTGGTCGACAC


 


AV140


(SEQ ID NO: 74)


CCTGACGGATGGCCTTTTCTATTATCACTGCCCGCTTTCCAGTCG


 


AV141


(SEQ ID NO: 75)


TTTCTTTGCTCTTCCGCTAGAAGGCCATCCTGACGGATGGCCTTTTCT


 


AV027


(SEQ ID NO: 76)


TTTCTGCTCTTCAAGCCGACACCATCGAATGGTGCA


 


AV169


(SEQ ID NO: 77)


TTTATTAGCGGAAGAGCCACGCGTGACTGCACGGTGCACCAATG


 


AV114


(SEQ ID NO: 78)


CCCTCGAATTCATGAATACTGTTTCCTGTGTGAAATTG


 


AV238


(SEQ ID NO: 79)


AACCCACGAAGACCTCATGAGCACCAATCAATACG


 


AV047


(SEQ ID NO: 80)


CGCCAGGGTTTTCCCAGTCACGAC


 


PRF13-F


(SEQ ID NO: 81)


TATCGAGAACTGCTGCTGCGGG


 


AV086


(SEQ ID NO: 82)


TCCTTGAATTCCGCTTGCTGCCGAAGTTCTT


 


AV118


(SEQ ID NO: 83)


CTTCCTTTCATGACGACCAATACTCCGAA


 


AV287


(SEQ ID NO: 84)


TCGGTAATGCCGTACCCGCCCAGGGTGGTCGGATTGCTGC


 


AV286


(SEQ ID NO: 85)


GCAGCAATCCGACCACCCTGGGCGGGTACGGCATTACCGA


 


AV293


(SEQ ID NO: 86)


AAACCAAGAGCTCTTAGTTGGTGCCTTCTTCGGC






Based on the restriction map in Shinomiya and Ina (1989), we cloned and sequenced a  ̃4.2 kb BglII fragment. A 1 μl sample of PS17 phage DNA was digested with BglII then electrophoresed in an agarose gel. The appropriate fragment was excised from the gel, purified, and ligated together with pUC 19 vector DNA digested with BamHI. Competent E. coli cells were transformed with the ligation products and transformants were selected on LB agar plates containing 100 μg/ml carbenicillin. Plasmid minipreps were prepared and used for DNA sequence analysis. Two overlapping open reading frames (SEQ. ID. NO.: 71) were found with significant homology to various tail fiber genes and chaperones. In plasmid pUC19-PS-B3, there were approximately 53 by between the termination codon of the presumed chaperone open reading frame and the Sad restriction enzyme recognition site derived from the vector polylinker.
pUCP30T was digested with BspHI, the ends were made blunt by treatment with the Klenow fragment of DNA polymerase I in the presence of dNTPs, and the vector was religated to form pSW107, which lacked a BspHI site.
A lacIq gene and a rrnBT2 terminator sequence were amplified by a two-step PCR using a suitable plasmid vector containing lacIq, such as pMAL-c2E, as template and primers AV140 and AV027 in the first step and primers AV141 and AV27 in the second step. The PCR product was digested with SapI and ligated together with SapI-digested pSW107 to form plasmid pDG19.
A tac promoter was amplified by PCR using a suitable plasmid vector pGEX-2T as template and primers AV169 and AV114. The PCR product was digested with SapI and EcoRI and ligated together with SapI- and EcoRI-digested pDG19 to form plasmid pDG35.
The presumed tail fiber and chaperone open reading frames were amplified by PCR from plasmid pUC19-PS-B3 using primers AV238 and AV047. The PCR product was digested with BspHI and SacI and ligated together with BspHI- and SacI-digested pDG35 to form pDG65.
A DNA fragment containing R2 prf15 and prf16 was amplified by PCR from PAO1 genomic DNA using the primers PRF13-F and AV086. The PCR product was cloned using a “Zero Blunt TOPO PCR Cloning Kit for Sequencing” from Invitrogen. The resulting clone was designated pTOPO-R2.
A fragment of the R2 prf15 open reading frame representing codons 1-223 was amplified by PCR using pTOPO-R2 as template and primers AV118 and AV287. A fragment of PS17 presumed tail fiber open reading frame representing the C-terminal portion from codon 220 through the termination codon after codon 779 plus the presumed chaperone open reading frame was amplified by PCR using pUC19-PS-B3 as template and primers AV286 and AV293. The resulting PCR products contained 20 by overlapping sequences. The two fragments were assembled by overlap PCR using primers AV118 and AV293. The resulting fragment was digested with BspHI and SacI and ligated together with BspHI- and SacI-digested pDG35 to form plasmid pSW122.
PS17 plaques normally have a turbid “bulls-eye” appearance on a lawn of sensitive cells. PS17 phages were plated on strain PML14, and a few rare plaques with a clear appearance were picked. The clear-plaque phage were purified by replating and picking isolated plaques with a clear appearance. An isolate designated PS17-c5 was chosen for further use.
P. aeruginosa strain PA01 was deleted of nucleotides 10-2067 of its prf15 coding sequence (SEQ. ID. NO.: 3) by a method analogous to that described to create PAO1Δprf15 in Example 1 to create PAO1-mΔprf15. A 50 ml culture of PAO1-mΔprf15 in tryptic soy broth was shaken at 37° C. until the optical density at 600 nm was approximately 0.2. One plaque of PS17-c5 was transferred from a plate to the liquid culture. After an additional 3 hours shaking at 37° C. the optical density at 600 nm dropped, and lysis was apparent. The culture was then left to shake overnight (16 hours). Following the overnight incubation, the culture had become turbid again. A sample of the culture was inoculated onto a tryptic soy agar plate and incubated overnight. Colonies were checked for PS17 lysogeny by colony PCR with primers AV168 and AV167 and appeared negative. A clonal isolate designated PAO1-mΔprf15-c5R was chosen for further use as a host production bacterium for R2-PS17 modified pyocins. Cells were made electrocompetent by a method similar to that described by Choi and Schweizer (2005) and transformed with pDG65 and pSW122. Transformants were selected and maintained with 100 μg/ml gentamicin.
For expression of R2-PS17 pyocins, overnight cultures of PAO1-mΔprf15-c5R in tryptic soy broth supplemented with 100 μg/ml gentamicin were diluted 1:100 into G medium (Shinomiya, 1972) containing 50 μg/ml gentamicin. The cultures were incubated at 37° C. with shaking (225 rpm) until the optical density at 600 nm was approximately 0.2. Mitomycin C was then added to a final concentration of 3 μg/ml, and the cultures were shaken at 37° C. 3-4 hours. Optionally, deoxyribonuclease was added at 1 unit per 40 ml, and the lysate was incubated at 37° C. for 15-30 minutes to decrease viscosity. Debris was removed by centrifugation at 12,000 rpm in a Beckman JA-25.50 rotor for 30 minutes at 4° C. The supernatant was transferred to a fresh centrifuge tube, and pyocins were pelleted at 22,000 rpm (approximately 58,500×g) for 1 hour at 4° C. The pellets were resuspended at 3% of the original volume in 10 mM Tris-HCl pH 7.5, 50 mM NaCl and stored at 4° C.
The bactericidal activity of the recombinant “R2-PS17” pyocin preparations were demonstrated by spotting dilutions on PS 17-sensitive Pseudomonas aeruginosa strains such as PML14.
h) Additional Fusion Proteins as Functional Tail Fibers on Pyocins: R2-MTD
The major tropism determinant (MTD) of the Bordetella bacteriophage BPP-1 has a C-type lectin (CTL) domain, which serves as a binding determinant for many different types of molecules and in many different biological contexts (Drickamer, 1999; McMahon et al., 2005). In BPP-1, MTD is incorporated as a homotrimeric globular domain located at the end of the phage tail, where it can bind to the surface protein pertactin, a virulence factor expressed on the outer surface of Bordetella bronchiseptica and Bordetella pertussis (Liu et al., 2004). In this context, MTD is also the target of phage-mediated homing mutagenesis, which can result in the bacteriophage acquiring a novel binding determinant for infecting its ever changing host.
Recent structural studies on the MTD domain and several of its diversified variants, have shown how the trimeric fiber tip forms a rigid scaffold that can contain more than 10 trillion variant binding ligands (McMahon et al. 2005). Fusing the MTD domain onto the pyocin tail fiber protein and then diversifying the MTD domain using the DGR system described by Miller and colleagues (Liu et al., 2004; Doulatov et al., 2004), creates a very large library of variants, from which to select and obtain the genes encoding pyocin tails with altered binding specificity.
Example 2
Assays of Fusion Proteins
a) Pyocin Purification and Assays
PAO1 or appropriate derivatives were grown shaking at 200 rpm at 37° C. in G medium supplemented with 50 μg/ml gentamicin when needed to maintain plasmids. When the cultures reached OD600 of about 0.250, mitomycin C was added to a final concentration of 3 μg/ml. Cultures were incubated for an addition 2.5 hours until lysis occurred. Five units (1 unit/μl) of DNase1 (Invitrogen) was added to 200 ml of culture, and the culture was allowed to incubate an additional 30 mins. Debris was removed by centrifugation at 12,000 rpm in a Beckman JLA-16.250 rotor for 1 hour. Saturated ammonium sulfate was slowly added, at a rate of 1 ml/min, to the supernatant stirring on ice, to a final added volume of 65 ml per 100 ml of the supernatant of the lysate. This was stored at 4° C. overnight. The ammonium sulfate precipitate was collected by centrifugation at 12,000 rpm in a Beckman JA-25.50 rotor for 1 hour, 4° C., and the pellet was resuspended in 10 ml of TN50 buffer (10 mM tris, 50 mM NaCl, pH 7.5). Pyocin particles in the resuspended solution were then sedimented at 22,000 rpm (58,500×g) in a Beckman JA-25.50 rotor for 1 hour, 4° C., and resuspended in 3-5 ml of TN50 buffer. Pyocin preps were judged to be >90% pure by SDS polyacrylamide gel electrophoretic analysis.
Quantitative pyocin assays were performed by counting bacterial survival in a slightly modified method as described by Kagayama et al., 1964. Pyocin samples were incubated with target bacteria (approximately 1×109 CFU/ml) for 40 minutes at 37° C. The samples were then diluted and plated to count survivors. The number of pyocin particles is related to the fraction of bacterial survivors in a Poisson distribution, m=−1 nS, where m=the average number of lethal events/cell and S is the fraction of survivors. The total number of active pyocin particles/ml=m×cells/ml. Strain13s was the Pseudomonas aeruginosa used in these assays and is a clinical isolate resistant to many anitibiotics, but sensitive to all 5 R-type pyocins. The E. coli target was C1a, kindly provided by Richard Calendar.
Semi-quantitative assays were also performed by a spot method where pyocin samples were serially diluted in TN50 buffer and spotted on lawns of target bacteria. After overnight incubation at 37° C., pyocin activity could be observed by a clear zone of killing on the lawn. FIG. 2 shows representative results from this assay format.
Example 3
Recombinant Bacteriophages to Screen Engineered Tail Fibers
The P4 bacteriophage was used as a surrogate to harbor a tail fiber fusion gene such that the genotype was coupled to the binding phenotype of the tail fiber. This has allowed efficient selection, transduction and isolation of the gene for the desired tail fiber.
Bacteriophage P2 is a temperate coliphage which can infect other enteric species, and can replicate in, but not infect, P. aeruginosa (Bertani & Six, 1988; Kahn et al., 1991). R-type pyocins are closely related genetically and structurally to P2, and the P2 tail fiber protein, encoded by gene H, shows homology to PRF15 at the N-terminal portion, where base plate attachment occurs (Haggard-Ljungquist et al., 1992; Nakayama et al., 2000). Deploying the P2 or P4 bacteriophage as a surrogate phage, in which plasmid-encoded tail fibers were incorporated in the phage particle in place of the P2 phage-encoded fibers, permitted the display and selection of fusion fibers in a context that closely resembled its intended functional context in the pyocin.
The tail fiber genotype was physically coupled to the binding phenotype in a transducing phage particle for genetic selection, similar to phage display technology. When a P2 phage with an amber mutation in its fiber protein gene H (made in an amber suppressor+E. coli) infected E. coli harboring a P4-based plasmid with a cos packaging site, which normally acts as a signal for packaging bacteriophage genomic DNA (Ziermann & Calendar, 1991; Kahn et al., 1991), it packaged the cos-containing P4 plasmid in the heads of newly synthesized P2/P4 phage particles. The P4-based plasmid, FIG. 12, encoded and expressed the tail fusion gene. The fusion tail fibers expressed from the P4 plasmid in the P2 infected E. coli were incorporated into the P2/P4 particles in place of the defective (amber truncated) gene H product (P2 tail fiber protein). Upon lysis of the infected bacteria by the expression of the P2 holin and lysozyme, the released P2/P4-based transducing particles carried the cos-containing P4 plasmid encoding the tail fiber fusion gene rather than the P2 genome and had attached the recombinant fusion tail fibers rather than the amber truncated P2 tail fibers.
Specifically, plasmid pSW166 was constructed by replacing the region corresponding to bases 226-2594 of bacteriophage P4sid1 (Shore et al. 1977) with the 763 by fragment consisting of the promoter and coding region of aacC1 (gentamicin acetyltransferase 3-1) from plasmid pUCP30T (Schweizer, 2001; NCBI accession U33752) flanked by restriction sites introduced by PCR amplification (MfeI and KpnI next to the promoter and EcoRI next to the termination codon), cloned in the same orientation as the P4 int gene.
Plasmid pDG211 was constructed by inserting between the MfeI and KpnI sites a 274 by fragment derived by PCR amplification and consisting of a P4 PLE promoter (Dello et al., 1988) corresponding to bases 8585-8835 (complementary strand) such that the promoter was in the same polarity as aacC1 and NheI and NcoI sites were created between the KpnI site and the PLE promoter.
DNA fragments derived by PCR amplification encoding amino acids 1-157 of the P2 gene H tail fiber gene and amino acids 218-875 of the phiV10 tail spike gene were inserted between the NcoI and KpnI sites of pDG211 to create pDG218, FIG. 12.
A 1 ml culture of E. coli C1a harboring plasmid pDG218 was grown to OD600 of 1.0, supplemented with 1 mM CaCl2 and infected with P2amH72vir20 (Sunshine et al., 1971) at a multiplicity of infection of approximately 2. After a 10 minute pre-adsorption, the cells were shaken at 225 rpm at 37° C. for 50 minutes. The bacteria and debris were removed by centrifugation in a microcentrifuge for 1 minute, and the lysate supernatant was saved.
Cultures (200 μl) of each E. coli TEA026 and E. coli EDL933 (Ho and Waldor, 2007) target cells were supplemented with 2.5 mM CaCl2 and 2.5 mM MgCl2. Supernatant (50 μl) from the lysate (previous step) was added and preadsorbed for 10 minutes. The cells were then diluted with 700 μl broth and shaken at 225 rpm at 37° C. for 1 hour. Aliquots (10 μl) of each cell suspension was plated on LB agar plates containing 15 μg gentamicin/ml. The plates were then incubated overnight at 37° C. While an estimated 1000 colonies grew on the EDL933 plate, none grew on the TEA026 plate.
A control P4-based, negative control plasmid, pDG212, which was constructed to contain the complete, unfused P2 gene H tail fiber gene rather than the P2-V10 fusion gene as in pDG218 (FIG. 14), was similarly packaged from E. coli C1a after infection with P2amH72vir20. When 10 μl of the control lysate was incubated with E. coli C1a on gentamicin-containing plates, more than 10,000 colonies grew but none appeared when the same control lysate was incubated with EDL933 on gentamicin containing plates. Thus, the false positive frequency for generating gentamicin-resistant colonies of EDL933 from transfection with P4 particles that do not harbor the O157-specific binding property is less than 10−4. When co-infected with P2 amberH, P4 particles are produced that can infect O157 strains and not C1a. It is important to note that unlike the PS17 system, phiV10 and its tail spike are completely unrelated genetically and structurally to P2. This indicates that a broad range of different phage types can be exploited by this system, further expanding the breadth of our applications.
Transducing phage particles with the ability to bind cells and trigger the bacteriophage injection mechanism conferred gentamicin resistance to successfully targeted bacteria, from which the selected fiber fusion gene was isolated from the plasmid after replication of the bacteria under gentamicin selection. The functional V 10-based RBD gene isolated by PCR was fused to the BPAR (aa 1-164) of R2 prf15, expressed in trans in PA01Δprf15 and recombinant pyocins isolated and assayed for bactericidal activity on E. coli TEA026 and E. coli EDL933. As described for the P2/P4 particle, the RBD from V10 tail spike protein when fused to BPAR from R2 pyocin PRF15, conveyed specificity to the resulting modified pyocin such that it was bactericidal for EDL933 but not for the mutant TEA026, lacking the O157 antigen. The tail fiber gene on the P4 plasmid is easily further manipulated to create many fusion junctions and to diversify the RBD in order to redesign and optimize the function of the modified tail fiber RBD.
A related P4 virion particle was made to carry recombinant tail fibers generated by fusing an BPAR portion of P2 gene H encoding aa 1-158 to the portion of the tail fiber gene of Pseudomonas phage, PS17, encoding an RBD of aa 164-779. The gene H-PS17 tail fiber fusion gene was co-expressed with the latter's cognate chaperone from a P4-based plasmid, pDG224, similar to pDG218. Once harvested from the lysate of a P2amH72vir20 infected E. coli C1a harboring pDG224, the P4 particles conveyed by transformation gentamicin resistance to P. aeruginosa strain PML14 but not to P. aeruginosa strain PA14. PS17 phage also infected the former but not the latter P. aeruginosa strain. Thus, the P4-based surrogate system has provided selection methods to couple recombinant genotype to recombinant tail fiber binding phenotype even across genera of bacteria.
This approach also overcomes many of the difficulties imposed by C-terminal display of a trimeric protein when using conventional phage display systems (Held & Sidhu, 2004). Bacteriophage P2 has tail fibers that genetically and morphologically resemble those of pyocins (Nakayama et al., 2000). Tail fibers attach to the base plates of P2 and pyocins via their N-termini, and there is significant sequence similarity of the N-termini of P2 and R2 pyocin tail fibers (Nakayama et al, 2000; Haggard-Ljungquist et al., 1992). Furthermore, the tail fiber gene of the P2-related phage, PS17, can complement the R2 pyocin tail fiber gene, prf15 (Shinomiya, 1984; Shinomiya & Ina, 1989).
Alternatively, portions of the tail fiber gene orf35 of VHML phage of Vibrio harveyii (which like BPP-1 also contains a functioning DGR) is fused to the N-terminal domain of P2 gene H. This recombinant construction will then allow the P4-based selection of RBDs of particular interest, as described above, after the DGR-driven diversification of the VHML VR embedded in the orf35 RBD.
Example 4
Methods to Recover the Desired Tail Fiber Gene
A P2 or P4 bacteriophage carrying an engineered tail fiber gene acted as a surrogate to couple pyocin tail fiber genotype to binding phenotype. By selecting or screening for specific binding phenotypes from the diversified or mutagenized libraries of the tail fiber genes harbored in such surrogate bacteriophages, one can isolate the tail fiber genes that encode a desired binding specificity. The selection may be carried out by single or multiple enrichment cycles of adsorbing the surrogate bacteriophages or transducing particles onto solid-phase target molecules, either by first removing undesired binders and then isolating, from among the remaining surrogates, those that bind to the intended target molecules, or visa versa. Alternatively, the selection may occur by applying either binding step alone. Ultimately, the surrogate exhibiting the desired binding phenotype can be subject to DNA extraction and isolation of the harbored tail fiber gene by cloning restriction enzyme fragments or by PCR reactions using oligonucleotide primers that bind specific DNA sequences peripheral to the diversified portion of the tail fiber gene.
Even though the surrogate phages or transducing P4 particles will not form plaques on the target-expressing bacteria, the infected or transduced bacteria will still acquire antibiotic resistance, such as P4 plasmid-encoded gentamicin resistance, along with the harbored plasmid or phasmid and therefore can be selectively grown and subsequently extracted to isolate the multi-copy plasmid and its desired tail fiber gene.
These techniques permitted the identification and isolation of surrogate bacteriophages or transducing particles exhibiting the desired, specific binding phenotypes from which we extracted and isolated the desired, specific, unnatural hmw bacteriocin tail fiber genes. Furthermore, the binding of surrogates to mammalian molecules, cells or tissues can be deployed to deplete from the libraries any genes encoding tail fibers that might cause adverse events if incorporated into therapeutic hmw bacteriocins.
There is an available library of insertional mutant Pseudomonas aeruginosa bacterial strains differing from highly pathogenic parental PA14 Pseudomonas aeruginosa only by the lack of expression of a series of specific virulence factors, one missing from each non-redundant, isogenic mutant (see the website at ausubellab.mgh.harvard.edu/cgi-bin/pa14/home.cgi). These isogenic mutant strains provide tools for ensuring the specificity of the surrogate bacteriophages for the targeted virulence factors and not for other prevalent surface molecules. For example, the population of surrogate P4 bacteriophages can be incubated with a high density culture of a Pseudomonas aeruginosa mutant missing a particular targeted virulence factor in order to adsorb and deplete from a population of surrogate bacteriophages or transducing particles, those that bind to surface molecules present on both the isogenic mutant and the virulent parental strain. The depleted population will be enriched in surrogates binding to the desired virulence factor. Once surrogate bacteriophages that do bind to and infect the bacteria expressing the particular virulence or fitness factor are isolated, each can be screened directly for its inability to infect the isogenic mutant strain lacking the targeted factor. The selected plasmid can be repackaged in surrogate transducing particles and recycled any number of times through the adsorption-depletion and infection process to further enrich and eventually purify the pUC-based plasmid encoding the desired tail fibers for targeting the virulence or fitness factor.
A tail fiber gene, recombinant or natural, encoded in a recombinant P4 genome can be subject to mutagenesis, particularly in the portion of the RBD domain that confers specificity, by any one of several methods familiar to one ordinarily skilled in the art. The mutagenized P4 genomic plasmid is transformed at low multiplicity into E. coli C, and the gentamicin-resistant transformants are subsequently infected by phage P2 amber H (P2amH72vir20). As described above, a library of P4 virion particles will be packaged and produced and will have tail fibers with mutant RBD portions, the gene for which will be encoded specifically within the packaged recombinant P4 genome. Some of these mutations will encode binding capabilities specific for a given target receptor on a target bacteria. The P4 genome harboring the mutant RBD with the desired, and even rare, binding specificity can be selected by infecting the target bacterial strain with the virion library and isolating gentamicin-resistant bacterial colonies. The resistant bacteria will harbor P4 genomes that encode a mutant RBD portion that has acquired specificity for the target bacterial strain.
An example of selecting a rare desired binding phenotype and thereby genotype from a large population of undesired P4 particles was demonstrated by mixing different proportions of lysates of P4 particles from E. coli C1a harboring pDG212 (P2 tail fiber) and E. coli C1a harboring pDG218 (P2-V10 recombinant tail fiber). When the mixtures contained 0%, 1%, 99%, or 100% of the P4 particles with the P2-V10 tail fibers or the converse number of P4 particles with P2 tail fibers, the appropriate numbers of EDL933 or E. coli C1a transformed colonies grew on gentamicin containing agar plates. That is the P4 particles harvested from E. coli harboring pDG218 could only transfect and convey gentamicin-resistance to EDL933 bacteria; while those harvested from E. coli harboring pDG212 could only transfect and convey gentamicin-resistance to E. coli C1a bacteria. The frequency of false positive growth, that is formation of gentamicin-resistant colonies of E. coli EDL933 after attempted transformation with P4 from pDG212-harboring E. coli, was less than 10−5. The converse was also observed, that is formation of gentamicin-resistant colonies of E. coli C1a after attempted transformation with P4 from pDG218-harboring E. coli, was less than 10−5.
The DNA encoding mutant RBDs with desired binding phenotype can be isolated by the PCR method using primers within the gene H sequence 5′ to the RBD and sequences 3′ to the RBD but immediately outside the RBD coding region. The selected RBD DNA sequence will be fused with the BPAR portion of an R-type pyocin prf15 gene, such as that portion encoding aa 1-164, and expressed in trans in bacteria such as PA01Δprf15 or a production strain as described below to make recombinant R-type pyocins with a novel, desired binding and bactericidal specificity.
Example 5
Methods for Producing Engineered hmw Bacteriocins
The modified tail fiber gene is recombined either (i) into a plasmid under a regulated promoter for expression in production bacteria also harboring, for example on a bacterial artificial chromosome (BAC), the R-pyocin gene cluster (including the endolysin genes) from which the resident prtR, prtN, prf15 and holin (prf9 or PA0614) genes have been deleted or otherwise disabled, or (ii) into the pyocin cluster containing BAC vector itself, using a plasmid-mediated allelic exchange reaction.
a) Expression of R-type Pyocins in E. coli 
The R2 pyocin gene cluster was cloned in four different variations using five different cloned fragments derived from PCR products.
Fragment 1 was amplified by PCR from PA01 genomic DNA using primers AV461 and PRF13R, then digested with restriction enzymes EcoRI and HindIII. The resulting fragment represented bases 4267-7856 of Genbank sequence AB030825. Primer AV461 added an EcoRI site. This fragment lacked genes prt-R and prt-N.
Fragment 2 was amplified by PCR from PA01 genomic DNA using primers AV529 and PRF13R, then digested with restriction enzymes EcoRI and HindIII. The resulting fragment represented bases 2975-7856 of Genbank sequence AB030825. Primer AV529 added an EcoRI site. This fragment contained genes prt-R and prt-N.
Fragment 3 was amplified from PA01 genomic DNA using primers AV333 and AV334, then digested with HindIII and NheI. The resulting fragment represented bases 7856-14280 of Genbank sequence AB030825. This fragment contains a full-length prf15 gene.
Fragment 4 was amplified from PA01-rΔprf15 genomic DNA using primers AV333 and AV334, then digested with HindIII and NheI. The resulting fragment represented bases 7856-9155 and 10028-14280 of Genbank sequence AB030825. This fragment contained a prf15 gene with an 873 by internal deletion.
Fragment 5 was amplified from PA01 genomic DNA using primers AV407 and AV404, then digested with NheI and PacI. The resulting fragment represented bases 14,280-19,860 of Genbank sequence AB030825. Primer AV404 added a PacI site.
A fragment of pBR322 (comprising nucleotides 2334-4353 of Genbank sequence SYNPBR322) including the origin of replication and the β-lactamase gene was amplified using primers AV337 and AV338. The resulting fragment was digested with NotI, and a multiple cloning site was created by ligating the NotI-digested vector with kinased and annealed oligos AV339 and AV340. The resulting plasmid was designated pDG121.









PCR primer sequences:



PRF13-R



(SEQ ID NO: 87)



GCACCGTTACCCGATCCGCGA



 



av333



(SEQ ID NO: 88)



TCGAGACGATTTACCAAGAGCTG



 



av334



(SEQ ID NO: 89)



TTCCACGACCAGTCCGGAAAATG



 



av337



(SEQ ID NO: 90)



TTTATTTGCGGCCGCGACGAAAGGGCCTCGTGATAC



 



av338



(SEQ ID NO: 91)



TTTATTTGCGGCCGCAAATACCGCATCAGGCGCTCTTC



 



av339



(SEQ ID NO: 92)



GGCCGCTTATTAACAAGCTTCACACACGCTAGCCCACCACGC



 



av340



(SEQ ID NO: 93)



GGCCGCGTGGTGGGCTAGCGTGTGTGAAGCTTGTTAATAAGC



 



av404



(SEQ ID NO: 94)



CCCCCCCTTAATTAACTTGAGTCAGGATGGACATG



 



av407



(SEQ ID NO: 95)



AAGGCATTCGAGACCGTCAAG



 



av461



(SEQ ID NO: 96)



TTTCCTTGAATTCGCTCGGCAATCTACAGACCGATG



 



AV529



(SEQ ID NO: 97)



TTTCCCTGAATTCATTACTTGCCCACGCAGAAGGCGCTTTC 






The plasmid pDG173 contained fragments 1, 3 and 5, inserted respectively between the EcoRI and PacI sites of pDG121.
The plasmid pDG174 contained fragments 2, 3 and 5, inserted respectively between the EcoRI and PacI sites of pDG121.
The plasmid pDG175 contained fragments 1, 4 and 5, inserted respectively between the EcoRI and PacI sites of pDG121.
The plasmid pDG176 contained fragments 2, 3 and 5, inserted respectively between the EcoRI and PacI sites of pDG121.
Chemically competent cells of E. coli strain BL21 (non-λDE3 lysogen; Novagen Cat. No. 69449-3) were transformed with plasmids pDG173, pDG174, pDG175 or pDG176. The retention of the plasmids was selected and maintained with 50 μg/ml carbenicillin.
For expression of pyocins, overnight cultures of strain BL21 in LB broth supplemented with 50 μg/ml carbenicillin were diluted 1:100 into G medium (Shinomiya, 1972) containing 25 μg/ml carbenicillin. The cultures were incubated at 37° C. with shaking (225 rpm) until the optical density at 600 nm was approximately 0.2. Mitomycin C was then added to a final concentration of 33.3 ng/ml, and the cultures were shaken at 37° C. overnight (15-22 hours). The cultures still appeared turbid. Cells and debris were removed by centrifugation at 12,000 rpm (approximately 17,400×g) in a Beckman JA-25.50 rotor for 30 minutes at 4° C. The supernatant was transferred to a fresh centrifuge tube, and pyocins were pelleted at 22,000 rpm (approximately 58,500×g) for 1 hour at 4° C. The pellets were resuspended at 3% of the original volume in 10 mM Tris-HCl pH 7.5, 50 mM NaCl and stored at 4° C. The bactericidal activity of each preparation was assayed on strain 13s of P. aeruginosa. 10 μl of each sample was electrophoresed on a 4-20% polyacrylamide tris-glycine SDS gel (SDS-PAGE) alongside molecular weight standards. The preparations from the E. coli transformants containing pDG173 and pDG174 exhibited potent bactericidal activities and clear R-type pyocin protein subunits on SDS-PAGE analyses. The preparations from the E. coli transformants containing pDG175 and pDG176 did not exhibit bactericidal activity and did not demonstrate substantive R-type pyocin protein subunits on SDS-PAGE analyses, all as predicted.
b) Expression of R-Type Pyocins in Pseudomonas fluorescens 
Kinased and annealed oligos AV530 and AV531 were ligated into EcoRI- and HindIII-digested broad-host range plasmid vector pUCP30T (Genbank XXU33752). The resulting plasmid was designated pDG171.







Primer sequences:


AV530


(SEQ ID NO: 98)


AGCTgcggccgcGAATTCacgcgtAAGCTTactagtGCTAGCTTAATTAA


 


AV531


(SEQ ID NO: 99)


aattTTAATTAAGCTAGCactagtAAGCTTacgcgtGAATTCgcggccgc






The  ̃15.6 kb EcoRI-PacI fragment from pDG173 was ligated into EcoRI- and PacI-digested pDG171 to create pDG193.
The  ̃16.9 kb EcoRI-PacI fragment from pDG174 was ligated into EcoRI- and PacI-digested pDG171 to create pDG194.
The  ̃14.7 kb EcoRI-PacI fragment from pDG175 was ligated into EcoRI- and PacI-digested pDG171 to create pDG195.
The  ̃16.0 kb EcoRI-PacI fragment from pDG176 was ligated into EcoRI- and PacI-digested pDG171 to create pDG196.
Pseudomonas fluorescens (ATCC Cat. No. 13525) were made electrocompetent by a method similar to that described by Choi and Schweizer (2005), and transformed with pDG193, pDG194, pDG195 or pDG196. Transformants were selected and maintained with 100 μg/ml gentamicin.
For expression of pyocins, overnight cultures in tryptic soy broth supplemented with 100 μg/ml gentamicin were diluted 1:100 into G medium (Shinomiya, 1972) containing 50 μg/ml gentamicin. The cultures were incubated at 37° C. with shaking (225 rpm) until the optical density at 600 nm was approximately 0.2. Mitomycin C was then added to a final concentration of 3 μg/ml, and the cultures were shaken at 37° C. 3-4 hours. Debris was removed by centrifugation at 12,000 rpm (approximately 17,400×g) in a Beckman JA-25.50 rotor for 30 minutes at 4° C. The supernatant was transferred to a fresh centrifuge tube, and pyocins were pelleted at 22,000 rpm (approximately 58,500×g) for 1 hour at 4° C. The pellets were resuspended at 3% of the original volume in 50 mM NaCl, 10 mM Tris-HCl, pH 7.5 and stored at 4° C. The bactericidal activity of each preparation was assayed on strain 13s of P. aeruginosa. 10 μl of each sample was electrophoresed on a 4-20% polyacrylamide tris-glycine SDS gel (SDS-PAGE) alongside molecular weight standards. The preparations from the E. coli transformants containing pDG193 and pDG194 exhibited potent bactericidal activities and clear R-type pyocin protein subunits on SDS-PAGE analyses. The preparations from the E. coli transformants containing pDG195 and pDG196 did not exhibit bactericidal activity and did not demonstrate substantive R-type pyocin protein subunits on SDS-PAGE analyses, all as predicted.
Upon induction of the pyocin genes and the engineered tail fiber gene, such as by inducing prtN directly via an engineered regulatable promoter such as lac or tac, the host cells synthesize pyocins until their nutrients are depleted and they cease growing (Young, Ry, 2006). The producing bacteria do not lyse in the absence of chloroform because the holin gene inactivation prevents cytoplasmic endolysin access to the bacterial cell wall, as is necessary for cell lysis. The exhausted cells are harvested by centrifugation or filtration and then frozen until one desires to harvest the soluble pyocins that have filled the cellular cytoplasm. Upon thawing, the inner cellular membrane ruptures, releasing endolysin to lyse the bacteria and thereby release the harvest of modified pyocins. The disruption of the bacterial membranes can be accelerated or completed if necessary by the addition of small quantities of chloroform to the aqueous solvent in which the bacterial paste is thawed.
Example 6
Targeting of Bacterial Strains with Recombinant P4/P2 Bacteriophage
When a large mixed population of bacteria, such as E. coli C1a and E. coli O157:H7, was contacted with P4 phage particles engineered as described above, containing the construct shown in FIG. 14, to target only one strain of the population, colonies of the target bacteria were isolated by growing the contacted population in the presence of gentamicin. In this experiment, known numbers of E. coli C-1a and EDL933 (O157:H7) were mixed in different proportions as indicated in the table (rows A-G) provided in FIG. 15. Each mixed population was contacted for 20 minutes with P4 particles engineered as shown in FIG. 14 to target the O157 antigen. Each mixed culture was then spread on agar plates containing 15 μg gentamicin/mL. The plates were incubated overnight at 37° C. and photographed the next morning (images of the plates are shown in FIG. 15). The numbers of colonies on each plate that could be counted are shown below each image. Five colonies each from plates E, F and G were tested for shiga toxin (Stx) genet by PCR analysis. All colonies tested, except those on plate G, were confirmed as EDL933. The 3 colonies on plate G were E. coli C-1a containing P4 plasmid that had contaminated the P4 phage lysate-preparation as evidenced by none having a Stx gene by PCR analysis. As shown in FIG. 15, a few as less than one in 1 million E. coli O157:H7 bacteria can be isolated from a population of at least 5 million non-O157 E. coli strains.
Conversely, it was demonstrated that, given a mixed population of P4 phages engineered to target and infect different bacterial strains, the novel system could be deployed to isolate a rare P4 phage containing an engineered tail fiber specific for a target bacterium. In this experiment, known numbers of engineered P4 phage particles generated by the methods described above and FIG. 12 and containing the P2 gene H (H) or the P2 gene H fused to the phiV10 tail spike gene (H-V10) were mixed in different proportions (as indicated to the left of the image in FIG. 16). The mixed P4 phage populations were contacted for 10 minutes with a culture of either E. coli C-1a or EDL933 (O157:H7), and the cultures were inoculated on plates containing 15 μg gentamicin/mL. The plates were incubated overnight at 37° C. and photographed the next morning (images provided in FIG. 16).
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All references cited herein are hereby incorporated by reference in their entireties, whether previously specifically incorporated or not. As used herein, the terms “a”, “an”, and “any” are each intended to include both the singular and plural forms.
Having now fully described the disclosed subject matter, it will be appreciated by those skilled in the art that the same can be performed within a wide range of equivalent parameters, concentrations, and conditions without departing from the spirit and scope of the disclosure and without undue experimentation. While this disclosure has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications. This application is intended to cover any variations, uses, or adaptations of the subject matter following, in general, the principles of the disclosure and including such departures from the disclosure as come within known or customary practice within the art to which the subject matter pertains and as may be applied to the essential features hereinbefore set forth.

## Claims

1. A recombinant P4 bacteriophage comprising, a recombinant P4 bacteriophage genome comprising an engineered tail fiber gene, wherein the engineered tail fiber gene comprises a polynucleotide encoding a base plate attachment region (BPAR) of P2 phage, wherein the BPAR comprises amino acids 1-157 or 1-158 of the P2 bacteriophage gene H product, and a heterologous polynucleotide encoding a receptor binding domain (RBD).

2. The recombinant P4 bacteriophage of claim 1, further comprising an antibiotic resistance gene.

3. The recombinant P4 bacteriophage of claim 1, wherein the BPAR comprises amino acids 1-158 of the P2 bacteriophage gene H product.

4. The recombinant P4 bacteriophage of claim 1, wherein the heterologous polynucleotide is from an L-413c, PS 17, BPP-1, CTX, VHML, CUS3, epsilon 15 HK620, sf6, ST64T, phiV10 phage, or encodes a tail spike-like protein.

5. The recombinant P4 bacteriophage of claim 1, wherein the heterologous polynucleotide encodes about 347 to 755 amino acids in length of the C-terminus of the RBD.

6. The recombinant P4 bacteriophage of claim 1, wherein the heterologous polynucleotide encodes amino acids 204-875, 211-875 or 217-875 from SEQ ID NO:60.

7. The recombinant bacteriophage of claim 1, wherein the recombinant P4 genome further comprises a second engineered tail fiber gene, and wherein the second engineered tail fiber gene comprises a polynucleotide encoding a base plate attachment region (BPAR) of a P2 phage, wherein the BPAR comprises amino acids 1-157 or 1-158 of the P2 bacteriophage gene H product, and a second, different, heterologous polynucleotide encoding a receptor binding domain (RBD), wherein the second engineered tail fiber encoded thereby has a different binding specificity than the first engineered tail fiber.

8. The recombinant P4 bacteriophage of claim 7, wherein the recombinant P4 bacteriophage is multivalent and binds more than one targeted receptor.

9. A mixture of the bacteriophage of claim 1 and a second bacteriophage that comprises a second engineered tail fiber gene, wherein the second engineered tail fiber gene comprises a polynucleotide encoding a base plate attachment region (BPAR) of a P2 phage, wherein the BPAR comprises amino acids 1-157 or 1-158 of the P2 bacteriophage gene H product, and a second, different, heterologous polynucleotide encoding a receptor binding domain (RBD), wherein the second engineered tail fiber encoded thereby has a different binding specificity than the engineered tail fiber of the first bacteriophage.

10. A bacteriophage library comprising a plurality of recombinant P4 bacteriophage members, wherein each member of the library comprises a recombinant P4 bacteriophage genome comprising an engineered tail fiber gene, wherein the engineered tail fiber gene comprises a polynucleotide encoding a base plate attachment region (BPAR) of a P2 phage, wherein the BPAR comprises amino acids 1-157 or 1-158 of the P2 bacteriophage gene H product, and a heterologous polynucleotide.

11. The library of claim 10, wherein the BPAR comprises amino acids 1-158 of SEQ ID NO:25.

12. The library of claim 10, wherein the heterologous polynucleotide encodes a receptor binding domain (RBD).

13. The library of claim 10, wherein the heterologous polynucleotide is from an L-413c, PS 17, BPP-1, CTX, VHML, CUS3, epsilon 15 HK620, sf6, ST64T, phiV10 phage, or encodes a tail spike-like protein.

14. The library of 10, wherein the members further comprise an antibiotic resistance gene.

15. The library of claim 12, wherein the receptor binding domain is a protein that binds and degrades cell surface structures.

16. The library of claim 15, wherein the protein that binds and degrades cell surface structures is an enzyme.

17. A nucleic acid molecule comprising a recombinant P4 bacteriophage genome comprising an engineered tail fiber gene, wherein the engineered tail fiber gene comprises a polynucleotide encoding a base plate attachment region (BPAR) of a P2 phage, wherein the BPAR comprises amino acids 1-157 or 1-158 of the P2 bacteriophage gene H product, and a heterologous polynucleotide encoding a receptor binding domain (RBD).

18. The nucleic acid molecule of claim 17, further comprising an antibiotic resistance gene.

19. The nucleic acid molecule of claim 17, wherein the heterologous polynucleotide is from an L-413c, PS 17, BPP-1, CTX, VHML, CUS3, epsilon 15 HK620, sf6, ST64T, phiV10 phage, or encodes a tail spike-like protein.

20. The nucleic acid molecule of claim 17, wherein the heterologous polynucleotide comprises amino acids 204-875, 211-875 or 217-875 from SEQ ID NO:60.

21. A method for detecting a target bacterium in a sample comprising,
contacting a sample suspected of containing a target bacterium with the recombinant P4 bacteriophage of claim 1, wherein the receptor binding domain binds to the target bacterium, and wherein the recombinant bacteriophage further comprises a gene encoding resistance to an antibiotic to which the target bacterium is sensitive;
culturing the sample and the recombinant P4 bacteriophage; and
detecting the presence of the target bacterium in the sample by detection of growth of the target bacterium in the presence of the antibiotic.

22. The method of claim 21, wherein the heterologous polynucleotide is from an L-413c, PS 17, BPP-1, CTX, VHML, CUS3, epsilon 15 HK620, sf6, ST64T, or phiV10 phage, or encodes a tail spike-like protein.

23. The method of claim 21, wherein the heterologous polynucleotide encodes about 347 to 755 amino acids in length of the C-terminus of the RBD.

24. The method of claim 21, wherein the heterologous polynucleotide encodes amino acids 204-875, 211-875 or 217-875 from SEQ ID NO:60.

25. The method of claim 21, wherein the recombinant P4 genome further comprises a second engineered tail fiber gene, wherein the second engineered tail fiber gene comprising a second, different, heterologous polynucleotide encoding a receptor binding domain (RBD).

26. The method of claim 25, wherein the recombinant P4 bacteriophage is multivalent and binds more than one targeted receptor.