Abstract:
Methods for improving binding of a proteinaceous substance to cell-wall material of a Gram-positive bacterium are disclosed. The proteinaceous substance includes an AcmA cell-wall binding domain, homolog or functional derivative thereof. The method includes treating the cell-wall material with a solution capable of removing a cell-wall component such as a protein, lipoteichoic acid or carbohydrate from the cell-wall material and contacting the proteinaceous substance with the cell-wall material.

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application is a divisional of U.S. patent application Ser. No. 11/299,304, filed Dec. 9, 2005, now U.S. patent Ser. No. 7,541,039, which application and this application is a divisional of U.S. patent application Ser. No. 10/321,857, filed Dec. 16, 2002, now U.S. Pat. No. 7,067,639, issued Jun. 27, 2006, which application and this application is a continuation of International Appl&#39;n No. PCT/NL02/000383 filed on Jun. 11, 2002, designating the United States of America, published in English on Dec. 19, 2002 as PCT International Publication WO 2002/101026 A2, which applications claim priority to EP 01202239.8, filed Jun. 11, 2001, the contents of the entirety of each of which are incorporated by reference. 
    
    
     STATEMENT ACCORDING TO 37 C.F.R. §1.52(e)(5)-SEQUENCE LISTING SUBMITTED ON COMPACT DISC 
     Pursuant to 37 C.F.R. §1.52(e)(1)(iii), a compact disc containing an electronic version of the Sequence Listing has been submitted concomitant with this application, the contents of which are hereby incorporated by reference. A second compact disc is submitted and is an identical copy of the first compact disc. The discs are labeled “copy 1” and “copy 2,” respectively, and each disc contains one file entitled “SeqListCRF.txt” which is 88 KB and created on Dec. 16, 2002. 
     TECHNICAL FIELD 
     The present invention relates generally to biotechnology, and, more particularly, pertains to a method for obtaining cell-wall material of Gram-positive bacteria with an improved capacity for binding a proteinaceous substance comprising an AcmA cell-wall binding domain, as well as pharmaceutical compositions including the obtained cell-wall material. 
     BACKGROUND 
     Heterologous surface display of proteins (Stahl and Uhlen, TIBTECH May 1997, 15, 185-192) on recombinant microorganisms via the targeting and anchoring of heterologous proteins to the outer surface or the cell wall of host cells, such as yeast, fungi, mammalian cells, plant cells, and bacteria, has been possible for several years. Display of heterologous proteins at the surface of these cells has taken many forms including the expression of reactive groups such as antigenic determinants, heterologous enzymes, single-chain antibodies, polyhistidyl tags, peptides, and other compounds. Heterologous surface display has been applied as a tool for applied and fundamental research in microbiology, molecular biology, vaccinology and biotechnology. Another application of bacterial surface display has been the development of live-bacterial-vaccine delivery systems. The cell-surface display of heterologous antigenic determinants has been considered advantageous for inducing antigen-specific immune responses in live recombinant cells used for immunization. Another application has been the use of bacterial surface display in generating whole-cell bioadsorbents or biofilters for environmental purposes, microbiocatalysts, and diagnostic tools. 
     Generally, chimeric proteins include an anchoring or targeting portion that is specific and selective for the recombinant organism, wherein the anchoring portion is combined with the reactive group, such as the antigenic determinant, heterologous enzyme, single-chain antibody, polyhistidyl tag, peptide, or other compound. A well-known anchoring portion comprises the so-called LPXTG (SEQ ID NO:1) box, which covalently binds to a  Staphylococcus  bacterial surface, i.e., in the form of a fully integrated membrane protein. In this manner, at least two polypeptides of different genetic origins may be joined by a normal peptide bond to produce a chimeric protein. For example, PCT International Patent Publication No. WO 94/18330, which relates to the isolation of compounds from complex mixtures and the preparation of immobilized ligands (bioadsorbents), discloses a method for obtaining a ligand comprising anchoring a binding protein in or at the exterior of a cell wall of a recombinant cell. The binding protein is essentially a chimeric protein produced by the recombinant cell and includes an N-terminal part derived from an antibody that is capable of binding to a specific compound, wherein the N-terminal part is joined to a C-terminal anchoring part, derived from an anchoring protein purposely selected for being functional in the specific recombinant cell chosen. PCT International Patent Publication No. WO 97/08553 discloses a method for selectively targeting proteins to the cell wall of  Staphylococcus  sp., using anchoring proteins which include long stretches of at least 80-90 amino acid long amino acid cell-wall-targeting signals. The signals are derived from the lysostaphin gene or amidase gene of  Staphylococcus  and encode for proteins that selectively bind to  Staphylococcus  cell-wall components. 
     Vaccine delivery or immunization systems with attenuated bacterial vector strains that express distinct antigenic determinants against a wide variety of diseases are currently being developed. Mucosal vaccines for nasal or oral passages using these attenuated bacterial vectors have received a great deal of attention. For example, both systemic and mucosal antibody responses against an antigenic determinant of hornet venom have been detected in mice orally colonized with a genetically engineered human oral commensal  Streptococcus gordonii  strain that expresses the hornet venom antigenic determinant on its surface (Medaglini et al., PNAS 1995, 2; 6868-6872). A protective immune response was also elicited by oral delivery of a recombinant bacterial vaccine that included tetanus toxin fragment C constitutively expressed in  Lactococcus lactis  (Robinson et al., Nature Biotechnology 1997, 15; 653-657). Mucosal immunization is considered an effective means of inducing IgG and secretory IgA antibodies directed against specific pathogens of mucosal surfaces. 
     Immunogens expressed by bacterial vectors may be presented in a particulate form to antigen-presenting cells, such as M-cells, of the immune system and therefore should be less likely to induce tolerance when compared to soluble antigens. Additionally, the existence of a common mucosal immune system permits immunization of one specific mucosal surface in order to induce secretion of antigen-specific IgA and other specific immune responses at distant mucosal sites. A drawback to using bacterial vectors for immunization is the potential of the bacterial strain causing inflammation or disease and potentially leading to fever or bacteremia. Instead of using attenuated bacterial strains that may become pathogenic, recombinant commensal bacteria, such as  Streptococcus  sp. or  Lactococcus  sp., may be used as vaccine carriers. 
     A potential problem with recombinant commensal microorganisms is that they may colonize the mucosal surfaces and generate a long-term exposure to the target antigens expressed and released by the recombinant microorganisms which may cause immune tolerance. 
     Additionally, the use of genetically modified microorganisms that contain recombinant nucleic acid has met considerable opposition from the public as a whole, stemming from a low-level acceptance of products which contain recombinant DNA or RNA. Similar objections exist against even the use of attenuated pathogenic strains or against proteins, or parts of proteins, derived from pathogenic strains. Further, the heterologous surface display of proteins described herein entails the use of anchoring or targeting proteins specific and selective for a limited set of microorganisms, which are of recombinant or pathogenic nature which greatly restricts their potential applications. 
     The protein anchor of  L. lactis , AcmA (cA), its homologs and functional derivatives (PCT International Patent Publication No. WO99/25836) bind in a non-covalent manner to a wide variety of Gram-positive bacteria. Binding also occurs to isolated cell-wall material. The ligand to which the protein anchor of  L. lactis  binds in these cell walls is currently unknown. 
     The use of a gram-positive, food-grade bacterium, such as  Lactococcus lactis , offers significant advantages over the use of other bacteria, such as  Salmonella , as a vaccine delivery vehicle. For instance,  L. lactis  does not replicate in or invade human tissues and reportedly possesses low intrinsic immunity (Norton et al. 1994). Further, mucosal -delivered  L. lactis  that expresses tetanus toxin fragment C has been shown to induce antibodies that protect mice against a lethal challenge with tetanus toxin even if the carrier bacteria was killed prior to administration (Robinson et al. 1997). The killed bacteria still contain recombinant DNA that will be spread into the environment, especially when used in wide-scale oral immunization programs. However, the uncontrollable shedding of recombinant DNA into the environment may have the risk of being taken up by other bacteria or other microorganisms. 
     SUMMARY OF THE INVENTION 
     Disclosed is a method for improving binding of a proteinaceous substance to cell-wall material of a Gram-positive bacterium. The proteinaceous substance comprises at least one repeat, but may comprise two or three repeat sequences of an AcmA cell-wall binding domain, homolog or functional derivative thereof. The method comprises treating the cell-wall material with a solution capable of removing a cell-wall component, such as a protein, lipoteichoic acid or carbohydrate, from the cell-wall material and contacting the proteinaceous substance with the treated cell-wall material. Improved binding may be obtained by treating the cell-wall material with a solution capable of removing a cell-wall component. The cell-wall material may be subsequently stored until it is contacted with a desired fusion protein. The fusion protein may comprise an AcmA cell-wall binding domain, homolog or functional derivative thereof where the cell-wall material is contacted with the fusion protein. The method of the present invention may be used to obtain cell-wall material with an improved capacity for binding a proteinaceous substance comprising the AcmA cell-wall binding domain, homolog or functional derivative thereof. 
     Also disclosed is a method for removing components from a bacterial cell wall comprising treating whole cells with a solution capable of removing a cell-wall component such as a protein, lipoteichoic acid or carbohydrate from the cell-wall material. The cell-wall material obtained by the present invention yields cell-wall material with at least 20%, better 30%, best 40% or even 50% of relatively empty, but intact, cell envelopes which include inert spherical microparticles. The inert spherical microparticles will be referred to herein as bacterial “ghosts.” The term “ghosts” reflects the size and shape of the bacterium from which the ghosts are obtained. 
     Also disclosed is a method for obtaining cell-wall material of a Gram-positive bacterium with an improved capacity for binding with a proteinaceous substance comprising an AcmA cell-wall binding domain, homolog or functional derivative thereof. The method comprises treating the cell-wall material with a solution capable of removing a cell-wall component such as a protein, lipoteichoic acid or carbohydrate from the cell-wall material, wherein the cell-wall material comprises spherical peptidoglycan microparticles referred to herein as ghosts. 
     Methods to extract bacterial cell-wall material with a solution have been described in EP 0 545 352 A and Brown et al. (Prep. Biochem. 6:479, 1976). A method to obtain purified soluble peptidoglycan from bacteria by exposure to TCA has been disclosed. The cited references describe procedures in which cells are mechanically disrupted, wherein the resulting cell fragments are treated with TCA to extract peptidoglycans from the cell wall. The cited methods provide a peptidoglycan preparation and a lysed, randomly fragmented cell-wall preparation from which cell-wall components have been removed. However, these methods do not yield ghosts. Furthermore, the methods do not allow targeting with a proteinaceous substance comprising an AcmA cell-wall binding domain, homolog or functional derivative thereof. 
     The method of the present invention is aimed at yielding ghosts from which cell-wall components have been removed. The use of ghosts for display of proteinaceous substances has advantages over the use of the disrupted cell-wall material. For example, binding the proteinaceous substance to bacterial ghosts results in a higher packing density when compared to binding a substance to mechanically disrupted cell-wall material. A high density surface display of proteins is favorable for application in industrial processes. In one embodiment, the present invention discloses a method for obtaining the cell-wall material not involving rupture. 
     Cell-wall material obtained by mechanical disruption methods suffers from several practical drawbacks. Because cells are completely broken with mechanical disruption, intracellular materials are released from the cell and cell-wall fragments need to be separated from a complex mixture of proteins, nucleic acids, and other cellular components. The released nucleic acids may increase the viscosity of the solution and complicate processing steps, especially chromatography. The cell debris produced by mechanical lysis also often includes small cell fragments which are difficult to remove. These problems are overcome when ghosts are produced using methods of the present invention. The uniform composition of a ghost preparation including particle size and shape offers other advantages for subsequent purification and isolation steps. The invention thus discloses a method of obtaining cell-wall material not involving rupture of the cell wall, wherein the resulting cell-wall material comprises ghosts. 
     The use of bacterial ghosts is often preferable when compared to the use of mechanically disrupted cell-wall bacteria for the surface display of immunogenic determinants. In contrast to mechanical disruption procedures, ghosts are produced by a process that preserves most of the bacteria&#39;s native spherical structure. Bacterial ghosts are better able to bind to and/or are more easily taken up by specific cells or tissues than mechanically disrupted cell-wall material. The ability of bacterial ghosts to target macrophages or dendritic cells enhances their functional efficacy. Thus, the non-recombinant, non-living ghost system disclosed by the present invention is well suited as a vaccine delivery vehicle. Accordingly, the invention discloses a method for obtaining ghosts, wherein the ghosts have an improved capacity for binding with a proteinaceous substance and have an enhanced induction of the cellular immune response. 
     The invention also discloses a method for binding a proteinaceous substance to the cell-wall material of a Gram-positive bacterium, wherein the proteinaceous substance comprises an AcmA cell-wall binding domain, homolog or functional derivative thereof. The method comprises treating the cell-wall material with a solution capable of removing a cell-wall component such as a protein, lipoteichoic acid or carbohydrate from the cell-wall material, and subsequently contacting the proteinaceous substance with the cell-wall material. The cell-wall material comprises ghosts which have been produced by the present invention which does not involve rupture of the bacterial cell-wall. 
     In another embodiment, the solution capable of removing the cell-wall material has a pH that is lower than the calculated Pi value of the AcmA cell-wall binding domain, homolog or functional derivative thereof. Particularly, the solution comprises an acid such as acetic acid (HAc), hydrochloric acid (HCl), sulphuric acid (H 2 SO 4 ), trichloro acetic acid (TCA), trifluoro acetic acid (TFA), and monochloroacetic acid (MCA). The concentration of the acid in the solution will be dependent on the desired pH value which may be determined by calculation using a computer program such as DNA star or Clone Manager. For instance, when the calculated pI is &gt;8, pH values of about 6 to 4 may suffice for effecting appropriate binding. When pI values are calculated to be lower, such as around 6, pH values of 3-4 may be selected. When domains with calculated pI values ranging from 8 to 12 are encountered, using the solution comprising 0.06 to 1.2 M TCA, or comparable acid, may suffice. 
     The binding may be improved by heating the cell-wall material or ghosts in the solution. However, precise requirements for the heating may vary depending on the cell-wall material or ghosts. However, heating for 5-25 minutes at approximately boiling temperature (i.e., 100° C.) will often generate the desired cell-wall material with improved binding capacity. The cell-wall material may then be washed and pelleted (e.g., by centrifugation) from the treatment solution and subsequently stored (e.g., by freezing or freeze-drying) until further use. Such cell-wall material includes spherical peptidoglycan microparticles that usually reflect the size and shape of the bacterium from which they were obtained. 
     In one embodiment, the cell-wall material is derived from a  Lactococcus , a  Lactobacillus , a  Bacillus  or a  Mycobacterium  sp. The cell walls of Gram -positive bacteria include complex networks of peptidoglycan layers, proteins, lipoteichoic acids and other modified carbohydrates. Generally, chemical treatment of the cell-wall material may be used to remove cell-wall components such as proteins, lipoteichoic acids and carbohydrates, wherein the chemical treatment yields purified peptidoglycan (Morata de Ambrosini et al. 1998). Sodium dodecyl sulphate (SDS) is also commonly used to remove proteins. Trichloro acid (TCA) is known to specifically remove lipoteichoic acids and carbohydrates from cell-wall isolates. Phenol, formamide and mixtures of chloroform and methanol are other examples of organic solvents that may be used to enhance the purification of peptidoglycan. 
     In the present invention, the effect of the pretreatment of whole cells of gram-positive bacteria with these and other chemicals in relation to binding technology provides the possibility to obtain bacterial ghosts or cell-wall material derived from the bacteria which possess new traits (i.e., different binding properties) without the introduction of recombinant DNA. 
     In another embodiment, the present invention discloses the incorporation of cell-wall material with improved binding capacity for AcmA-type anchors into a composition, such as a pharmaceutical composition, with a proteinaceous substance comprising an AcmA-type anchor. Reactive groups, such as antigenic determinants, heterologous enzymes, single-chain antibodies, polyhistidyl tags, peptides, and other compounds may be bound to the cell-wall material as disclosed herein by providing reactive groups with an AcmA-type anchor, and subsequently contacting the cell-wall material with the reactive groups to improve binding capacity. Other reactive groups include fluorescing protein, luciferase, binding protein or peptide, antibiotics, hormones, non-peptide antigenic determinants, carbohydrates, fatty acids, aromatic substances or reporter molecules. 
     In another embodiment, the invention discloses the use of cell-wall material in generating bioadsorbents or biofilters for environmental purposes, microbiocatalysts, and diagnostic tools. For instance, the use of immobilized biocatalysts, such as enzymes or whole microbial cells, has increased steadily during the past decade in the food, pharmaceutical and chemical industries. The immobilized biocatalysts are more stable, easier to handle, and can be used repeatedly in industrial processes in comparison to their free counterparts. Immobilization of enzymes typically requires a chemical step to link the enzyme to an insoluble support. However, chemical treatments may negatively affect the enzymes. Alternatively, enzymes may be immobilized by incorporation in gels with the disadvantage that diffusion of the substrate into the gel slows down the process. 
     As disclosed herein, large-scale immobilization of enzymatically active proteins may be accomplished by surface displaying proteins on gram-positive cells or cell-wall material. For instance, the immobilization of a fusion protein comprising α-amylase or β-lactamase fused to the AcmA-protein anchor domain has been demonstrated herein in  L. lactis . The addition of the AcmA-anchor fusion protein resulted in the stable attachment of heterologous proteins to the surface of  L. lactis  and other gram-positive bacteria. Further, pre-treating  L. lactis  cells and other gram-positive cells with acid as described herein results in a high density surface display of heterologous proteins and is a prerequisite for application in industrial processes. Further, the carrier or gram-positive cells may be obtained in high yield and be non-recombinant. Thus, a method disclosed herein may be used to economically produce the immobilized enzyme and make the AcmA-protein anchor a useful approach for the surface display of enzymes on gram-positive cells. 
     Another industrial application of an immobilized enzyme is the isomerization of glucose which is catalyzed by glucose isomerase and used during the production of high-fructose corn syrup. This process may be made economically feasible by immobilizing the glucose isomerase. The productivity of glucose isomerase is improved by increasing the stability of epoxide hydrolase in organic solvents by immobilization to microbial cells or cell-wall material as described herein. 
     Immobilized enzymes may also be used to treat waste water or industrial effluent. For instance, industrial effluents containing low value chemicals produced during synthesis of the commodity chemicals epichlorohydrin and propylene oxide may be treated by using immobilized haloalkane dehalogenase to recycle these low value products into the manufacturing process. 
     The invention further discloses chimeric or hybrid AcmA-type anchors for the preparation of a composition that has new binding properties. The AcmA-type anchors can be divided into two groups of hybrids based on their pI (see, Table 3). A large group includes hybrids with a pI higher than 8, but lower than 10, and a smaller group includes hybrids with a relatively low pI (i.e., &lt;5). Hybrid AcmA-type anchors are disclosed with at least one AcmA-type domain and a relatively high calculated pI, and another AcmA-type domain is disclosed with a relatively lower calculated pI. The resulting hybrid anchor has an intermediate calculated pI which is useful when release of the bound proteinaceous substance at a higher pH is contemplated. Such a composition may be routed through the stomach, which has a relative low pH, such that the composition releases its anchor bound reactive groups in the intestines, which have a higher pH. 
     The invention also discloses a proteinaceous substance comprising an AcmA cell-wall binding domain, homolog or functional derivative thereof wherein the binding domain is a hybrid of at least two different AcmA-type cell-wall binding domains, homologs or functional derivatives thereof. The proteinaceous substance may comprise an AcmA cell-wall binding domain, homolog or functional derivative thereof where the binding domain is a hybrid of at least two different AcmA repeat sequences and has a calculated pI lower than 10. For instance, a hybrid protein anchor including the A1 and A2 repeat sequences of AcmA and the D1 repeat sequence of AcmD may be constructed. Such a hybrid domain may comprise at least one AcmA-type domain with a relatively high calculated pI and another AcmA-type domain with a relatively lower calculated pI. The domain with the relatively high pI may be derived from, or be functionally equivalent to, the AcmA-type domain of the lactococcal cell-wall hydrolase AcmA. Of course; many other domains with a high pI are known, such as those disclosed in Table 3. A domain with a relatively low pI may be derived from, or be functionally equivalent to, the AcmA-type domain of the lactococcal cell-wall hydrolase AcmD. However, other domains with relatively low pI are known, including those disclosed in Table 3. 
     The invention further discloses a proteinaceous substance comprising a hybrid domain with at least two stretches of amino acids, wherein each stretch corresponds to a domain repeat sequence and is located adjacent to each other. The stretches may be separated by one or more amino acid residues of a short distance, i.e., 3-6 to 10-15 amino acids apart, by a medium distance, i.e., 15-100 amino acids apart, or by longer distances, i.e., &gt;100 amino acid residues apart. 
     In another embodiment, the invention discloses a proteinaceous substance with a hybrid AcmA domain that further comprises a reactive group. Reactive groups that may be used include, without limitation, antigenic determinants, heterologous enzymes, single-chain antibodies or fragments thereof, polyhistidyl tags, fluorescing proteins, luciferase, binding proteins or peptides, antibiotics, hormones, non-peptide antigenic determinants, carbohydrates, fatty acids, aromatic substances, inorganic particles such as latex, and reporter molecules. The reactive group may also include AcmA cell-wall binding domains, homologs or functional derivatives thereof wherein the binding domain is a hybrid of at least two different AcmA cell-wall binding domains, homologs or functional derivatives thereof that are useful in heterologous surface display and are broadly reactive with cell-wall components of a broad range of micro-organisms. As used herein, the AcmA cell-wall binding domains, homologs and functional derivatives thereof will also be referred to as hybrid AcmA domains. 
     The invention further discloses reactive groups which are non-protein moieties, including substances such as antibiotics, hormones, aromatic substances, inorganic particles, or reporter molecules. The substances may be constructed by binding an antibiotic, such as penicillin, tetracycline or various other antibiotics, a hormone, such as a steroid hormone, or any other compound to a binding domain produced by the present invention. Such binding may be achieved using various techniques known in the art and may function to label or “flag” the binding domain. For instance, a binding domain may be bound to a reporter molecule such as fluorescent nanoparticles, i.e., FITC or HRPO, wherein tools are generated that may be used in diagnostic assays to detect microorganisms possessing peptidoglycan. Similarly, a binding domain may be bound to an antibiotic and used for in vivo parenteral administration into the bloodstream of humans or animals, or used in vitro to bind microorganisms with peptidoglycan in order to increase the concentration of the antibiotic around the microorganism which may be killed by the antibiotics. 
     The invention further discloses a reactive group which is a protein moiety which may include, without limitation, antigenic determinants, enzymes, single-chain antibodies or fragments thereof, polyhistidyl tags, fluorescing proteins, binding proteins or peptides. For instance, a protein including a reactive group which is another protein or polypeptide is disclosed. The invention also discloses a nucleic acid molecule encoding the protein produced using the methods of the invention. Such a nucleic acid molecule, comprising single-stranded or double-stranded DNA, RNA or DNA-RNA duplex, comprises nucleic acid sequences which encode a hybrid binding domain. The nucleic acid molecule may also comprise nucleic acid sequences encoding the reactive group polypeptide and may further comprise other nucleic acid sequences encoding a signal peptide comprising promoter sequences or regulatory nucleic acid sequences. 
     A vector comprising a nucleic acid molecule encoding a proteinaceous substance provided by the invention is also disclosed. Examples of vectors include, without limitation, a plasmid, a phage or a virus, wherein the vectors may be constructed using nucleic acids of the invention and routine skills known in the art. Viral vectors include baculovirus vectors or comparable vector viruses through which a protein produced by the present invention may be expressed or produced in cells, such as insect cells. 
     A host cell or expression system including a nucleic acid molecule or a vector produced using methods of the present invention is also disclosed. The host cell expressing a protein of the present invention may be a microorganism to which the protein is attached. The host cell, or expression system, may be a Gram-positive bacterium, a Gram-negative bacterium, a yeast cell, an insect cell, a plant cell, a mammalian cell, or a cell-free expression system, such as a reticulocyte lysate. The host cell or expression system may be constructed or obtained using a nucleic acid or vector of the present invention and routine skills known in the art. 
     In a further embodiment, the invention discloses a pharmaceutical composition comprising cell-wall material with an improved binding capacity with an immunogen bound thereto which may be useful for vaccination purposes, i.e., a vaccine. The vaccine may be used to invoke immunity against pathogens, such as malaria, which undergo life cycle stages where the pathogen is not in the blood but hides in cells. 
     The vaccines may be delivered to mucosal surfaces instead of being injected since mucosal surface vaccines are easier and safer to administer. An  L. lactis -derived cell-wall material may be used for mucosal vaccination since this bacterium is of intestinal origin and no adverse immune reactions are generally expected from  L. lactis.    
     The vaccine of the invention may also be administered by injection. When the vaccine is administered through injection, cell-wall material may be derived from a  Mycobacterium  sp. since mycobacterial cell-wall preparations have beneficial adjuvant properties. The mycobacterial cell-wall vaccine may be mixed with the proteinaceous substance carrying the immunogenic determinants used in the vaccine. 
     A vaccine produced using a method of the present invention will likely have a reduced risk of generating undesirable immune responses against cell-wall compounds of unwanted immunogens because the unwanted immunogens are not included in the vaccine. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1 . Schematic map of plasmid pNG3041 that encodes the reporter protein MSA2::cA that is secreted as a proprotein using the lactococcal PrtP signal- and prosequences (PrtP.sspro). Pnis represents the nisin inducible promoter of the nisA gene. T represents the transcriptional terminator. CmR is the chloramphenicol resistance gene. repC and repA are genes involved in the replication of the plasmid. 
         FIG. 2A . Fluorescence microscopic images of bacterial cells with externally bound MSA2::cA.  Lb. curvatis, Lb. sake  and  L. lactis  cells that were not pretreated prior to binding. 
         FIG. 2B . Fluorescence microscopic images of bacterial cells with externally bound MSA2::cA.  L. lactis  cells that were TCA-pretreated prior to binding. The light colored areas indicate the position where the reporter protein MSA2::cA binds. The difference between  L. lactis  cells that were not pretreated with TCA (in  FIG. 2A ) and those that were TCA pretreated is apparent (in  FIG. 2B ). 
         FIG. 3 . Western blots of chemically pretreated  L. lactis  cells that were washed after the pretreatment and incubated with MSA2::cA to allow binding. Unbound MSA2::cA was removed by washing. The drawing shows the MSA2::cA that was bound to the chemically pretreated cells and detected using an antibody specific for MSA2. The different pretreatments are indicated above the lanes. MSA2::cA is produced by the producer cells as a proprotein, pro-MSA2::cA. Some pro-MSA2::cA is present in the medium used for binding and binds as indicated by the arrow. A membrane bound protease, HtrA, of the producer cells cleaves off the prosequence, resulting in mature MSA2::cA, which also binds to the pretreated cells as indicated by the asterisk. HtrA also cleaves off the repeats of the cA anchor. Since there are three repeats, MSA2 proteins of several sizes are present in the medium of the producer. As long as more than one repeat is present, binding can still occur. The double asterisks point to MSA2::cA from which one or two repeats have been cleaved. M is a molecular weight marker. The molecular weights are indicated in the left margin. The two blots have different signal intensities. As a reference, both blots contain the same TCA-pretreated samples. The difference in signal intensity is due to differences in stain developing time. It is apparent that the TCA and other acid pretreatments produce pronounced effects on the subsequent binding of MSA2::cA. The conclusions for all chemical pretreatments are summarized in Table 1. 
         FIG. 4 . Coomassie stained SDS-PAGE gel with chemically pretreated  L. lactis  cells. Pretreatments: (1) no-treatment; (2) HCl; (3) H 2 SO 4 ; (4) HAc; (5) TFA; and (6) TCA. It is apparent that treatment of the cells with HCl, H 2 SO 4 , TFA or TCA significantly removes an amount of protein from the cells. 
         FIG. 5 . Western blot of  L. lactis  cells pretreated with different TCA concentrations and externally bound with MSA2::cA. Arrow and asterisks: as in  FIG. 3 . Pretreatments: (1) no TCA treatment; (2) 1% TCA; (3) 5% TCA; (4) 10% TCA; and (5) 20% TCA. An increase in the binding of MSA2::cA is shown to correlate with increasing amounts of TCA used in the pretreatment. 
         FIG. 6 . Alignment of cA repeats with cD repeats. AcmA (A1) (SEQ ID NO:16) is aligned to AcmD (D1) (SEQ ID NO:19). AcmA (A2) (SEQ ID NO:17) is aligned to AcmD (D2) (SEQ ID NO:20). AcmA (A3) (SEQ ID NO:18) is aligned to AcmD (D3) (SEQ ID NO:21). Consensus repeats SEQ ID NOS: 163, 164 and 165 are aligned. The amino acids that are in agreement with the consensus sequence are shown at the bottom of the figure (defined in PCT Publication WO99/25836) are underlined. The asterisks indicate residues that are identical between the compared repeats. 
         FIG. 7 . Binding of various anchor-fusion proteins to  L. Lactis  with and without TCA pretreatment. Multiple bands shown in one lane are caused by the different processed forms of MSA2 fusions. Lanes: (1) non-pretreated  L. lactis +MSA2::cA; (2) non-treated  L. lactis +MSA2::cD; (3) non-pretreated  L. lactis +MSA2; (4) TCA-pretreated  L. lactis +MSA2::cA; (5) TCA-pretreated  L. lactis +MSA2::cD; and (6) TCA -pretreated  L. lactis +MSA2. The effect of TCA pretreatment on the binding of MSA2::cA is shown (i.e., compare lanes 1 and 4). A minor improvement for MSA2::cD and no improvement for MSA2 without anchor is observed. Since there is a signal for MSA2 without the anchor means that MSA2 by itself has a weak affinity for bacterial cell walls. However, MSA2::cD or MSA2 binding to the pretreated cells cannot be detected using fluorescence or electron microscopy (see text). The difference in results is probably due to a difference in sensitivity of the techniques. 
         FIG. 8 . Fluorescence microscopy image of TCA-pretreated  L. lactis  cells incubated with MSA2::cA or MSA2::cD. Light colored areas indicate the position were the reporter fusion protein binds. It appears that binding only occurred with MSA2::cA and not with MSA2::cD. 
         FIG. 9A . Electron microscopy images of  L. lactis  cells incubated with different MSA2 constructs. The black dots represent the position of bound MSA2 fusion protein. Image A depicts non-pretreated cells incubated with MSA2::cA. 
         FIG. 9B . Electron microscopy images of  L. lactis  cells incubated with different MSA2 constructs. The black dots represent the position of bound MSA2 fusion protein. Image B depicts TCA-pre-treated cells incubated with MSA2::cA. Significant binding, shown by black dots, is only visible in the TCA-pre-treated cells incubated with MSA2::cA. 
         FIG. 9C . Electron microscopy images of  L. lactis  cells incubated with different MSA2 constructs. The black dots represent the position of bound MSA2 fusion protein. Image C depicts TCA-pre-treated cells incubated with MSA2::cD. 
         FIG. 9D . Electron microscopy images of  L. lactis  cells incubated with different MSA2 constructs. The black dots represent the position of bound MSA2 fusion protein. Image D depicts TCA-pre-treated cells incubated with MSA2. 
         FIG. 10 . Binding of different anchor-fusion proteins to  B. subtilis  with and without TCA pretreatment. The drawing is a Western blot similar to  FIGS. 3 and 7 . Lanes: (1) non-pretreated cells+MSA2::cA; (2) non-pretreated cells+MSA2::cD; (3) non-pretreated cells+MSA2; (4) TCA-pretreated cells+MSA2::cA; (5) TCA-pretreated cells+MSA2::cD; (6) TCA-pretreated cells+MSA2; and (7) non-pretreated  B. subtilis  (negative control). TCA pretreatment improves the binding of MSA2::cA in a manner similar to  L. lactis  (i.e., compare lanes 1 and 4). Only background binding is observed for MSA2::cD and MSA2 without anchor. 
         FIG. 11 . Fluorescence microscopy image of MSA2::cA binding to  Lb. casei  with or without TCA pretreatment. The light colored areas represent bound MSA2::cA. TCA pretreatment improves binding of MSA2::cA and  Lb. casei.    
         FIG. 12 . Fluorescence microscopy image of MSA2::cA and MSA2::cD binding to  M. smegmatis  pretreated with TCA. The light colored areas represent bound MSA2 fusion protein. As illustrated, only MSA2::cA binds. 
         FIG. 13 . Western blot of  L. lactis  cells with externally bound MSA2::cA treated with LiCl or stored under different conditions. The bands in the various lanes represent the amount of MSA2::cA that remained bound to the TCA-pretreated cells. Arrow and asterisks: as in  FIG. 3 . Lanes: (1) marker; (2) non-pretreated  L. lactis  incubated without MSA2::cA; (3) non-pretreated  L. lactis  incubated with MSA2::cA; (4) TCA-pretreated  L. lactis  incubated with MSA2::cA; (5) TCA-pretreated  L. lactis  incubated with MSA2::cA, subsequently washed with 8 M LiCl; (6) TCA-pretreated  L. lactis  incubated with MSA2::cA, subsequently stored in water for 3 weeks at 4° C.; (7) TCA-pretreated  L. lactis  incubated with MSA2::cA, subsequently stored in 10% glycerol for 3 weeks at −80° C.; and (8) TCA -pretreated  L. lactis  incubated with MSA2::cA, subsequently stored in water for three weeks at −80° C. As illustrated, TCA pretreatment improves binding of MSA2::cA to  L. lactis  cells (i.e., compare lanes 3 and 4). Washing with 8 M LiCl and storage in water for 3 weeks at 4° C. has minor effects on the bound MSA2::cA (i.e., compare lane 4 with 5 and 6). Storage at −80° C. has no effect on the bound MSA2::cA (i.e., compare lane 4 with 7 and 8). 
         FIG. 14A . Fluorescence microscopy image of MSA2::cA surface expression in the recombinant strain NZ9000(pNG3041). The light colored areas indicate the position of MSA2 fusion protein. The recombinant strain producing MSA2::cA has the protein on the surface in some specific spots. 
         FIG. 14B . Fluorescence microscopy image of MSA2::cP surface expression in the recombinant strain NZ9000(pNG3043). The recombinant strain producing MSA2::cP has more on the surface organized in several areas. 
         FIG. 14C . Fluorescence microscopy image of MSA2::cA binding to TCA pretreated  L. lactis  cells. The surface of the TCA-pretreated non-recombinant  L. lactis  with bound MSA2::cA is completely covered with the protein. 
         FIG. 15 . Western blots of  L. lactis  total protein extracts reacted with rabbit immune serum diluted at 1:100. 0: preimmune serum. 2 and 3: serum after the second and third immunization, respectively. A1: subcutaneously immunized rabbit with NZ9000Δ acmA (pNG3041) cells (recombinant, MSA2::cA surface anchored). B1: subcutaneously immunized rabbit with NZ9000ΔacmA (negative control). C2: orally immunized rabbit with NZ9000ΔacmA(pNG3043) cells (recombinant, MSA2::cP surface anchored). E1: orally immunized rabbit with TCA-pretreated NZ9000ΔacmA to which MSA2::cA had been externally bound (non-recombinant, MSA2::cA surface anchored). The staining bands in the lanes illustrates that  L. lactis  proteins react with the indicated rabbit antiserum. It is visible that the non-recombinant TCA-pretreated strain with bound MSA2::cA (E1) evokes a minimal response to  L. lactis  proteins indicating that the response to the carrier is reduced, while the response to the malaria antigen is not negatively influenced (see, Table 2). 
         FIG. 16 . Schematic representation of the domains in AcmA and AcmD. SS represents signal sequence. Both enzymes include a cell-wall binding domain that includes 3 repeats indicated by A1, 2, 3 and D1, 2, 3. The alignments of these repeats are shown in  FIG. 6 . In addition, an example of one of the hybrid protein anchors is described in Table 5. 
         FIG. 17 . Western blot showing the effect of pH supernatant on binding of MSA2::cD to TCA-pretreated  L. lactis  cells. As previously described, the Western blot shows the amount of MSA2::cD bound by the cells. In addition, the amount of MSA2::cD that was not bound and remained in the medium after binding is shown. The arrow indicates the expected position for pro-MSA2::cD and the asterisk indicates the position of mature MSA2::cD. Lanes: (1) pH during binding 6.2, cells; (2) pH during binding 6.2, supernatant after binding; (3) pH during binding 3.2, cells; (4) pH during binding 3.2, supernatant after binding; and (5) positive control:  L. lactis , TCA-pretreated with bound MSA2::cA at pH 6.2. It is visible that MSA2::cD binds better at pH 3.2 than at pH 6.2 (i.e., compare lanes 1 and 3). 
         FIG. 18 . Western blot of medium supernatant (S) after binding to ghost cells at the indicated pH and ghost (G) with the bound protein anchor. Lanes 1 and 2 illustrate binding at pH 3; lanes 3 and 4 illustrate binding at pH 5; lanes 5 and 6 illustrate binding at pH 7. The drawing shows considerable binding at pH 5. At pH 5, the native cD anchor (D1D2D3) shows little binding. The addition of the A3 repeat, which has a high pI value, results in increased binding at pH 5. 
         FIG. 19 . Immunization schedule. Mice immunizations were started at day 1 and repeated after 14 and 28 days. A lethal nasal challenge with  S. pneumoniae  was given 14 days after the last oral immunization. S.c. represents subcutaneous immunization. 
         FIG. 20 . Serum antibody response. Mean anti-PpmA serum antibody titers. OV represents orally immunized; IN represents intranasally immunized; SC represents subcutaneously immunized; Freund&#39;s PpmA refers to soluble PpmA subcutaneously administered with Freund&#39;s complete adjuvants. High titers were obtained with the intranasally and subcutaneously administered Ghosts-PpmA::cA. 
         FIG. 21 . Survival times. The orally vaccinated mice were challenged with a lethal dose of  S. pneumonia . Mice vaccinated with soluble PpmA or Ghost alone died within 72 hours. Forty percent of the mice immunized with Ghosts-PpmA::cA survived the challenge, indicating they were protected by the vaccination. 
     
    
    
     DETAILED DESCRIPTION 
     EXAMPLE 1 
     Acid Pretreatment of Gram-positive Bacteria Enhances Binding of AcmA Protein Anchor Fusions 
     Materials and Methods 
     Bacterial Strains and Growth Conditions.  Lactococcus lactis  strain MG1363 (Gasson 1983) or derivatives thereof, such as MG1363ΔacmA (Buist et al. 1995) or NZ9000Δ acmA, were used as recipients for binding of reporter fusion protein. NZ9000 (Kuipers et al. 1997), which carries one of the reporter plasmids, was used as a production strain.  L. lactis  strains were grown in M17 broth (Oxoid) supplemented with 0.5% glucose in standing cultures at 30° C. Chloramphenicol was added to the M17 medium to an end-concentration of 5 μg/ml when appropriate. For expression, mid-log phase cultures were induced for 2 hours with the culture supernatant of the nisin producing  L. lactis  strain NZ9700 as described by Kuipers et al. (1997).  Lactobacillus casei , ATCC393, was grown in MRS broth (Oxoid) in standing cultures at 30° C.  Mycobacterium smegmatis , ATCC700084, was grown in Middlebrook medium (Oxoid) at 37° C. in aerated cultures.  Bacillus subtilis,  168, was grown in TY broth (per liter: 10 g tryptone, 5 g yeast extract, 5 g NaCl pH 7.4) at 37° C. in aerated cultures. 
     Construction of Reporter Plasmids. The merozoite surface antigen 2 (MSA2) of  Plasmodium falciparum  strain 3D7 (Ramasamy et al. 1999) fused to the three repeats of AcmA (MSA2::cA) was used as the reporter anchor protein. The reporter anchor protein is encoded by plasmid pNG3041 based on the nisin inducible expression vector pNZ8048 (Kuipers et al. 1997) and contains a modified multiple cloning site in which the hybrid reporter gene was cloned. An in-frame fusion of the reporter was made at the 5′ end, the lactococcal PrtP signal—and prosequence, and at the 3′ end, the AcmA protein anchor sequence. The sequence of the MSA2 gene that was included in the construct corresponds to nucleotides (nt) 61 to 708 in GenBank accession number A06129. Primers used for the amplification of the MSA2 gene were MSA2.1 (5′-ACCATGGCAAAAAATGAAAGTAAATATAGC (SEQ ID NO:2)) and MSA2.4 (5′-CGGTCTCTAGCTTATAAGCTTAGAATTCGGGATGTTGCTGCTCC ACAG (SEQ ID NO:3)). The primers contain tags with restriction endonuclease recognition sites that were used for cloning. For cloning of the PrtP signal and prosequence (nt 1206 to 1766 in Kok et al. 1988), the primers PrtP.sspro.fw (5′-CCGTCTCCCATGCAAAGGAAAAAAGA AAGGGC (SEQ ID NO:4)) and PrtP.sspro.rev (AAAAAAAGCTTGAATTCCCAT GGCAGTCGGATAATAAACTTTCGCC (SEQ ID NO:5)) were used. The primers include restriction sites that were used for cloning. The AcmA protein anchor gene fragment (nt 833 to 1875) was obtained by subcloning a PvuII-HindIII fragment from plasmid pAL01 (Buist et al. 1995). Restriction endonuclease enzymes and Expand High Fidelity PCR polymerase were used in accordance with the instructions of the supplier (Roche). The final expression vector was designated pNG3041 ( FIG. 1 ). 
     A construct including a stop codon introduced after the MSA2 sequence in pNG3041 was designated pNG304. The protein secreted using this construct is substantially the same as the protein expressed from the pNG3041 plasmid except that the protein produced from pNG304 does not contain the AcmA protein anchor. The protein produced from pNG304 is used as a negative control in the binding assays. A vector was also made in which the AcmA protein anchor was exchanged for a protein anchor. The putative cell-wall binding domain of  L. lactis  AcmD (Bolotin et al. 2001) was cloned (nt 1796 to 2371 in GenBank accession number AE006288) using primers pACMB2 (5′-CGCAAGCTTCTGCAGAGCTCTTAGATTCTAATTGTTTGTCCTGG (SEQ ID NO:6)) and pACMB3 (5′-CGGAATTCAAGGAGGAGAAATATCAGGAGG (SEQ ID NO:7)) to produce the plasmid pNG3042. pNG3042 contains an in-frame fusion between MSA2 and the protein anchor of AcmD (MSA2::cD) and differs from plasmid pNG3041 only in the gene fragment encoding the protein anchor. 
     Cell Pretreatment and Binding Conditions. Chemical pretreatment of  L. lactis  NZ9000ÄacmA was done with 10% TCA (0.6 M) in the following manner. Cells of 0.5 ml stationary phase cultures were sedimented by centrifugation and washed once with 2 volumes of demineralized water. Cells were resuspended in 1 volume of a 10% TCA solution and incubated by placing the reaction tube in boiling water for 15 minutes. Subsequently, cells were washed once with 2 volumes PBS (58 mM Na 2 HPO 4 .2H 2 O, 17 mM NaH 2 PO 4 .H 2 O, 68 mM NaCl; pH 7.2) and three times with 2 volumes demineralized water. The cells were used directly for binding experiments or stored (as described herein) until further use. 
     The following chemicals and conditions were used to examine the effect of different chemicals on the binding capacity of  L. lactis  cells for AcmA-type protein anchor fusions: acetic acid (HAc), hydrochloric acid (HCl), sulfuric acid (H 2 SO 4 ), TCA, trifluoroacetic acid (TFA), and monochloro acetic acid (MCA). The acids were used at a final concentration of 0.6 M and incubated for 15 minutes in boiling water. SDS, dimethyl formamide (DMF) and dimethyl sulfoxide (DMSO) were used at a concentration of 10%. The SDS pretreatment was incubated for 15 minutes in boiling water and DMF and DMSO treatments were incubated at room temperature for 15 minutes. Cells were also pretreated with phenol (Tris buffer saturated) and incubated for 15 minutes at 55° C. Other chemicals pretreated at the 55° C. incubation temperature were: 4 M guanidine hydrochloride (GnHCl), 37% formaldehyde, chloroform:methanol (CHCL 3 :CH 3 OH (2:1)) and 0.1% sodium hypochlorite (NaOCl). In addition, incubation with 25 mM dithiothrietol (DTT) for 30 minutes at 37° C. and a pretreatment with hexane (100%) were analyzed. 
     The effect of enzymatic pretreatment of cells with lysozyme was also tested. For lysozyme pretreatment, the cells were resuspended in buffer (20% sucrose, 10 mM Tris pH 8.1, 10 mM EDTA, 50 mM NaCl) with lysozyme (2 mg/ml) and incubated at 55° C. for 15 minutes. After the chemical and enzymatic pretreatments, the washing steps were the same as the washing steps used for the TCA-treated cells. TCA pretreatment of  Bacillus subtilis, Lactobacillus casei  and  Mycobacterium smegmatis  was done as described herein for  L. lactis.    
     Cell-free culture supernatants containing MSA2::cA, MSA2::cD or MSA2 without anchor were incubated in four-fold excess for 10 minutes at room temperature with pretreated cells (e.g., cells from 0.5 ml culture were incubated with 2.0 ml culture supernatant). After binding, cells were sedimented by centrifugation, washed twice in 2 volumes of demineralized water, resuspended in SDS-denaturation buffer, heated for 5 minutes at 98° C., subjected to SDS-PAGE, and analyzed by Western blot analysis. 
     Storage Conditions. Cell-free supernatants containing MSA2::cA, MSA2::cD or MSA2 were stored at −20° C. with or without 10% glycerol prior to binding. TCA-pretreated  L. lactis  cells were stored at −80° C. in 10% glycerol prior to binding. TCA pretreated  L. lactis  cells with bound MSA2::cA were stored at +4° C. or −80° C. with or without 10% glycerol. Cells stored in 10% glycerol were washed once with 1 volume of demineralized water prior to binding. 
     Cell pellets (in demineralized water) of TCA-pretreated  L. lactis  cells with or without bound MSA2::cA were frozen by contacting the vials with liquid nitrogen and removing the water with lyophilization. Alternatively, non-frozen cell pellets were dried under vacuum at 30° C. for 2 hours prior to binding. 
     Western Blotting. For detection of MSA2 proteins, cell pellets corresponding to 500 μl culture were resuspended in 50 μl SDS-denaturation buffer. Cell-free culture supernatants (1 ml) were concentrated by phenol-ether precipitation (Sauvé et al. 1995), vacuum dried and resuspended in 50 μl SDS-denaturation buffer. Proteins were separated with standard SDS-PAGE techniques. After separation, proteins were electroblotted onto PVDF membranes (Roche). In immunoblots, MSA2 proteins were detected with 1:10,000 diluted rabbit MSA2-specific antiserum (Ramasamy et al. 1999) and 1:5,000 diluted anti-rabbit IgG-conjugated alkaline phosphatase (Roche) using known procedures. 
     Fluorescence Microscopy. 100 μl cell suspensions incubated with MSA2::cA, MSA2::cD or MSA2 fusion proteins were washed twice with demineralized water and resuspended in an equal volume of PBS containing 1% BSA and MSA2-specific rabbit antiserum diluted to 1:200. After incubation for 20 minutes at room temperature, the cells were washed three times with 2 volumes PBS. Subsequently, the cells were incubated for 20 minutes in 1 volume PBS with 1% BSA and 1:100 diluted Oregon green labeled goat anti-rabbit immunoglobulin G (Molecular Probes). After washing once with 2 volumes PBS and twice with 2 volumes demineralized water, the cells were resuspended in 100 μl demineralized water. A 10 μl aliquot of the resuspended cells was spread onto a Polysin microslide (Menzel-Gläser), air dried, and examined under a fluorescence microscope (Zeiss). 
     Electron microscopy. TCA-pretreated  L. lactis  cells incubated with MSA2::cA, MSA2::cD or MSA2 were collected and washed as described herein. Immunogold labeling was performed on whole mount preparations of glutaraldehyde fixed cells on Formvar-carbon coated nickel grids using Auroprobe 15 nm goat anti-rabbit IgG gold marker (Amersham). Primary antibodies against MSA2 were diluted 1:1000 in PBS-glycine buffer. The labeled samples were stained with 0.1% uranyl acetate (W/V in water) and examined in a Philips CM10 transmission electron microscope at 100 kV. 
     Pretreatment of  L. Lactis  Cells with Different Chemicals. The cA protein anchor of  L. lactis  AcmA can be used to bind fusion proteins to a wide variety of Gram -positive bacteria. However, the amount of fusion protein that binds varies greatly among this group of bacteria. Binding of MSA2::cA that covers the entire cell surface of some lactobacilli was observed, whereas other bacteria such as  L. lactis  showed only limited localized binding ( FIG. 2A ). This phenomenon may be due to the fact that the cell walls of some bacterial species contain components that interfere with cA anchor binding. Since chemicals like SDS, TCA, chloroform/methanol and others may be used to remove components from isolated bacterial cell walls (Morata de Ambrosini et al. 1998), the effect of the removal of cell-wall components from  L. lactis  whole cells on the binding of the reporter fusion protein MSA2::cA was investigated.  L. lactis  cells were pretreated as described herein with various chemicals or with lysozyme. 
       FIG. 3  shows typical Western blots of pretreated whole cells to which MSA2::cA was bound. Mature MSA2::cA migrates at a position of a 75 kDa protein (indicated by an asterisk). The arrow represents MSA2::cA that contains the PrtP prosequence. The double asterisks represent MSA2::cA from which one or two of the repeats have been removed. A cell membrane anchored protease HtrA has been shown to be involved in processing proproteins and in removing repeats from AcmA (Poquet et al. 2000). From the results of  FIG. 3 , it may be concluded that pretreatment with TCA (lanes 8 and 16 contain the same samples, the difference in signal intensity is due to differences in stain developing time), HCl, H 2 SO 4  and HAc substantially improves the subsequent binding of MSA2::cA (compare with the negative control in lane 15). Other tested acids, TFA and MCA, had similar effects (not shown). Phenol, GnHCl, formamide and chloroform/methanol pretreatments showed a moderate improvement of binding (lanes 4, 5, 6, 7, respectively). Minor binding improvements were observed after pretreatment with SDS, DMF, DMSO and DTT. The results are summarized in Table 1. Based on the results, it appears that pretreatment of  L. lactis  cells with the acids TCA, TFA, MCA, HCl, H 2 SO 4  and HAc are the most effective agents for improving binding of cA anchor fusion proteins to lactococcal cells. Acids such as TCA are known to remove lipoteichoic acids from cell walls. 
     Whether proteins are removed from the cell walls by these acid treatments was also analyzed.  FIG. 4  shows a Coomassie stained gel of lysed pretreated cells. Most of the acid treatments, except for HAc, removed a substantial amount of proteins from the lactococcal cells. Since HAc removed only a trace amount of proteins (compare lane 1 and 4) and SDS pretreatment (which is known to remove proteins from the cell walls) showed only a minor improvement of MSA2::cA binding ( FIG. 3 , lane 1), it may be concluded that removal of proteins from the cell wall is not critical for improving the binding of cA anchor fusions. This conclusion may be due to the fact that lipoteichoic acids or carbohydrates occupy sites in the cell walls of  L. lactis  that interfere with efficient binding. Alternatively, acid pretreatment may result in altering the compactness of peptidoglycan strands that make cA binding sites more available. 
     TCA pretreatment was also used in all other experiments. The optimal TCA concentration in the boiling procedure was determined. TCA percentages of 1, 5, 10 and 20% were tested. Although 1% TCA pretreatment already showed a significant improvement in binding of MSA2::cA and 5% TCA pretreatment showed a further increase, no further improvement was observed at concentrations higher than 10% TCA ( FIG. 5 ). Therefore, the boiling procedure with 10% TCA was selected as the standard procedure for the experiments. 
     The binding characteristics of the lactococcal cA homolog cD in an MSA2 fusion were analyzed using the standard TCA pretreatment procedure. Two of the three AcmD repeats are highly homologous to those of AcmA. An alignment is shown in  FIG. 6 . Secreted MSA2 without an anchoring domain was included in these experiments as a negative control. In Western blots, the effect of TCA pretreatment on the binding of MSA2::cA was evident ( FIG. 7 , compare lanes 1 and 4). The effect of TCA pretreatment was also studied using fluorescence microscopy ( FIG. 2 , compare  L. lactis  in A and B;  FIG. 8 ) and electron microscopy ( FIG. 9 , compare A and B). Independent of the technique used, the effect of TCA pretreatment on the binding of MSA2::cA can be detected. 
     The binding of MSA2::cD to non-TCA-pretreated  L. lactis  cells was low as detected in Western blots ( FIG. 7 , lane 2) and was undetectable in fluorescence microscopy and electron microscopy ( FIG. 9A ). TCA pretreatment only had minor effects on the intensity of the MSA2::cD signal in Western blots ( FIG. 7 , lane 5). At the same time, no MSA2::cD specific signal associated with the pretreated cells could be observed in fluorescence microscopy ( FIG. 8 ) and only low levels of labeling were observed in electron microscopy ( FIG. 9C ). Some cell-associated signal was observed for MSA2 without anchoring domain for both non-TCA pretreated and TCA-pretreated  L. lactis  cells ( FIG. 7 , lanes 3 and 6, respectively). However, for MSA2::cD, this was not observed in fluorescence microscopy (not shown) and only minor labeling signals were found in electron microscopy ( FIG. 9D ). Taken together, it may be concluded that: (i) the reporter protein MSA2 does have some low degree of affinity for bacterial cell walls that can be detected in Western blots; (ii) the cA anchor domain specifically stimulates the binding of the reporter fusion to non-pretreated cells; (iii) chemical pretreatment, especially with acids, enhances this binding; and (iv) the cD anchor domain does not promote binding of fusion proteins under the conditions applied. 
     The fluorescence microscopic images and electron microscopic images of TCA pretreated lactococcal cells ( FIGS. 2 ,  8  and  9 ) showed that pretreatment leaves the integrity of the cell intact. However, cells are no longer viable (plating efficiency 0) and therefore may be considered as inert spherical peptidoglycan microparticles with a diameter of approximately 1 μm, “ghost cells.” 
     Binding to Other Gram-Positives. The binding of MSA2::cA, MSA2::cD and MSA2 without anchor domain to the Gram-positive bacteria  B. subtilis, Lb. casei  and  M. smegmatis  was also analyzed.  FIG. 10  shows a Western blot summarizing binding of MSA2::cA, MSA2::cD and MSA2 to non-pretreated and TCA-pretreated  B. subtilis  cells. As for  L. lactis , an increase in binding is observed for MSA2::cA. An MSA::cA specific signal could also be visualized in fluorescence microscopy of non-pretreated  B. subtilis  cells, but with a highly improved signal for the TCA-pretreated cells (not shown). Binding of MSA2::cD and MSA2 to non-pretreated or TCA-pretreated cells could not be demonstrated in fluorescence microscopy (not shown). 
     Similar results were obtained for  Lb. casei  and  M. smegmatis . The improved binding of MSA2::cA to TCA-pretreated  Lb. casei  cells is shown in  FIG. 11 . For MSA2::cD and MSA2, no fluorescence signals were detected (not shown). The TCA pretreatment of  M. smegmatis  also had a positive effect on the binding of MSA2::cA, whereas no binding was observed for MSA2::cD or MSA2 ( FIG. 12 ). Taken together, it may be concluded that acid pretreatment, such as with TCA, improves the binding of cA protein anchor fusions to the cell surface of Gram-positive bacteria. 
     Binding strength and storage conditions. The strength of the MSA2::cA binding to TCA-pretreated  L. lactis  cells was analyzed with a treatment of LiCl after the binding. LiCl is commonly used to remove proteins from bacterial cell walls. From the Western blot of  FIG. 13 , it may be concluded that 8 M LiCl partially removes MSA2::cA from the  L. lactis  cells (compare lanes 4 and 5). Therefore, although MSA2::cA binds non-covalently to cell walls, the binding interactions are most likely very strong. 
     Cell-free culture supernatants with MSA2::cA were stored with or without 10% glycerol at −20° C. MSA2::cA stored in this manner for several weeks had the same capacity to bind to TCA-pretreated  L. lactis  cells (not shown). 
     TCA-pretreated  L. lactis  cells with bound MSA2::cA were stored for 3 weeks at +4° C. in demineralized water or at −80° C. in demineralized water with or without 10% glycerol. The samples were analyzed in Western blots. Storing pretreated cells with bound MSA2::cA for 3 weeks in water at +4° C. only resulted in a loss of signal of about 50% ( FIG. 13 , compare lanes 4 and 6). Whether this loss of signal was due to degradation or due to release of the protein into the water was not determined. Storage at −80° C. with or without 10% glycerol had no effect on the binding ( FIG. 13 , compare lanes 4, 7 and 8). 
     In addition, the effects of drying and lyophilization on the binding of MSA2::cA to TCA-pretreated  L. lactis  cells were studied. Drying of pretreated cells had no observable negative effect on binding of MSA2::cA afterwards. Dried pretreated cells with bound MSA2::cA could be resuspended in water without losing bound fusion protein. This was also observed for lyophilized cells with bound MSA2::cA. Lyophilization of TCA-pretreated cells prior to binding resulted in loss of the binding capacity for MSA2::cA (results not shown). 
     From these data, it may be concluded that: (i) in spite of the non-covalent character of cA anchor binding to cell walls, the binding is very strong; (ii) cell-free culture supernatants can be stored safely at −20° C.; and (iii) drying of TCA-pretreated cells provides an efficient and simple method for storage of such cells either with or without bound cA-anchor fusions. 
     EXAMPLE 2 
     Oral Immunizations of Rabbits with Non-recombinant  Lactococcus Lactis  Preloaded with the  Plasmodium falciparum  Malaria Antigen MSA2 Fused to the Lactococcal AcmA Protein Anchor 
     In Example 1, a technology is described that efficiently binds protein hybrids when externally added to the cell surface of non-recombinant gram-positive bacteria by means of an AcmA-type protein anchor. This technology provides the possibility to provide bacteria or bacterial cell walls with new traits without introducing recombinant DNA into them. The immunogenicity in rabbits of the  Plasmodium falciparum  merozoite surface protein, MSA2 of strain 3D7 (Ramasamy et al. 1999), presented on the cell surface of non -recombinant non-living  L. lactis  cells as an AcmA anchor fusion protein was investigated. 
     Materials and Methods 
     Bacterial Strains and Growth Conditions. The  L. lactis  strain which produces MSA2::cA, the strain&#39;s growth conditions, the induction for expression, the TCA pretreatment of the  L. lactis  recipient cells and the binding of MSA2::cA to the cells was described in Example 1 with the following modification: a ratio of 1 (TCA-pretreated cells) to 5 (cell-free culture supernatant with MSA2::cA) was used for binding. An  L. lactis  NZ9000 strain carrying plasmid pNG3043 was used as a positive control in the immunization experiments (was positive in a previous, unpublished experiment). Plasmid pNG3043 encodes an MSA2 hybrid protein that contains the lactococcal PrtP cell-wall anchoring domain at its C-terminus (MSA2::cP) instead of the AcmA protein anchor. The PrtP cell-wall anchoring domain contains the LPXTG (SEQ ID NO: 1) motif that enables a membrane-linked sortase to covalently couple the protein to the cell wall (Navarre and Schneewind 1994). The cP domain used in construct pNG3043 corresponds to nt 6539 to 6914 in Kok et al. (1988). Primers used for the amplification of this fragment were PrtP.cwa.fw3 (5′-ATATAAAGCTTGCAAAGTCTGAAAACGAAGG (SEQ ID NO:8)) and PrtP.cwa.rev (5′-CCGTCTCAAGCTCACTATTCTTCACGTTGTTTCCG (SEQ ID NO:9)). The primers include restriction endonuclease recognition sites for cloning. Plasmid pNG3043 differs from plasmid pNG3041 in the cell-wall binding domain. Growth conditions and induction of expression of strain NZ9000ΔacmA(pNG3043) were the same as for strain NZ9000Δ acmA(pNG3041). 
     Rabbit Immunizations. Ten barrier-reared, New Zealand white rabbits obtained from Harlan laboratories, The Netherlands, were used in groups of 2 for experimental immunizations. The care and use of animals were according to WHO guidelines (WHO/LAB/88.1). The rabbits were ear bled prior to immunization to obtain preimmune sera. Details of the rabbits and immunogens are as follows: 
     Rabbits A1 and A2 were subcutaneously immunized with NZ9000Δ acmA(pNG3041) cells (recombinant, MSA2::cA partly surface anchored). 
     Rabbits B1 and B2 were subcutaneously immunized with NZ9000ΔacmA (negative control). 
     Rabbits C1 and C2 were orally immunized with NZ9000ΔacmA(pNG3043) cells (recombinant, MSA2::cP surface anchored). 
     Rabbits D1 and D2 were orally immunized with NZ9000ΔacmA(pNG3041) cells (recombinant, MSA2::cA surface anchored). 
     Rabbits E1 and E2 were orally immunized with TCA treated NZ9000ΔacmA to which MSA2::cA had been bound from NZ9000ΔacmA(pNG3041) culture supernatant (non-recombinant, MSA2::cA surface anchored). 
     Stocks of NZ9000ΔacmA(pNG3043) with MSA2::cP expressed at its surface were stored in aliquots of 10 11  cells in growth medium containing 10% glycerol at −80° C. The cells remain viable under these conditions and retain MSA2 on the surface as demonstrated by immunofluorescence (not shown). The first immunization was carried out with freshly grown bacteria. For subsequent immunizations, stocks of bacteria were freshly thawed, washed and resuspended in buffer at the appropriate concentration for immunizations. 
     On the other hand, the non-pretreated NZ9000ΔacmA (negative control), the non-pretreated NZ9000ΔacmA(pNG3041) and the TCA-pretreated NZ9000ΔacmA with the externally bound MSA2::cA were prepared daily from fresh cultures. 
     Subcutaneous injections were performed with a total of 5×10 9  cells in 100 μl PBS without any adjuvant into two sides on either side of the spine. The subcutaneous injections were repeated two more times at three-week intervals. Prior to oral immunization, the rabbits were deprived of water and food for two to four hours. The rabbits were then fed 5×10 10  cells resuspended in 1 ml of 0.5% sucrose. Each dose was repeated for three successive days to obtain reproducible oral immunization. Altogether, three series of oral immunizations were given at three-week intervals. Adverse effects consequent to the immunizations, including granulomas at the sites of subcutaneous injections, were not observed, indicating that  L. lactis  was well tolerated by the animals. 
     Serum Antibody Responses. Rabbits were ear bled two weeks after each immunization to obtain sera for antibody assays. The sera were stored at −20° C. until use. Ten-fold serial dilutions of the antisera in 2% BSA in PBS were used in immunofluorescence assays (IFA) to determine the titer of the antibodies against MSA2 on the surface of 3D7  P. falciparum  merozoites. IFA was performed on acetone-methanol fixed late stage 3D7  P. falciparum  parasites as previously described (Ramasamy 1987). For detection of antibody isotypes, Oregon Green conjugated goat anti-rabbit Ig (Molecular Probes) was used as the second antibody. For detection of IgG antibodies, a fluorescein conjugated, affinity purified, mouse monoclonal with specificity against rabbit IgG chains (Rockland) was used. 
     Results and Discussion 
     Surface Expression of MSA2 in Different  L. Lactis  Strains. Coomassie staining of SDS-PAGE gels and fluorescence microscopy were used to determine, in a semi-quantitative way, the number of MSA2 molecules expressed and surface exposed by the recombinant lactococcal strains carrying plasmid pNG3041 or pNG3043 that produce MSA2::cA or MSA2::cP, respectively, and by the non-recombinant TCA-pretreated  L. lactis  cells to which MSA2::cA had been bound from the outside. The recombinant strains were estimated to produce approximately 1.4×10 5  molecules of MSA2::cA or MSA2::cP. The surface exposure of MSA2::cA and MSA2::cP differed considerably as shown by fluorescence microscopy in  FIG. 14 . The non-recombinant TCA-pretreated  L. lactis  cells with bound MSA2::cA showed a uniform staining of the entire cell surface. However, the semiquantitative SDS-PAGE analysis indicated that about 1×10 4  molecules of MSA2::cA per cell were represented. 
     Accordingly, it may be concluded that the number of surface-exposed MSA2::cA and MSA2::cP on the recombinant lactococcal strains is less than 10% of the total number of molecules produced by these strains. The other molecules are most likely trapped in the membrane or the cell wall. Similar observations were made by Norton et al. (1996) for the expression of TTFC fused to the cP cell-wall anchoring domain. In that study, only membrane-associated or cell-wall-associated TTFC could be demonstrated and no surface-exposed TTFC::cP was demonstrated. Thus, it appears that binding from the outside to TCA-pretreated cells is a more efficient method to surface-exposed proteins on  L. lactis  cells. 
     Anti-MSA2 Antibody Responses in Orally Immunized Rabbits. Characteristics of the anti-MSA2 antibody response to the immunizations are summarized in Table 2. The oral immunizations with the recombinant  L. lactis  that produces MSA2::cP (rabbits C1 and C2) were done before (unpublished results) and used as a positive control. In the previous experiment, a similar antibody response was found. The present experiment showed that specific antibodies against near native MSA2 were detectable after two immunizations for group A, D and E rabbits, and that antibody titers increased in all instances after a third immunization. IgG antibodies were predominant after three immunizations in either the subcutaneous or oral route. A comparatively weak anti-MSA2 surface IFA, attributable to the generation of cross-reactive antibodies (as described herein), was also observed after three control subcutaneous immunizations with  L. lactis  cells alone. 
     Taken together, the results indicate that: (i) MSA2 produced by lactococcal cells elicits serum antibodies that recognize native  P. falciparum  parasite MSA2; (ii) MSA2-specific T h  cells are activated through mucosal immunization due to the presence of systemic IgG antibodies (Table 2) that can be boosted (unpublished results); and (iii) oral immunizations with MSA2::cA bound to non-recombinant non-living TCA-pretreated  L. lactis  cells are as efficient in evoking specific serum antibody responses as the live recombinant strain producing MSA2::cA that was administered subcutaneously or orally, or as efficient as the live recombinant strain producing MSA2::cP that binds MSA2 covalently to its cell wall delivered orally. 
     Anti-lactococcal Antibody Responses. Western blots ( FIG. 15 ) demonstrated significant antibody responses against  L. lactis  antigens after two and three immunizations of the rabbits. The responses were notably greater after subcutaneous (group A and B rabbits) than oral immunization with  L. lactis  (group C rabbits). Oral immunization with the TCA-pretreated lactococcal cells (group E rabbits) elicited antibodies that reacted at a lower intensity with fewer  L. lactis  antigens than oral immunization with viable  L. lactis  cells. This is most likely due to the fact that proteins are removed from the lactococcal cells by the TCA pretreatment (see, Example 1). The lower anti-carrier response observed for the TCA-pretreated (non -recombinant) cells renders this type of delivery vehicle more suitable for repeated immunization strategies than its untreated (recombinant) counterpart. 
     EXAMPLE 3 
     pH-dependent Cell-wall Binding of AcmA Protein Anchor Homologs and Hybrids 
     The cell-wall binding domain or anchor of the lactococcal cell-wall hydrolase unization strategies than AcmA includes three repeats of 45 amino acids that show a high degree of homology (Buist et al. 1995). These three repeats belong to a family of domains that meet the consensus criteria as defined in PCT publication WO 99/25836 and can be found in various surface-located proteins in a wide variety of organisms. Another feature that most of these domains have in common is that their calculated pI values are high, approximately 8 or higher (Table 3). The pH used in previous binding experiments with MSA2::cA (i.e., Examples 1 and 2) was approximately 6, indicating that the binding domain was positively charged. 
     The AcmA protein anchor homolog of the lactococcal cell-wall hydrolase AcmD (cD) (Bolotin et al. 2001) also includes three repeats ( FIG. 16 ) with a calculated pI that is lower (approximately pI 3.8) than that of the cA domain (Table 4). Consequently, the cD anchor was negatively charged at the binding conditions used in Example 1. No binding of the MSA2::cD reporter protein occurred under these conditions as demonstrated herein. Therefore, the influence of the pH during binding of a cD fusion protein (MSA2::cD) was investigated. Furthermore, a hybrid protein anchor including the three cD repeats and one cA repeat that has a calculated pI value that is higher than that of the cD repeats alone was constructed. The hybrid protein anchor showed better binding pH values above the pI of the cD repeats alone, indicating that the pH binding range of AcmA-type protein anchors can be manipulated by using the pI values of the individual repeats in hybrids. 
     Materials and Methods 
     Bacterial strains, growth and induction conditions, TCA pretreatment of  L. lactis  cells, incubation of the MSA2 protein anchor fusion proteins to TCA-pretreated cells, washing conditions, protein gel electrophoresis, Western blotting and immunodetection were the same as described herein with reference to Example 1. The cell-free culture supernatants with MSA2::cA, MSA2::cD or A3D1D2D3 have a pH of approximately 6.2. The influence of pH was examined by adjusting the pH of the cultures by the addition of HCl or NaOH to obtain the required pH. 
     Plasmid Constructions. The plasmid that expresses the MSA2::cD fusion was described herein with reference to Example 1. Plasmid pPA43 is based on the same expression plasmid and contains an in-frame fusion of the lactococcal signal sequence of Usp45 (ssUsp; van Asseldonk et al. 1990. Gene 95: 155-160), the c-myc epitope for detection purposes, the A3 cA repeat and repeats D1, D2 and D3 of cD. Primers used for cloning A3 were cA repeat3.fw (CCG TCT CCA ATT CAA TCT GCT GCT GCT TCA AAT CC (SEQ ID NO: 10)) and cA repeat3.rev (TAA TAA GCT TAA AGG TCT CCA ATT CCT TTT ATT CGT AGA TAC TGA CCA ATT AAA ATA G (SEQ ID NO: 11)) (the primers include the A3 specific sequences). The primers used for cloning the three cD repeats were cDrepeat1.fw (CCGTCTCCAATTTCAGGAGGAACTGCTGTTACAACTAG) (SEQ ID NO: 12) and cDrepeat3.rev (TAATAAGCTTAAAGGTCTCCAATTCCAGCAACTTGCAAAACTTCTCCTAC) (SEQ ID NO: 13) (the primers include the cD specific sequences). 
     Results and Discussion 
     Binding of MSA2::cD at Low pH. Since binding of MSA2::cD was not observed at a pH (the pH of the culture medium after growth and induction is about 6.2) higher than the calculated pI for the cD domain (i.e., pI 3.85), binding was studied when the pH of the medium was adjusted to pH 3.2. TCA-pretreated  L. lactis  cells were used as the binding substrate and the relative amounts of bound MSA2::cD were analyzed in Western blots. The amounts of unbound reporter protein remaining in the culture supernatant after binding were also analyzed.  FIG. 17  shows a clear increase in bound MSA2::cD when binding is performed at pH 3.2 (compare lanes 1 and 3). At the same time, less unbound reporter protein remained in the supernatant (compare lanes 2 and 4). This result indicates that positive charges are important for binding of cA-type anchoring domains. 
     Binding of cAcD Hybrid Anchors. Analysis of the pI values of the cA homologs in Table 3 indicates that two classes of repeats can be distinguished: a majority (99 out of 148) of homologs that have a high pI value (&gt;8) and a smaller group (33 out 148), of which cD is a representative, that has pI values lower than 6. Based on the experimental results, it is shown that these types of anchoring domains only bind to bacterial cell walls at a pH that is lower than the anchoring domains pI. Notably, most cell-wall binding domain homologs include repeats with a pI that are representatives of one of the two groups, i.e., only repeats with a high or low pI. Some proteins with cell-wall binding domains, e.g., those of DniR of  Trepanoma pallidum  and an amidase of  Borrelia burgdorferi , include repeats with high and low pI. Since the binding pH of such “natural hybrid” cell-wall binding domains is below the intermediate pI value of the total number of repeats present in the domain, a hybrid cell-wall protein anchor was constructed using the cA and cD repeats with an intermediate pI value. Table 5 lists the native AcmA and AcmD anchors and a number of examples of cA/cD hybrids. The constructed hybrid protein anchor (A3 D1D2D3) has a calculated pI value of approximately 5.1. A protein anchor including only D1D2D3 shows little binding at a pH above its calculated pI (as described herein). The A3 (pI 10) domain shows similar binding at pH 5 and pH 7. 
     The binding of the hybrid anchor A3D1D2D3 was tested at pH 3, pH 5 and pH 7. At pH 3, most protein had been bound to the ghost cells ( FIG. 18 ). At pH 5, there was considerable binding (+/−40%), whereas there was only minimal binding at pH 7 (+/−20%). This result indicates the pH range of binding for cD repeats was shifted to higher pH values by the addition of one cA repeat (A3) that caused a shift in calculated pI values of 3.8 to 5.1. The increase of binding at pH 5 for the A3D1D2D3 hybrid cannot be attributed to binding of the A3 repeat alone. If this was the case, then the same level of binding should occur at pH 7 since the A repeats show the same binding at these pH values. In addition, the increased binding at pH 5 is not an additive effect in the sense that an extra binding domain results in increased binding. It has previously been shown that addition of one repeat to the cA anchor did not result in increased binding. The binding at the higher pH values of the A3D1D2D3 repeats, as compared to the D1D2D3 repeats alone, thus may be attributed to the increase in the calculated pI value of the hybrid cA/cD anchor. This demonstrates that pH binding properties of these types of protein anchors may be manipulated on the basis of the pI values of individual repeats present in the hybrid anchor. 
     EXAMPLE 4 
     Induction of Cellular Immune Responses in Mice after Oral Immunizations with Lactococcal Ghosts Displaying the Malaria  Plasmodium Falciparum  Antigen MSA2 Fused to the Lactococcal AcmA Protein Anchor 
     Non-genetically modified non-living  Lactococcus lactis  cells (ghosts) preloaded with the  Plasmodium falciparum  MSA2 antigen fused to the AcmA protein anchor (MSA2::cA) were used to orally immunize mice in a similar way as described herein with reference to Example 2. In this experiment, the question of whether immunizations through the oral route with the non-recombinant non-living Ghosts carrying MSA2::cA on their surface (Ghosts-MSA2::cA) can elicit typical Th1-type immune responses, such as IgG2 antibodies and gamma-interferon (γIFN)-producing T cells in the spleen is addressed. These responses are particularly relevant to obtain immunity for pathogens, such as malaria, that undergo stages in their life cycle where they are not in the blood but hide in cells. 
     Materials and Methods 
     Groups of five mice of different strains were used for immunization. The strains of mice used were Balb/c (with the major histocompatibility locus allotype of H2d), C57 Black (H2b), C3H (H2k) and ICR (outbred, i.e., of varying H2 types). Oral immunizations were performed at three weekly intervals. Immunizations were performed with MSA2::cA absorbed onto the surfaces of TCA-treated  Lactococcus lactis  cells (Ghosts-MSA2::cA) or with recombinant  L. lactis  that displayed MSA2 on the surface through the use of a covalently linked cell-wall anchor ( L. lactis (MSA2::cP)) as described herein with reference to Example 2. The mice were tail bled to obtain serum samples two weeks after the second, third and fourth immunizations. Fecal pellets were collected and extracted to examine intestinal IgA antibody production. The mice were sacrificed at the end of each experiment and the spleens were removed for examining T-cell responses by ELISPOT. MSA2-his tag produced in  E. coli  was used as antigen in the ELISA and ELISPOT assay. The growth of bacterial strains and the preparation of Ghost cells were as described herein with reference to Example 2. 
     Results and Discussion 
     Kinetics and Isotypes of the Serum IgG Antibodies Generated Oral Immunizations. Differences in the kinetics of the antibody response and the isotype distribution were observed between different murine strains. The antibody response was also different when living recombinant  L. lactis  (MSA2::cP) or Ghosts-MSA2::cA were used as immunogens. With Ghosts-MSA2::cA, high serum antibody levels were detectable in the C3H mice after two immunizations. IgG antibodies were detectable in all four murine strains after three and four immunizations. Antibody titers were highest in C3H mice. IgG antibodies that reacted with native MSA2 on parasites were detected in the sera of immune mice by fluorescence microscopy (IFA) confirming that the immunizing form of the protein elicits biologically relevant antibodies. Control immunizations were performed with Ghosts alone where no MSA2-specific antibodies were elicited. In parallel experiments using MSA2cP as the immunogen, high serum IgG antibody levels were only seen with Balb/c mice after two immunizations. After three and four immunizations, good antibody responses developed in C3H mice. Antibody titers were highest in Balb/c mice. 
     Significant differences existed between the strains in the isotypes of the elicited serum IgG antibodies in response to immunization with Ghosts-MSA2::cA. Balb/c mice showed higher levels of IgG2a and IgG2b antibodies, some IgG3 antibodies and negligible IgG1, which demonstrates a possible Th1 bias. On the other hand, C57 Black and C3H mice had high IgG1, IgG2a and IgG2b, and lower IgG3 antibodies to MSA2, which is more characteristic of a mixed Th1 and Th2 response. ICR mice, as expected, showed a range of responses. Some ICR mice had the Balb/c and others the C3H/C57 Black pattern of IgG isotypes. 
     Formation of Mucosal Antibodies. IgA antibodies were detected by ELISA in the fecal pellets of the ICR and Balb/c mice, but were not detected in C3H or C57 Black mice when immunization was performed with living recombinant  L. lactis (MSA2::cP) or Ghost-MSA2::cA. 
     T-Cell Responses. The increase of the intensity of the IgG ELISA reactions seen in mice immunized with Ghosts-MSA2::cA with each immunization demonstrates that boosting takes place and that a Th-dependent antibody response exists in these animals. The IgG isotype distribution further confirms this conclusion. Therefore, Th cells are generated in ICR, Balb/c, C57 Black and C3H mice. 
     The ELISPOT assay for detecting gamma-interferon (γIFN) producing cells detects mainly CD8 +  Tc cells, which are an important component of the immune response to many pathogens, including malaria parasites. His-tagged MSA2 produced in  E. coli  was used as antigen in the assay. MSA2-specific γIFN producing cells could be detected in the spleens of Balb/c, C57 Black and C3H mice that were immunized with Ghosts-MSA2::cA. MSA2-specific γIFN producing cells were not observed in the spleens of control mice immunized with Ghosts alone or with the living recombinant  L. lactis (MSA2-cP). The latter group showed a high level of non-specific γIFN producing cells. The high background observed may be due to ongoing inflammation. 
     The sensitization of MSA2-specific Tc cells in the spleen after immunization with the non-recombinant non-living  L. lactis  Ghost system carrying a foreign protein is a novel finding which is applicable to malaria since protection against sporozoite-infection is associated with γIFN producing cells being produced in the spleen. 
     The non-recombinant non-living Ghost system can be used in oral immunizations to elicit typical Th1-type immune responses. These types of responses are particularly relevant to obtain immunity for pathogens that undergo stages in their life cycle where the pathogens are not in the blood but rather hide in cells. The responses are more pronounced and more specific for the Ghost system than for the living recombinant system. The Ghost system has the additional advantage of eliminating the risk of spreading recombinant DNA into the environment. 
     EXAMPLE 5 
     Protection of Mice for Lethal  Streptococcus pneumoniae  Challenge after Oral Immunizations with Lactococcal Ghosts Preloaded with PpmA Antigen Fused to the Lactococcal AcmA Protein Anchor 
       Streptococcus pneumoniae  is the leading etiological agent of severe infections including septicemia, meningitis, pneumonia, and otitis media. Recent studies on the molecular epidemiology and pathogenesis of  S. pneumoniae  have identified pneumococcal proteins with vaccine potential. One of these proteins, the protease maturation protein PpmA, has been shown to elicit immune protective potential in a mouse pneumonia model. 
     The non-genetically modified lactococcal ghosts have been shown to be an efficient carrier for use in oral immunizations of rabbits and mice in order to elicit strong anti-malaria immune responses. The construction of lactococcal ghosts that display the  S. pneumoniae  PpmA fused to the lactococcal AcmA cell-wall binding domain on their surface is described herein. The ability of these ghosts to protect orally immunized mice from a lethal nasal dose of  S. pneumoniae  was investigated. 
     Materials and Methods 
     Bacterial Strains and Growth Conditions.  L. lactis  was grown and ghost cells were prepared as described herein with reference to Example 1.  S. pneumoniae  was grown as described before (Gingles et al. 2001 , Infect. Immun.  69: 426-434). 
     Construction of ppmA Protein Anchor Fusion Expression Plasmid. The expression plasmid for ppmA protein anchor fusion (PpmA::cA) was substantially similar to the expression plasmid for the MSA2 protein anchor fusion as described herein with reference to Example 2. For the secretion of PpmA::cA, the secretion signal sequence of the Usp45 protein (ssUsp) of  L. lactis  (van Asseldonk et al. 1990. Gene 95: 155-160) was used. The PpmA gene was cloned by PCR using primers ppmA.1 (CGGTCTCACATGTCGAAAGGGTCAGAAGGTGCAGACC) (SEQ ID NO: 14) and ppmA.2 (CGGTCTCGAATTGCTTCGTTTGATGTACTACTG CTTGAG) (SEQ ID NO:15) resulting in plasmid pPA32 which contains ppmA as an in-frame fusion with ssUsp45 and the protein anchor (ssUsp::ppmA::cA). Expression of the fusion gene results in the secreted product PpmA::cA. The primers include an Eco31I restriction enzyme recognition site that was used for digestion of the PCR fragment. This restriction digest produced NcoI and EcoRI sticky ends which were used for cloning. The primers also included the ppmA sequences. Chromosomal DNA of  S. pneumoniae  strain D39 was used as a template for the PCR reactions. 
     Preparation of the Vaccine. Three liters of M17 medium with PpmA::cA, obtained after growth and used to induce producer cells for expression of  L. lactis  (pPA32) was centrifuged and filter sterilized (0.2 μm) to remove the producer cells. Ghost cells were prepared from 0.5 liter of  L. lactis  NZ9000(ΔacmA). After binding, the ghost cells with PpmA::cA (Ghosts-PpmA::cA) were isolated by centrifugation and washed with PBS. The ghost cells were stored in PBS in aliquots of 2.5×10 10  Ghosts/ml at −80° C. Two control groups included: (i) Ghosts without bound PpmA::cA; for the sample preparation, the same amounts of ghost cells were used and the same centrifugation and washing steps were performed, but the binding step was omitted; and (ii) soluble PpmA was isolated as a his-tagged fusion. 
     Mice Immunizations. Groups of 10 mice (CD-1) were used in the immunizations. Oral doses included 5×10 9  Ghosts with or without PpmA::cA (50 μg) or 50 μg soluble PpmA in PBS. Nasal doses included 5×10 8  Ghosts with or without PpmA::cA (5 μg) or 5 μg soluble PpmA. 10 8  Ghosts-PpmA::cA (1 μg) were subcutaneously injected. For intranasal immunizations, the mice were slightly anesthetized with Isofluorane. 
     Intranasal Challenge. The groups of orally immunized mice were intranasally challenged 14 days after the last booster immunization with a dose of 10 6  colony forming units (CFU)  S. pneumoniae  D39 as described (Kadioglu et al. 2000 , Infect. Immun.  68: 492-501). Mice were monitored after the challenge for visible clinical symptoms for 7 days, at which point the experiment was ended. Mice that were alive after 7 days were considered to have survived the pneumococcal challenge and mice that became moribund during the 7-day period were judged to have reached the endpoint of the assay. The time the animal became moribund was recorded, and the animal was sacrificed by cervical dislocation. 
     ELISA Analysis. Serum samples were taken from each mouse before the intranasal challenge and stored at −20° C. before use. Microtiter plates were coated with 100 μg PpmA/ml in 0.05 carbonate buffer. Serial 10-fold dilutions of pooled serum of each group were incubated on the plates as described (Gingles et al. 2001 , Infect. Immun.  69: 426-434). Anti-mouse immunoglobulin-horseradish peroxidase conjugate was used for detection and the absorbance was measured at 492 nm. 
     Results and Discussion 
     Serum Antibody Response. Mice were immunized orally, nasally and subcutaneously according to the scheme shown in  FIG. 19 . Anti-PpmA antibody titers in the blood serum were determined for each group by ELISA assays. The results are given in  FIG. 20 . As expected, ghosts alone administered orally or nasally, OV Ghosts or IN Ghosts, respectively, did not induce anti-PpmA antibodies. Soluble PpmA given by the nasal route resulted in only a low anti-PpmA antibody titer, which agrees with the general findings that soluble antigens are not very immunogenic when given by the mucosal routes. Ghosts-PpmA::cA provided by the oral route (OV PpmA+Ghost) induced only a low level of anti-PpmA serum antibodies. This contrasts the results for the oral immunization experiments described herein with reference to Examples 2 and 4 with MSA2::cA. However, the contrast may be antigen-type related. 
     Intranasal administration of Ghosts-PpmA::cA resulted in a high titer of anti-PpmA antibodies (IN PpmA+Ghosts). A high titer was also obtained by subcutaneous administration of Ghosts-PpmA::cA. These titers were lower by a factor of 5 to 10 when compared to soluble PpmA that was subcutaneously administered and formulated with the strong Freund&#39;s complete adjuvant (Peter Adrian, Erasmus University Rotterdam, The Netherlands, unpublished results). In addition, the Freund&#39;s PpmA vaccine contained 50 μg PpmA per dose, whereas the intranasally administered Ghosts-PpmA:cA contains only 5 μg/dose and the subcutaneous Ghost-PpmA::cA vaccine contains only 1 μg PpmA/dose. This result demonstrates the adjuvant effect of the ghost cells. Side effects of the orally, nasally or subcutaneously administered ghosts were not observed, which is in contrast to the severe side effects that are usually seen with the use of Freund&#39;s adjuvants. 
     The results demonstrate that high titer serum antibodies can be obtained by the mucosal route of administration. These data also show that ghost cells may be safely used in traditionally injected vaccines without side effects in order to induce high titer serum antibodies. 
     Protection Against Challenge. The mice orally immunized with soluble PpmA, Ghosts alone or Ghosts-PpmA::cA were challenged 14 days post-immunization with a lethal intranasal dose of  S. pneumoniae . The mice immunized with soluble PpmA or Ghosts alone died within 72 hours after challenge. The group immunized with Ghosts-PpmA::cA showed a survival rate of 40% ( FIG. 21 ). These results show that mucosal immunization of mice with Ghosts-PpmA induces protective immunity against a lethal  S. pneumoniae  challenge. In conclusion, the non-recombinant non-living Ghost system may be used to elicit high titer serum antibodies and the mucosal route of administration may be used to obtain protective immunity against a mucosally acquired pathogen. 
     
       
         
               
             
               
               
               
             
           
               
                 TABLE 1 
               
             
             
               
                   
               
               
                 Effect of different pretreatments of  L. lactis  on binding of MSA2::cA. 
               
             
          
           
               
                   
                 Treatment 
                 Signal on Western blot 
               
               
                   
                   
               
               
                   
                 H 2 O 
                 − 
               
               
                   
                 10% TCA (0.6 M) 
                 ++++ 
               
               
                   
                 0.6 M HAc 
                 ++++ 
               
               
                   
                 0.6 M HCl 
                 ++++ 
               
               
                   
                 0.6 M H 2 SO 4   
                 ++++ 
               
               
                   
                 0.6 M TFA 
                 ++++ 
               
               
                   
                 0.6 M MCA 
                 ++++ 
               
               
                   
                 Phenol 
                 ++ 
               
               
                   
                 4 M GnHCl 
                 ++ 
               
               
                   
                 37% formaldehyde 
                 ++ 
               
               
                   
                 CHCl 3 /MeOH 
                 ++ 
               
               
                   
                 10% SDS 
                 + 
               
               
                   
                 10% DMF 
                 + 
               
               
                   
                 10% DMSO 
                 + 
               
               
                   
                 25 mM DTT 
                 + 
               
               
                   
                 0.1% NaHC1O* 
                 − 
               
               
                   
                 Hexane 
                 − 
               
               
                   
                 Lysozyme* 
                 − 
               
               
                   
                   
               
               
                   
                 *Lysis of cells occurred during treatment or washing steps. 
               
             
          
         
       
     
     
       
         
               
             
               
               
             
               
               
               
               
               
               
             
           
               
                 TABLE 2 
               
             
             
               
                   
               
               
                 MSA2 antibody titers of rabbit serum determined by IFA on 
               
               
                   Plasmodium falciparum  3D7 asexual blood stage parasites. 
               
             
          
           
               
                   
                 Immunization 
               
             
          
           
               
                 Rabbit 
                   
                   
                   
                   
                 3 rd   
               
               
                 serum 
                 Immunogen 
                 P 
                 2 nd   
                 3 rd   
                 IgG 
               
               
                   
               
               
                 A1 
                 s.c.  L. lactis  [MSA2::cA] 
                 0 
                 2 
                 4 
                 4 
               
               
                 A2 
                 s.c.  L. lactis  [MSA2::cA] 
                 0 
                 2 
                 5 
                 5 
               
               
                 B1 
                 s.c.  L. lactis   
                 0 
                 0 
                 1 
                 n.d. 
               
               
                 B2 
                 s.c.  L. lactis   
                 0 
                 0 
                 1 
                 n.d. 
               
               
                 C1 
                 oral  L. lactis  [MSA2::cP] 
                 0 
                 3 
                 5 
                 5 
               
               
                 C2 
                 oral  L. lactis  [MSA2::cP] 
                 0 
                 2 
                 5 
                 5 
               
               
                 D1 
                 oral  L. lactis  [MSA2::cA] 
                 0 
                 2 
                 4 
                 5 
               
               
                 D2 
                 oral  L. lactis  [MSA2::cA] 
                 0 
                 2 
                 4 
                 5 
               
               
                 E1 
                 oral TCA  L. lactis  + MSA2::cA 
                 0 
                 2 
                 5 
                 5 
               
               
                 E2 
                 oral TCA  L. lactis  + MSA2::cA 
                 0 
                 2 
                 5 
                 4 
               
               
                   
               
               
                   L. lactis  strain used: NZ9000ΔacmA (lactococcal cells lacking the cell wall hydrolase AcmA). 
               
               
                   L. lactis  [MSA2::cA] and  L. lactis  [MSA2::cP] are the recombinant strains with surface-expressed MSA2, cell wall anchored through the non-covalent AcmA binding domain (cA) or the covalent PrtP anchoring domain (cP), respectively. 
               
               
                 TCA  L. lactis  + MSA2::cA are the non-recombinant TCA-pretreated lactococcal cells to which MSA2::cA had been bound externally. 
               
               
                 P: pre-immune serum. 
               
               
                 S.C.: subcutaneous injection. 
               
               
                 Titers are expressed as the negative logarithms of the lowest ten-fold dilution of sera giving a detectable reaction on the merozoite surface. The last column represents the IgG fraction of the antibody response. 
               
               
                 0: indicates no detectable reaction at a 1:10 dilution of the serum. 
               
               
                 n.d.: not done. 
               
             
          
         
       
     
     
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
               
               
               
             
           
               
                 TABLE 3 
               
               
                   
               
               
                 AcmA cell wall binding domain homologs and their calculated pI values. 
               
               
                 (the pI values are indicated directly behind the amino acid sequences) 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                 
                   Lactococcus 
                 
                 * acmA 
                 YTVKSGDTLWGISQRYGISVAQIQSAN 
                 SEQ ID NO: 16 
                 9.75 
               
               
                 
                   lactis 
                 
                   
                 NLKST IIYIGQKLVLT 
                   
                   
               
               
                   
                   
                 VKVKSGDTLWALSVKYKTSIAQLKSWN 
                 SEQ ID NO: 17 
                 9.64 
               
               
                   
                   
                 HLSSD TIYIGQNLIVS 
                   
                   
               
               
                   
                   
                 HKVVKGDTLWGLSQKSGSPIASIKAWN 
                 SEQ ID NO: 18 
                 10.06 
               
               
                   
                   
                 HLSSD TILIGQYLRIK 
                   
                   
               
               
                   
                 * acmD 
                 YKVQEGDSLSAIAAQYGTTVDALVSAN 
                 SEQ ID NO: 19 
                 4.15 
               
               
                   
                   
                 SLENANDIHVGEVLQVA 
                   
                   
               
               
                   
                   
                 YTVKSGDSLYSIAEQYGMTVSSLMSAN 
                 SEQ ID NO: 20 
                 3.78 
               
               
                   
                   
                 GIYDVNSMLQVGQVLQVTV 
                   
                   
               
               
                   
                   
                 YTIQNGDSIYSIATANGMTADQLAALN 
                 SEQ ID NO: 21 
                 4.15 
               
               
                   
                   
                 GFGIND MIHPGQTIRI 
                   
                   
               
               
                   
               
               
                 ØTuc2009 
                 * lys 
                 YVVKQGDTLSGIASNWGTNWQELARQN 
                 SEQ ID NO: 22 
                 6.31 
               
               
                   
                   
                 SLSNPNMIYAGQVISFT 
                   
                   
               
               
                   
                   
                 YTVQSGDNLSSIAILLGTTVQSLVSMN 
                 SEQ ID NO: 23 
                 3.45 
               
               
                   
                   
                 GISNPNLIYAGQTLNY 
                   
                   
               
               
                   
               
               
                 Ø-LC3 
                 * lysB 
                 YIVKQGDTLSGIASNLGTNWQELARQN 
                 SEQ ID NO: 24 
                 6.31 
               
               
                   
                   
                 SLSNPNMIYSGQVISLT 
                   
                   
               
               
                   
                   
                 YTVQSGDNLSSIARRLGTTVQSLVSMN 
                 SEQ ID NO: 25 
                 8.79 
               
               
                   
                   
                 GISNPNLIYAGQTLNY 
                   
                   
               
               
                   
               
               
                 
                   Enterococcus 
                 
                 * autolysin 
                 YTVKSGDTLNKIAAQYGVSVANLRSWN 
                 SEQ ID NO: 26 
                 9.74 
               
               
                 
                   faecalis 
                 
                   
                 GISGD LIFVGQKLIVK 
                   
                   
               
               
                   
                   
                 YTVKSGDTLNKIAAQYGVTVANLRSWN 
                 SEQ ID NO: 27 
                 9.74 
               
               
                   
                   
                 GISGD LIFVGQKLIVK 
                   
                   
               
               
                   
                   
                 YTIKSGDTLNKIAAQYGVSVANLRSWN 
                 SEQ ID NO: 28 
                 9.74 
               
               
                   
                   
                 GISGD LIFAGQKIIVK 
                   
                   
               
               
                   
                   
                 YTIKSGDTLNKISAQFGVSVANLRSWN 
                 SEQ ID NO: 29 
                 9.85 
               
               
                   
                   
                 GIKGD LIFAGQTIIVK 
                   
                   
               
               
                   
                   
                 HTVKSGDSLWGLSMQYGISIQKIKQLN 
                 SEQ ID NO: 30 
                 9.35 
               
               
                   
                   
                 GLSGD TIYIGQTLKVG 
                   
                   
               
               
                   
               
               
                 
                   hirae 
                 
                 * mur2 
                 YTVKSGDSVWGISHSFGITMAQLIEWN 
                 SEQ ID NO: 31 
                 9.35 
               
               
                   
                   
                 NIKNN FIYPGQKLTIK 
                   
                   
               
               
                   
                   
                 YTVKSGDSVWKIANDHGISMNQLIEWN 
                 SEQ ID NO: 32 
                 7.14 
               
               
                   
                   
                 NIKNN FVYPGQQLVVS 
                   
                   
               
               
                   
                   
                 YTVKAGESVWSVSNKFGISMNQLIQWN 
                 SEQ ID NO: 33 
                 9.91 
               
               
                   
                   
                 NIKNN FIYPGQKLIVK 
                   
                   
               
               
                   
                   
                 YTVKAGESVWGVANKNGISMNQLIEWN 
                 SEQ ID NO: 34 
                 9.64 
               
               
                   
                   
                 NIKNN FIYPGQKLIVK 
                   
                   
               
               
                   
                   
                 YTVKAGESVWGVANKHHITMDQLIEWN 
                 SEQ ID NO: 35 
                 7.31 
               
               
                   
                   
                 NIKNN FIYPGQEVIVK 
                   
                   
               
               
                   
                   
                 YTVKAGESVWGVADSHGITMNQLIEWN 
                 SEQ ID NO: 36 
                 7.15 
               
               
                   
                   
                 NIKNN FIYPGQQLIVK 
                   
                   
               
               
                 
                   Listeria 
                 
                 * P60 
                 VVVEAGDTLWGIAQSKGTTVDAIKKAN 
                 SEQ ID NO: 37 
                 8.61 
               
               
                 
                   monocytogenes 
                 
                   
                 NLTTD KIVPGQKLQVN 
                   
                   
               
               
                   
                   
                 NAVKSGDTIWALSVKYGVSVQDIMSWN 
                 SEQ ID NO: 38 
                 9.35 
               
               
                   
                   
                 NLSSS SIYVGQKLAIK 
                   
                   
               
               
                   
               
               
                 
                   innocua 
                 
                 * P60 
                 VVVEAGDTLWGIAQSKGTTVDAIKKAN 
                 SEQ ID NO: 39 
                 8.61 
               
               
                   
                   
                 NLTTD KIVPGQKLQVN 
                   
                   
               
               
                   
                   
                 HNVKSGDTIWALSVKYGVSVQDIMSWN 
                 SEQ ID NO: 40 
                 8.35 
               
               
                   
                   
                 NLSSS SIYVGQKPAIK 
                   
                   
               
               
                   
               
               
                 
                   ivanovii 
                 
                 * P60 
                 VVVEAGDTLWGIAQDKGTTVDALKKAN 
                 SEQ ID NO: 41 
                 6.35 
               
               
                   
                   
                 NLTSD KIVPGQKLQIT 
                   
                   
               
               
                   
                   
                 YTVKSGDTIWALSSKYGTSVQNIMSWN 
                 SEQ ID NO: 42 
                 9.37 
               
               
                   
                   
                 NLSSS SIYVGQVLAVK 
                   
                   
               
               
                   
                   
                 YTVKSGDTLSKIATTFGTTVSKIKALN 
                 SEQ ID NO: 43 
                 9.89 
               
               
                   
                   
                 GLNSD NLQVGQVLKVK 
                   
                   
               
               
                   
               
               
                 
                   seeligeri 
                 
                 * P60 
                 VVVEAGDTLWGIAQDNGTTVDALKKAN 
                 SEQ ID NO: 44 
                 6.35 
               
               
                   
                   
                 KLTTD KIVPGQKLQVT 
                   
                   
               
               
                   
                   
                 HTVKSGDTIWALSVKYGASVQDLMSWN 
                 SEQ ID NO: 45 
                 8.64 
               
               
                   
                   
                 NLSSS SIYVGQNIAVK 
                   
                   
               
               
                   
                   
                 YTVKSGDTLGKIASTFGTTVSKIKALN 
                 SEQ ID NO: 46 
                 9.62 
               
               
                   
                   
                 GLTSD NLQVGDVLKVK 
                   
                   
               
               
                   
               
               
                 
                   welshimeri 
                 
                 * P60 
                 VVVEAGDTLWGIAQSKGTTVDALKKAN 
                 SEQ ID NO: 47 
                 8.61 
               
               
                   
                   
                 NLTSD KIVPGQKLQVT 
                   
                   
               
               
                   
                   
                 HTVKSGDTIWALSVKYGASVQDLMSWN 
                 SEQ ID NO: 48 
                 9.35 
               
               
                   
                   
                 NLSSS SIYVGQKIAVK 
                   
                   
               
               
                   
                   
                 YTVKSGDSLSKIANTFGTSVSKIKALN 
                 SEQ ID NO: 49 
                 9.89 
               
               
                   
                   
                 NLTSD NLQVGTVLKVK 
                   
                   
               
               
                   
               
               
                 
                   grayi 
                 
                 * P60 
                 VVVASGDTLWGIASKTGTTVDQLKQLN 
                 SEQ ID NO: 50 
                 9.42 
               
               
                   
                   
                 KLDSD RIVPGQKLTIK 
                   
                   
               
               
                   
                   
                 YKVKSGDTIWALSVKYGVPVQKLIEWN 
                 SEQ ID NO: 51 
                 9.57 
               
               
                   
                   
                 NLSSS SIYVGQTIAVK 
                   
                   
               
               
                   
                   
                 YKVQNGDSLGKIASLFKVSVADLTNWN 
                 SEQ ID NO: 52 
                 8.59 
               
               
                   
                   
                 NLNATITIYAGQELSVK 
                   
                   
               
               
                   
               
               
                 
                   Haemophilus 
                 
                 * amiB 
                 HIVKKGESLGSLSNKYHVKVSDIIKLN 
                 SEQ ID NO: 53 
                 10.11 
               
               
                 
                   influenzae 
                 
                   
                 QLKRK TLWLNESIKIP 
                   
                   
               
               
                   
                   
                 HKVTKNQTLYAISREYNIPVNILLSLN 
                 SEQ ID NO: 54 
                 10.49 
               
               
                   
                   
                 PHLKNG KVITGQKIKLR 
                   
                   
               
               
                   
                 * yebA 
                 YTVTEGDTLKDVLVLSGLDDSSVQPLI 
                 SEQ ID NO: 55 
                 3.87 
               
               
                   
                   
                 ALDPELAHLKAGQQFYWI 
                   
                   
               
               
                   
                 lppB 
                 YKVNKGDTMFLIAYLAGIDVKELAALN 
                 SEQ ID NO: 56 
                 6.40 
               
               
                   
                   
                 NLSEPNYNLSLGQVLKIS 
                   
                   
               
               
                   
               
               
                 
                   somnus 
                 
                 lppB 
                 YKVRKGDTMFLIAYISGMDIKELATLN 
                 SEQ ID NO: 57 
                 8.56 
               
               
                   
                   
                 NMSEPYHLSIGQVLKIA 
                   
                   
               
               
                   
               
               
                 
                   Helicobacter 
                 
                 dniR 
                 HVVLPKETLSSIAKRYQVSISNIQLAN 
                 SEQ ID NO: 58 
                 10.02 
               
               
                 
                   pylori 
                 
                   
                 DLKDS NIFIHQRLIIR 
                   
                   
               
               
                   
               
               
                 
                   Pseudomonas 
                 
                 lppB 
                 YIVRRGDTLYSIAFRFGWDWKALAARN 
                 SEQ ID NO: 59 
                 10.06 
               
               
                 
                   aeruginosa 
                 
                   
                 GIAPPYTIQVGQAIQFG 
                   
                   
               
               
                   
               
               
                 
                   Putida 
                 
                 nlpD 
                 YIVKPGDTLFSIAFRYGWDYKELAARN 
                 SEQ ID NO: 60 
                 9.77 
               
               
                   
                   
                 GIPAPYTIRPGQPIRFS 
                   
                   
               
               
                   
               
               
                 
                   Sinorhizoblum 
                 
                 nlpD 
                 IMVRQGDTVTVLARRFGVPEKEILKAN 
                 SEQ ID NO: 61 
                 10.27 
               
               
                 
                   meliloti 
                 
                   
                 GLKSASQVEPGQRLVIP 
                   
                   
               
               
                   
               
               
                 
                   Synechocystis 
                 
                 nlpD 
                 HQVKEGESLWQISQAFQVDAKAIALAN 
                 SEQ ID NO: 62 
                 4.38 
               
               
                 sp. 
                   
                 SISTDTELQAGQVLNIP 
                   
                   
               
               
                   
                 slr0878 
                 HVVKAGETIDSIAAQYQLVPATLISVN 
                 SEQ ID NO: 63 
                 5.41 
               
               
                   
                   
                 NQLSSGQVTPGQTILIP 
                   
                   
               
               
                   
               
               
                 
                   Aquifex 
                 
                 nlpD1 
                 YKVKKGDSLWKIAKEYKTSIGKLLELN 
                 SEQ ID NO: 64 
                 10.08 
               
               
                 
                   acolicus 
                 
                   
                 PKLKNRKYLRPGEKICLK 
                   
                   
               
               
                   
                   
                 YRVKRGDSLIKIAKKFGVSVKEIKRVN 
                 SEQ ID NO: 65 
                 10.95 
               
               
                   
                   
                 KLKGN RIYVGQKLKIP 
                   
                   
               
               
                   
                   
                 YRVRRGDTLIKIAKRFRTSVKEIKRIN 
                 SEQ ID NO: 66 
                 12.11 
               
               
                   
                   
                 RLKGN LIRVGQKLKIP 
                   
                   
               
               
                   
               
               
                 
                   Volvox 
                 
                   
                 YTIQPGDTFWAIAQRRGTTVDVIQSLN 
                 SEQ ID NO: 67 
                 9.03 
               
               
                 
                   carteri 
                 
                   
                 PGVVPTRLQVGQVINVP 
                   
                   
               
               
                   
               
               
                 
                   f. 
                 
                   
                 YTIQPGDTFWAIAQRRGTTVDVIQSLN 
                 SEQ ID NO: 68 
                 9.03 
               
               
                 
                   nagariensis 
                 
                   
                 PGVNPARLQVGQVINVP 
                   
                   
               
               
                   
               
               
                   Staphylo - 
                 ProtA 
                 HVVKPGDTVNDIAKANGTTADKIAADN 
                 SEQ ID NO: 69 
                 5.58 
               
               
                 
                   coccus 
                 
                   
                 KLADKNMIKPGQELVVD 
                   
                   
               
               
                 
                   aureus 
                 
                 lytN 
                 YTVKKGDTLSAIALKYKTTVSNIQNTN 
                 SEQ ID NO: 70 
                 10.03 
               
               
                   
                   
                 NIANPNLIFIGQKLKVP 
                   
                   
               
               
                   
               
               
                 
                   Colletotrichum 
                 
                 cih1 
                 HKVKSGESLTTIAEKYDTGICNIAKLN 
                 SEQ ID NO: 71 
                 4.76 
               
               
                   
                   
                 NLADPNFIDLNQDLQIP 
                   
                   
               
               
                   
               
               
                 
                   lindemuthianum 
                 
                   
                 YSVVSGDTLTSIAQALQITLQSLKDAN 
                 SEQ ID NO: 72 
                 5.46 
               
               
                   
                   
                 PGVVPENLNVGQKLNVP 
                   
                   
               
               
                   
               
               
                 
                   Chlamydophila 
                 
                 aniB 
                 IVYREGDSLSKIAKKYKLSVTELKKIN 
                 SEQ ID NO: 73 
                 9.46 
               
               
                   
                   
                 KLDSD AIYAGQRLCLQ 
                   
                   
               
               
                   
               
               
                 
                   Pneumoniae 
                 
                 CPn0593 
                 YVVQDGDSLWLIAKRFGIPMDKIIQKN 
                 SEQ ID NO: 74 
                 10.01 
               
               
                   
                   
                 GLNHH RLFPGKVLKLP 
                   
                   
               
               
                   
                 NlpD 
                 VVVKKGDFLERIARANNTTVAKLMQIN 
                 SEQ ID NO: 75 
                 10.17 
               
               
                   
                   
                 DLTTT QLKIGQVIKVP 
                   
                   
               
               
                   
                   
                 YIVQEGDSPWTIALRNHIRLDDLLKMN 
                 SEQ ID NO: 76 
                 8.64 
               
               
                   
                   
                 DLDEYKARRLKPGDQLRIR 
                   
                   
               
               
                   
               
               
                 
                   Chlamydia 
                 
                 NlpD 
                 VIVKKGDFLERIARSNHTTVSALMQLN 
                 SEQ ID NO: 77 
                 9.99 
               
               
                 
                   trachomatis 
                 
                   
                 DLSST QLQIGQVLRVP 
                   
                   
               
               
                   
                   
                 YVVKEGDSPWAIALSNGIRLDELLKLN 
                 SEQ ID NO: 78 
                 10.00 
               
               
                   
                   
                 GLDEQKARRLRPGDRLRIR 
                   
                   
               
               
                   
                 papQ 
                 HIVKQGETLSKIASKYNIPVVELKKLN 
                 SEQ ID NO: 79 
                 9.89 
               
               
                   
                   
                 KLNSD TIFTDQRIRLP 
                   
                   
               
               
                 
                   Prevotella 
                 
                 phg 
                 HTVRSNESLYDISQQYGVRLKNIMKAN 
                 SEQ ID NO: 80 
                 10.72 
               
               
                 
                   intermedia 
                 
                   
                 RKIVKRGIKAGDRVVL 
                   
                   
               
               
                   
               
               
                 
                   Leuconostoc 
                 
                 lys 
                 YTVQSGDTLGAIAAKYGTTYQKLASLN 
                 SEQ ID NO: 81 
                 9.23 
               
               
                   oenos  Ø10MC 
                   
                 GIGSPYIIIPGEKLKVS 
                   
                   
               
               
                   
                   
                 YKVASGDTLSAIASKYGTSVSKLVSLN 
                 SEQ ID NO: 82 
                 9.68 
               
               
                   
                   
                 GLKNANYIYVGENLKIK 
                   
                   
               
               
                 
                   Oenococcus 
                 
                 Lys44 
                 YTVRSGDTLGAIAAKYGTTYQKLASLN 
                 SEQ ID NO: 83 
                 9.58 
               
               
                   oeni  ØfOg44 
                   
                 GIGSPYIIIPGEKLKVS 
                   
                   
               
               
                   
                   
                 YKVASGDTLSAIASKYGTSVSKLVSLN 
                 SEQ ID NO: 84 
                 9.95 
               
               
                   
                   
                 GLKNANYIYVGQTLRIK 
                   
                   
               
               
                   
               
               
                 
                   Thermotoga 
                 
                 TM0409 
                 YKVQKNDTLYSISLNFGISPSLLLDWN 
                 SEQ ID NO: 85 
                 5.49 
               
               
                 
                   maritime 
                 
                   
                 PGLDPHSLRVGQEIVIP 
                   
                   
               
               
                   
                   
                 YTVKKGDTLDAIAKRFFTTATFIKEAN 
                 SEQ ID NO: 86 
                 9.73 
               
               
                   
                   
                 QLKSY TIYAGQKLFIP 
                   
                   
               
               
                   
                 TM1686 
                 HVVKRGETLWSIANQYGVRVGDIVLIN 
                 SEQ ID NO: 87 
                 8.76 
               
               
                   
                   
                 RLEDPDRIVAGQVLKIG 
                   
                   
               
               
                   
               
               
                 
                   Treponema 
                 
                 dniR 
                 HTIRSGDTLYALARRYGLGVDTLKAHN 
                 SEQ ID NO: 88 
                 10.58 
               
               
                 
                   pallidum 
                 
                   
                 RAHSATHLKIGQKLIIP 
                   
                   
               
               
                   
                   
                 HVVQQGDTLWSLAKRYGVSVENLAEEN 
                 SEQ ID NO: 89 
                 4.81 
               
               
                   
                   
                 NLAVDATLSLGMILKTP 
                   
                   
               
               
                   
                 TP0155 
                 YEVREGDVVGRIAQRYDISQDAIISLN 
                 SEQ ID NO: 90 
                 9.58 
               
               
                   
                   
                 KLRSTRALQVGQLLKIP 
                   
                   
               
               
                   
                 TP0444 
                 HVIAKGETLFSLSRRYGVPLSALAQAN 
                 SEQ ID NO: 91 
                 10.98 
               
               
                   
                   
                 NLANVHQLVPGQRIVVP 
                   
                   
               
               
                   
               
               
                 
                   Borrelia 
                 
                 BB0262 
                 HKIKPGETLSHVAARYQITSETLISFN 
                 SEQ ID NO: 92 
                 9.72 
               
               
                 
                   burgdorferi 
                 
                   
                 EIKDVRNIKPNSVIKVP 
                   
                   
               
               
                   
                   
                 YIVKKNDSISSIASAYNVPKVDILDSN 
                 SEQ ID NO: 93 
                 4.58 
               
               
                   
                   
                 NLDNE VLFLGQKLFIP 
                   
                   
               
               
                   
                 * B80625 
                 YKVVKGDTLFSIAIKYKVKVSDLKRIN 
                 SEQ ID NO: 94 
                 10.02 
               
               
                   
                   
                 KLNVD NIKAGQILIIP 
                   
                   
               
               
                   
                   
                 YTAKEGDTIESISKLVGLSQEEIIAWN 
                 SEQ ID NO: 95 
                 5.00 
               
               
                   
                   
                 DLRSK DLKVGMKLVLT 
                   
                   
               
               
                   
                   
                 YMVRKGDSLSKLSQDFDISSKDILKFN 
                 SEQ ID NO: 96 
                 9.20 
               
               
                   
                   
                 FLNDD KLKIGQQLFLK 
                   
                   
               
               
                   
                   
                 HYVKRGETLGRIAYIYGVTAKDLVALN 
                 SEQ ID NO: 97 
                 10.05 
               
               
                   
                   
                 GNRAI NLKAGSLLNVL 
                   
                   
               
               
                   
                   
                 HSVAVGETLYSIARHYGVLIEDLKNWN 
                 SEQ ID NO: 98 
                 7.41 
               
               
                   
                   
                 NLSSN NIMHDQKLKIF 
                   
                   
               
               
                   
                 BB0761 
                 YKVKKGDTFFKIANKINGWQSGIATIN 
                 SEQ ID NO: 99 
                 9.34 
               
               
                   
                   
                 LLDSP AVSVGQEILIP 
                   
                   
               
               
                   
               
               
                 
                   Lactobacillus 
                 
                 * lys 
                 YTVVSGDSWNKIAQRNGLSMYTLASQN 
                 SEQ ID NO: 100 
                 9.83 
               
               
                 Øgle 
                   
                 GKSIYSTIYPGNKLIIK 
                   
                   
               
               
                   
               
               
                 
                   Bacillus 
                 
                 * lytE 
                 IKVKKGDTLWDLSRKYDTTISKIKSEN 
                 SEQ ID NO: 101 
                 9.55 
               
               
                 
                   subtilis 
                 
                   
                 HLRSD IIYVGQTLSIN 
                   
                   
               
               
                   
                   
                 YKVKSGDSLWKISKKYGMTINELKKLN 
                 SEQ ID NO: 102 
                 10.16 
               
               
                   
                   
                 GLKSD LLRVGQVLKLK 
                   
                   
               
               
                   
                   
                 YKVKSGDSLSKIASKYGTTVSKLKSLN 
                 SEQ ID NO: 103 
                 10.03 
               
               
                   
                   
                 GLKSD VIYVNQVLKVK 
                   
                   
               
               
                   
                 spoV1D 
                 CIVQQEDTIERLCERYEITSQQLIRMN 
                 SEQ ID NO: 104 
                 4.20 
               
               
                   
                   
                 SLALDDELKAGQILYIP 
                   
                   
               
               
                   
                 yaaH 
                 MVKQGDTLSAIASQYRTTTNDITETN 
                 SEQ ID NO: 105 
                 3.89 
               
               
                   
                   
                 EIPNPDSLVVGQTIVIP 
                   
                   
               
               
                   
                   
                 YDVKRGDTLTSIARQFNTTAAELARVN 
                 SEQ ID NO: 106 
                 10.32 
               
               
                   
                   
                 RIQLNTVLQIGFRLYIP 
                   
                   
               
               
                   
                 yhdD 
                 IKVKSGDSLWKLAQTYNTSVAALTSAN 
                 SEQ ID NO: 107 
                 9.56 
               
               
                   
                   
                 HLSTT VLSIGQTLTIP 
                   
                   
               
               
                   
                   
                 YTVKSGDSLWLIANEFKNTVQELKKLN 
                 SEQ ID NO: 108 
                 9.62 
               
               
                   
                   
                 GLSSD LIRAGQKLKVS 
                   
                   
               
               
                   
                   
                 YKVQLGDSLWKIANKVNMSIAELKVLN 
                 SEQ ID NO: 109 
                 9.72 
               
               
                   
                   
                 NLKSD TIYVNQVLKTK 
                   
                   
               
               
                   
                   
                 YTVKSGDSLWKIANNYNLTVQQIRNIN 
                 SEQ ID NO: 110 
                 9.65 
               
               
                   
                   
                 NLKSD VLYVGQVLKLT 
                   
                   
               
               
                   
                   
                 YTVKSGDSLWVIAQKFNVTAQQIREKN 
                 SEQ ID NO: 111 
                 9.72 
               
               
                   
                   
                 NLKTD VLGVGQKLVIS 
                   
                   
               
               
                   
                 yojL 
                 IKVKSGDSLWKLSRQYDTTISALKSEN 
                 SEQ ID NO: 112 
                 9.93 
               
               
                   
                   
                 KLKST VLYVGQSLKVP 
                   
                   
               
               
                   
                   
                 YTVAYGDSLWMIAKNHKMSVSELKSLN 
                 SEQ ID NO: 113 
                 9.81 
               
               
                   
                   
                 SLSSD LIRPGQKLKIK 
                   
                   
               
               
                   
                   
                 YTVKLGDSLWKIANSLNMTVAELKTLN 
                 SEQ ID NO: 114 
                 9.27 
               
               
                   
                   
                 GLTSD TLYPKQVLKIG 
                   
                   
               
               
                   
                   
                 YKVKAGDSLWKIANRLGVTVQSIRDKN 
                 SEQ ID NO: 115 
                 9.84 
               
               
                   
                   
                 NLSSD VLQIGQVLTIS 
                   
                   
               
               
                   
                 yocH 
                 ITVQKGDTLWGISQKNGVNLKDLKEWN 
                 SEQ ID NO: 116 
                 9.25 
               
               
                   
                   
                 KLTSD KIIAGEKLTIS 
                   
                   
               
               
                   
                   
                 YTIKAGDTLSKIAQKFGTTVNNLKVWN 
                 SEQ ID NO: 117 
                 9.64 
               
               
                   
                   
                 NLSSD MIYAGSTLSVK 
                   
                   
               
               
                   
                 ykvP 
                 HHVTPGETLSIIASKYNVSLQQLMELN 
                 SEQ ID NO: 118 
                 8.65 
               
               
                   
                   
                 HFKSD QIYAGQIIKIR 
                   
                   
               
               
                   
                 * xlyB 
                 YHVKKGDTLSGIAASHGASVKTLQSIN 
                 SEQ ID NO: 119 
                 9.72 
               
               
                   
                   
                 HITDPNHIKIGQVIKLP 
                   
                   
               
               
                   
                 yrbA 
                 NIVQKGDSLWKIAEKYGVDVEEVKKLN 
                 SEQ ID NO: 120 
                 8.51 
               
               
                   
                   
                 TQLSNPDLIMPGMKIKVP 
                   
                   
               
               
                   
                 ydhD 
                 HIVGPGDSLFSIGRRYGASVDQIRGVN 
                 SEQ ID NO: 121 
                 5.49 
               
               
                   
                   
                 GLDET NIVPGQALLIP 
                   
                   
               
               
                   
                 ykuD 
                 YQVKQGDTLNSIAADFRISTAALLQAN 
                 SEQ ID NO: 122 
                 6.10 
               
               
                   
                   
                 PSLQA GLTAGQSIVIP 
                   
                   
               
               
                   
               
               
                 ØPBSX 
                 * xlyA 
                 YVVKQGDTLTSIARAFGVTVAQLQEWN 
                 SEQ ID NO: 123 
                 4.65 
               
               
                   
                   
                 NIEDPNLIRVGQVLIVS 
                   
                   
               
               
                   
               
               
                 Ø PZA 
                 * orf15 
                 YKVKSGDNLTKIAKKHNTTVATLLKLN 
                 SEQ ID NO: 124 
                 10.23 
               
               
                   
                   
                 PSIKDPNMIRVGQTINVT 
                   
                   
               
               
                 (= Ø-29) 
                   
                 HKVKSGDTLSKIAVDNKTTVSRLMSLN 
                 SEQ ID NO: 125 
                 10.17 
               
               
                   
                   
                 PEITNPNHIKVGQTIRLS 
                   
                   
               
               
                   
               
               
                 Ø B103 
                 * orf15 
                 HVVKKGDTLSEIAKKIKTSTKTLLELN 
                 SEQ ID NO: 126 
                 10.11 
               
               
                   
                   
                 PTIKNPNKIYVGQRINVG 
                   
                   
               
               
                   
                   
                 YKIKRGETLTGIAKKNKTTVSQLMKLN 
                 SEQ ID NO: 127 
                 10.61 
               
               
                   
                   
                 PNIKNANNIYAGQTIRLK 
                   
                   
               
               
                   
               
               
                 
                   sphaericus 
                 
                 * Pep I 
                 ILIRPGDSLWYFSDLFKIPLQLLLDSN 
                 SEQ ID NO: 128 
                 8.86 
               
               
                   
                   
                 RNINPQ LLQVGQRIQIP 
                   
                   
               
               
                   
                   
                 YTITQGDSLWQIAQNKNLPLNAILLVN 
                 SEQ ID NO: 129 
                 7.15 
               
               
                   
                   
                 PEIQPS RLHIGQTIQVP 
                   
                   
               
               
                   
               
               
                 
                   Salmonella 
                 
                 nlpD 
                 YTVKKGDTLFYIAWITGNDFRDLAQRN 
                 SEQ ID NO: 130 
                 8.64 
               
               
                 
                   dublin 
                 
                   
                 SISAPYSLNVGQTLQVG 
                   
                   
               
               
                   
               
               
                 
                   Escherichia 
                 
                 * yebA 
                 YVVSTGDTLSSILNQYGIDMGDISQLA 
                 SEQ ID NO: 131 
                 4.13 
               
               
                 
                   coli 
                 
                   
                 AADKELRNLKIGQQLSWT 
                   
                   
               
               
                   
                 mltD 
                 YTVRSGDTLSSIASRLGVSTKDLQQWN 
                 SEQ ID NO: 132 
                 10.58 
               
               
                   
                   
                 KLRGS KLKPGQSLTIG 
                   
                   
               
               
                   
                   
                 YRVRKGDSLSSIAKRHGVNIKDVMRWN 
                 SEQ ID NO: 133 
                 10.18 
               
               
                   
                   
                 SDTAN LQPGDKLTLF 
                   
                   
               
               
                   
                 UUG 
                 YTVKRGDTLYRISRTTGTSVKELARLN 
                 SEQ ID NO: 134 
                 10.16 
               
               
                   
                   
                 GISPPYTIEVGQKLKLG 
                   
                   
               
               
                   
                 nlpD 
                 YTVKKGDTLFYIAWITGNDFRDLAQRN 
                 SEQ ID NO: 135 
                 8.64 
               
               
                   
                   
                 NIQAPYALNVGQTLQVG 
                   
                   
               
               
                 
                   Drosophila 
                 
                 Q9VNAI 
                 YTVGNRDTLTSVAARFDTTPSELTHLN 
                 SEQ ID NO: 136 
                 7.15 
               
               
                 
                   melanogaster 
                 
                   
                 RLNSS FIYPGQQLLVP 
                   
                   
               
               
                   
               
               
                 
                   Drosophila 
                 
                 Q961P8 
                 YTVGNRDTLTSVAARFDTTPSELTHLN 
                 SEQ ID NO: 136 
                 7.15 
               
               
                 
                   melanogaster 
                 
                   
                 RLNSS FIYPGQQLLVP 
                   
                   
               
               
                   
               
               
                 
                   Caenorhabditis 
                 
                 F43G9.2 
                 RKVKNGDTLNKLAIKYQVNVAEIKRVN 
                 SEQ ID NO: 137 
                 10.01 
               
               
                 
                   elegans 
                 
                   
                 NMVSEQDFMALSKVKIP 
                   
                   
               
               
                   
               
               
                 
                   Caenorhabditis 
                 
                 F52E1.13 
                 YTITETDTLERVAASNDCTVGELMKLN 
                 SEQ ID NO: 138 
                 7.08 
               
               
                 
                   elegans 
                 
                   
                 KMASR MVFPGQKILVP 
                   
                   
               
               
                   
               
               
                 
                   Caenorhabditis 
                 
                 F07G11.9 
                 TEIKSGDSCWNIASNAKISVERLQQLN 
                 SEQ ID NO: 139 
                 8.32 
               
               
                 
                   elegans 
                 
                   
                 KGMKCDKLPLGDKLCLA 
                   
                   
               
               
                   
                   
                 LKLKAEDTCFKIWSSQKLSERQFLGMN 
                 SEQ ID NO: 140 
                 7.84 
               
               
                   
                   
                 EGMDCDKLKVGKEVCVA 
                   
                   
               
               
                   
                   
                 HKIQKGDTCFKIWTTNKISEKQFRNLN 
                 SEQ ID NO: 141 
                 8.65 
               
               
                   
                   
                 KGLDCDKLEIGKEVCIS 
                   
                   
               
               
                   
                   
                 LKIKEGDTCYNIWTSQKISEQEFMELN 
                 SEQ ID NO: 142 
                 4.54 
               
               
                   
                   
                 KGLDCDKLEIGKEVCVT 
                   
                   
               
               
                   
                   
                 YRFKKGDTCYKIWTSHKMSEKQFRALN 
                 SEQ ID NO: 143 
                 9.35 
               
               
                   
                   
                 RGIDCDRLVPGKELCVG 
                   
                   
               
               
                   
                   
                 ITVKPGDTCFSIWTSQKMTQQQFMDIN 
                 SEQ ID NO: 144 
                 4.21 
               
               
                   
                   
                 PELDCDKLEIGKEVCVT 
                   
                   
               
               
                   
                   
                 VKINPGDTCFNIWTSQRMTQQQFMDLN 
                 SEQ ID NO: 145 
                 6.30 
               
               
                   
                   
                 KRLDCDKLEVGKEVCVA 
                   
                   
               
               
                   
                   
                 VQINPGDTCFKIWSAQKLTEQQFMELN 
                 SEQ ID NO: 146 
                 4.60 
               
               
                   
                   
                 KGLDCDRLEVGKEVCIA 
                   
                   
               
               
                   
                   
                 TEVKEGDTCFKIWSAHKITEQQFMEMN 
                 SEQ ID NO: 147 
                 5.12 
               
               
                   
                   
                 RGLDCNRLEVGKEVCIV 
                   
                   
               
               
                   
                   
                 IKVKEGDTCFKIWSAQKMTEQQFMEMN 
                 SEQ ID NO: 148 
                 7.85 
               
               
                   
                   
                 RGLDCNKLMVGKEVCVS 
                   
                   
               
               
                   
                   
                 ATITPGNTCFNISVAYGINLT   DLQ 
                 SEQ ID NO: 149 
                 3.99 
               
               
                   
                   
                 KTYDCKALEVGDTICVS 
                   
                   
               
               
                   
                   
                 IEVIKGDTCWFLENAFKTNQTEMERAN 
                 SEQ ID NO: 150 
                 4.67 
               
               
                   
                   
                 EGVKCDNLPIGRMMCVW 
                   
                   
               
               
                   
               
               
                 
                   Caenorhabditis 
                 
                 T01C4.1 
                 HTIKSGDTCWKIASEASISVQELEGLN 
                 SEQ ID NO: 151 
                 5.01 
               
               
                 
                   elegans 
                 
                   
                 SKKSCANLAVGLSEQEF 
                   
                   
               
               
                   
                   
                 IHVKEGDTCYTIWTSQHLTEKQFMDMN 
                 SEQ ID NO: 152 
                 4.12 
               
               
                   
                   
                 EELNCGMLEIGNEVCVD 
                   
                   
               
               
                   
                   
                 ATVTPGSSCYTISASYGLNLAELQTTY 
                 SEQ ID NO: 153 
                 3.07 
               
               
                   
                   
                 NCDALQVDDTICVS 
                   
                   
               
               
                   
                   
                 IEILNGDTCGFLENAFQTNNTEMEIAN 
                 SEQ ID NO: 154 
                 3.85 
               
               
                   
                   
                 EGVKCDNLPIGRMMCVW 
                   
                   
               
               
                   
               
               
                 
                   Bacillus 
                 
                 # ypbE 
                 HTVQKKETLYRISMKYYKSRTGEEKIR 
                 SEQ ID NO: 155 
                 9.45 
               
               
                 
                   subtilis 
                 
                   
                 AYNHLNGNDVYTGQVLDIP 
                   
                   
               
               
                   
               
               
                 
                   Citrobacter 
                 
                 # eae 
                 YTLKTGESVAQLSKSQGISVPVIWSLN 
                 SEQ ID NO: 156 
                 8.59 
               
               
                 
                   fruendii 
                 
                   
                 KHLYSSESEMMKASPGQQIILP 
                   
                   
               
               
                   
               
               
                 
                   Escherichia 
                 
                 # eae 
                 YTLKTGETVADLSKSQDINLSTIWSLN 
                 SEQ ID NO: 157 
                 5.65 
               
               
                 
                   coli 
                 
                   
                 KNLYSSESEMMKAAPGQQIILP 
                   
                   
               
               
                 
                   Micrococcus 
                 
                 # rpf 
                 IVVKSGDSLWTLANEYEVEGGWTALYE 
                 SEQ ID NO: 158 
                 3.85 
               
               
                 
                   luteus 
                 
                   
                 ANKGAVSDAAVIYVGQELVL 
                   
                   
               
               
                   
               
               
                 
                   Bacillus 
                 
                 # yneA 
                 IEVQQGDTLWSIADQVADTKKINKNDF 
                 SEQ ID NO: 159 
                 3.81 
               
               
                 
                   subtilis 
                 
                   
                 IEWVADKNQLQTSDIQPGDELVIP 
                   
                   
               
               
                   
               
               
                 
                   Streptococcus 
                 
                 # 
                 YTVKYGDTLSTIAEAMGIDVHVLGDIN 
                 SEQ ID NO: 160 
                 4.23 
               
               
                 
                   pyogenes 
                 
                   
                 HIANIDLIFPDTILTANYNQHGQATTL 
                   
                   
               
               
                   
                   
                 T 
                   
                   
               
               
                   
               
               
                 
                   Bacillus 
                 
                 # xkdP 
                 YTVKKGDTLWDIAGRFYGNETQWRKIW 
                 SEQ ID NO: 161 
                 11.23 
               
               
                 
                   subtilis 
                 
                   
                 NANKTAMIKRSKRNIRQPGHWIFPGQK 
                   
                   
               
               
                   
                   
                 LKIP 
                   
                   
               
               
                   
               
               
                 
                   Bacillus 
                 
                 # yqbP 
                 YTVKKGDTLWDIAGRFYGNSTQWRKIW 
                 SEQ ID NO: 161 
                 11.23 
               
               
                 
                   subtilis 
                 
                   
                 NANKTAMIKRSKRNIRQPGHWIFPGQK 
                   
                   
               
               
                   
                   
                 LKIP 
                   
                   
               
               
                   
               
               
                 
                   Bacillus 
                 
                 # 
                 YTVKKGDTLWDLAGKFYGDSTKWRKIW 
                 SEQ ID NO: 162 
                 10.75 
               
               
                 
                   subtilis 
                 
                   
                 KVNKKAMIKRSKRNIRQPGHWIFPGQK 
                   
                   
               
               
                   
                   
                 LKIP 
               
               
                   
               
             
          
           
               
                 
                   Lactococcus 
                 
                 245-287 (33) 
                 437 
                 U1769600 
                 muramidase 
               
               
                 
                   lactis 
                 
                 321-363 (31) 
                   
                   
                   
               
               
                   
                 395-437 
                   
                   
                   
               
               
                   
                 194-237 
                   
                 QGCI25 
                   
               
               
                   
                 258-303 
                   
                   
                   
               
               
                   
                 319-361 
                   
                   
                   
               
               
                   
               
               
                 ØTuc2009 
                 332-375 (10) 
                 428 
                 L31364 
                 glycosidase 
               
               
                   
                   
                   
                   
                 (muramidase) 
               
               
                   
                 386-428 
                   
                   
                   
               
               
                   
               
               
                 Ø-LC3 
                 333-376 (10) 
                 429 
                 U04309 
                 muramidase 
               
               
                   
                 387-429 
                   
                   
                   
               
               
                   
               
               
                 
                   Enterococcus 
                 
                 363-405 (25) 
                 671 
                 P37710 
                 muramidase 
               
               
                 
                   faecalis 
                 
                 431-473 (25) 
                   
                   
                   
               
               
                   
                 499-541 (25) 
                   
                   
                   
               
               
                   
                 567-609 (19) 
                   
                   
                   
               
               
                   
                 629-671 
                   
                   
                   
               
               
                   
               
               
                 
                   hirae 
                 
                 257-299 (38) 
                 666 
                 P39046 
                 muramidase 
               
               
                   
                 338-380 (33) 
                   
                   
                   
               
               
                   
                 414-456 (32) 
                   
                   
                   
               
               
                   
                 489-531 (33) 
                   
                   
                   
               
               
                   
                 565-607 (15) 
                   
                   
                   
               
               
                   
                 623-665 
                   
                   
                   
               
               
                   
               
               
                 
                   Listeria 
                 
                  30-72  (130) 
                 484 
                 P21171 
                 adherence and 
               
               
                 
                   monocytogenes 
                 
                   
                   
                   
                 invasion protein 
               
               
                   
                   
                   
                   
                 P60 
               
               
                   
                 203-245 
                   
                   
                   
               
               
                   
               
               
                 
                   innocua 
                 
                  30-72  (129) 
                 481 
                 Q01836 
                 adherence and 
               
               
                   
                   
                   
                   
                 invasion protein 
               
               
                   
                   
                   
                   
                 P60 
               
               
                   
                 201-243 
                   
                   
                   
               
               
                   
               
               
                 
                   ivanovii 
                 
                  30-72  (125) 
                 524 
                 Q01837 
                 adherence and 
               
               
                   
                   
                   
                   
                 invasion protein 
               
               
                   
                   
                   
                   
                 P60 
               
               
                   
                 198-240 (73) 
                   
                   
                   
               
               
                   
                 314-356 
                   
                   
                   
               
               
                   
               
               
                 
                   seeligeri 
                 
                  30-72  (127) 
                 523 
                 Q01838 
                 adherence and 
               
               
                   
                   
                   
                   
                 invasion protein 
               
               
                   
                   
                   
                   
                 P60 
               
               
                   
                 200-242 (77) 
                   
                   
                   
               
               
                   
                 320-362 
                   
                   
                   
               
               
                   
               
               
                 
                   welshimeri 
                 
                  30-72  (125) 
                 524 
                 M80348 
                 adherence and 
               
               
                   
                   
                   
                   
                 invasion protein 
               
               
                   
                   
                   
                   
                 P60 
               
               
                   
                 198-240 (75) 
                   
                   
                   
               
               
                   
                 316-358 
                   
                   
                   
               
               
                   
               
               
                 
                   grayi 
                 
                  30-72  (104) 
                 511 
                 Q01835 
                 adherence and 
               
               
                   
                   
                   
                   
                 invasion protein 
               
               
                   
                   
                   
                   
                 P60 
               
               
                   
                 177-219 (79) 
                   
                   
                   
               
               
                   
                 299-342 
                   
                   
                   
               
               
                   
               
               
                 
                   Haemophilus 
                 
                 294-336 
                 432 
                 P44493 
                 N—acetylmuramoyl- 
               
               
                 
                   influenzae 
                 
                   
                   
                   
                 L-alanine amidase 
               
               
                   
                 387-430 
                   
                   
                   
               
               
                   
                 131-174 
                 475 
                 P44693 
                 homologous to 
               
               
                   
                   
                   
                   
                 endopeptidase of 
               
               
                   
                   
                   
                   
                 Staphylococcus 
               
               
                   
                 147-190 
                 405 
                 P44833 
                 outer membrane 
               
               
                   
                   
                   
                   
                 lipoprotein 
               
               
                   
               
               
                 
                   somnus 
                 
                 120-164 
                 279 
                 L10653 
                 outer membrane 
               
               
                   
                   
                   
                   
                 lipoprotein 
               
               
                   
               
               
                 
                   Helicobacter 
                 
                 319-361 
                 372 
                 AE000654 
                 regulatory protein 
               
               
                 
                   pylori 
                 
                   
                   
                   
                 DniR 
               
               
                   
               
               
                 
                   Pseudomonas 
                 
                  69-113 
                 297 
                 P45682 
                 Lipoprotein 
               
               
                 
                   aeruginosa 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Putida 
                 
                  44-87 
                 244 
                 Y19122 
                 lipoprotein 
               
               
                   
               
               
                 
                   Sinorhizoblum 
                 
                 166-209 
                 512 
                 U81296 
                 Lipoprotein 
               
               
                 
                   meliloti 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Synechocystis 
                 
                  87-130 
                 715 
                 D90915 
                 Lipoprotein 
               
               
                 sp. 
                   4-47 
                 245 
                 D90907 
                 Hypothetical protein 
               
               
                   
               
               
                 
                   Aquifex 
                 
                  26-70  (24) 
                 349 
                 AE000700 
                 Lipoprotein 
               
               
                 
                   acolicus 
                 
                  95-137 (37) 
                   
                   
                   
               
               
                   
                 174-216 
                   
                   
                   
               
               
                   
               
               
                 
                   Volvox 
                 
                  42-85 
                 309 
                 AF058716 
                 chitinase 
               
               
                 
                   carteri 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   f. 
                 
                 106-149 
                   
                   
                   
               
               
                 
                   nagariensis 
                 
                   
                   
                   
                   
               
               
                   
               
               
                   Staphylo - 
                 431-474 
                 524 
                 A04512 
                 protein A 
               
               
                 
                   coccus 
                 
                 177-220 
                 383 
                 AF106851 
                 autolysin homolog 
               
               
                 
                   aureus 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Colletotrichum 
                 
                 110-153 (31) 
                 230 
                 AJ001441 
                 glycoprotein 
               
               
                   
               
               
                 
                   lindemuthianum 
                 
                 185-228 
                   
                   
                   
               
               
                   
               
               
                 
                   Chlamydophila 
                 
                 159-201 
                 205 
                 AE001659.1 
                 N—Acetylmuramoyl- 
               
               
                   
                   
                   
                   
                 L-Ala Amidase 
               
               
                   
               
               
                 
                   Pneumoniae 
                 
                 316-358 
                 362 
                 AE001643 
                   
               
               
                   
                 124-166 
                 233 
                 AE001670 
                 Muramidase 
               
               
                   
                 188-233 
                   
                   
                   
               
               
                   
               
               
                 
                   Chlamydia 
                 
                 138-180 
                 245 
                 AE001348 
                 Muramidase 
               
               
                 
                   trachomatis 
                 
                 200-245 
                   
                   
                   
               
               
                   
                 155-197 
                 200 
                 AE001330 
                   
               
               
                   
               
               
                 
                   Prevotella 
                 
                 266-309 
                 309 
                 AF017417 
                 hemagglutinin 
               
               
                 
                   intermedia 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Leuconostoc 
                 
                 335-378 
                 432 
                   
                 endolysin 
               
               
                   oenos  Ø10MC 
                 389-432 
                   
                   
                   
               
               
                   
               
               
                 
                   Oenococcus 
                 
                 335-378 
                 432 
                 AF047001 
                 Lysin 
               
               
                   oeni  ØfOg44 
                 389-432 
                   
                   
                   
               
               
                   
               
               
                 
                   Thermotoga 
                 
                  26-69 
                 271 
                 AE001720 
                   
               
               
                 
                   maritime 
                 
                  76-118 
                   
                   
                   
               
               
                   
                 212-255 
                 395 
                 AE001809 
                   
               
               
                   
               
               
                 
                   Treponema 
                 
                 607-650 
                 779 
                 AE001237 
                 membrane-bound 
               
               
                 
                   pallidum 
                 
                   
                   
                   
                 lytic murein 
               
               
                   
                   
                   
                   
                 transglycosylase D 
               
               
                   
                 734-777 
                   
                   
                   
               
               
                   
                  87-130 
                 371 
                 AE001200 
                   
               
               
                   
                  67-110 
                 342 
                 AE001221 
                   
               
               
                   
               
               
                 
                   Borrelia 
                 
                 183-226 (6) 
                 417 
                 AE001137 
                 Hypothetical protein 
               
               
                 
                   burgdorferi 
                 
                 233-275 
                   
                   
                   
               
               
                   
                  44-86  (28) 
                 697 
                 AE001164 
                 N—acetylmuramoyl- 
               
               
                   
                   
                   
                   
                 L-alanine amidase 
               
               
                   
                 115-157 (7) 
                   
                   
                   
               
               
                   
                 165-207 (8) 
                   
                   
                   
               
               
                   
                 216-258 (27) 
                   
                   
                   
               
               
                   
                 286-328 
                   
                   
                   
               
               
                   
                  59-102 
                 295 
                 AE001176 
                   
               
               
                   
               
               
                 
                   Lactobacillus 
                 
                 399-442 
                 442 
                 X90511 
                 lysin 
               
               
                 Øgle 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Bacillus 
                 
                  28-70  (17) 
                 334 
                 U38819.1 
                 D-Glutamate-M- 
               
               
                 
                   subtilis 
                 
                   
                   
                   
                 diam inopimlate 
               
               
                   
                   
                   
                   
                 endopeptidase 
               
               
                   
                  88-130 (20) 
                   
                   
                   
               
               
                   
                 151-193 
                   
                   
                   
               
               
                   
                 525-568 
                 575 
                 P37963 
                 stage VI sporulation 
               
               
                   
                   
                   
                   
                 protein D 
               
               
                   
                   1-43  (5) 
                 427 
                 P37531 
                 Hypothetical protein 
               
               
                   
                  49-92 
                   
                   
                   
               
               
                   
                  29-71  (22) 
                 488 
                 Y14079 
                 Hypothetical protein 
               
               
                   
                  94-136 (39) 
                   
                   
                   
               
               
                   
                 176-218 (23) 
                   
                   
                   
               
               
                   
                 242-284 (24) 
                   
                   
                   
               
               
                   
                 309-351 
                   
                   
                   
               
               
                   
                  29-71  (18) 
                 414 
                 Z99114 
                 similar to cell wall 
               
               
                   
                   
                   
                   
                 binding protein 
               
               
                   
                  90-132 (26) 
                   
                   
                   
               
               
                   
                 159-201 (25) 
                   
                   
                   
               
               
                   
                 227-269 
                   
                   
                   
               
               
                   
                  28-70  (9) 
                 287 
                 AF027868 
                 similar to papQ 
               
               
                   
                  80-122 
                   
                   
                   
               
               
                   
                 345-387 
                 399 
                 Z99111 
                 Hypothetical protein 
               
               
                   
                 179-222 
                 317 
                 Z99110 
                 N—acetylmuramoyl- 
               
               
                   
                   
                   
                   
                 L-alanine amidase 
               
               
                   
                   4-48 
                 387 
                 Z99118 
                 similar to spore coat 
               
               
                   
                   
                   
                   
                 protein 
               
               
                   
                   4-46 
                 439 
                 Z99107 
                   
               
               
                   
                   4-46 
                 164 
                 Z99111 
                   
               
               
                   
               
               
                 ØPBSX 
                 161-204 
                 297 
                 P39800 
                 N—acetylmuramoyl- 
               
               
                   
                   
                   
                   
                 L-alanine amidase 
               
               
                   
               
               
                 Ø PZA 
                 163-207 (6) 
                 258 
                 P11187 
                   
               
               
                   
               
               
                 (=Ø-29) 
                 214-258 
                   
                 P07540 
                   
               
               
                   
               
               
                 Ø B103 
                 165-209 (9) 
                 263 
                 X99260 
                 lysozyme 
               
               
                   
                 219-263 
                   
                   
                   
               
               
                   
               
               
                 
                   sphaericus 
                 
                   3-46  (6) 
                 396 
                 X69507 
                 carboxypeptidase 1 
               
               
                   
                  53-96 
                   
                   
                   
               
               
                   
               
               
                 
                   Salmonella 
                 
                 121-164 
                 377 
                 AJ006131 
                   
               
               
                 
                   dublin 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Escherichia 
                 
                  77-121 
                 419 
                 p24204 
                 homologous to 
               
               
                 
                   coli 
                 
                   
                   
                   
                 endopeptidase of 
               
               
                   
                   
                   
                   
                 Staphylococcus 
               
               
                   
                 343-385 (16) 
                 452 
                 P23931 
                 membrane-bound 
               
               
                   
                   
                   
                   
                 lytic murein 
               
               
                   
                   
                   
                   
                 transglycosylase 
               
               
                   
                   
                   
                   
                 d precursor 
               
               
                   
                 402-443 
                   
                   
                   
               
               
                   
                  50-93 
                 259 
                 U28375 
                 Hypothetical protein 
               
               
                   
                 123-166 
                 379 
                 P33648 
                 Lipoprotein 
               
               
                   
               
               
                 
                   Drosophila 
                 
                 329-371 
                 1325 
                 AF125384 
                 Lethal 82FD protein 
               
               
                 
                   melanogaster 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Drosophila 
                 
                 104-146 
                 678 
                 AAK92873 
                   
               
               
                 
                   melanogaster 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Caenorhabditis 
                 
                  12-55 
                 179 
                 Z79755 
                   
               
               
                 
                   elegans 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Caenorhabditis 
                 
                  24-66 
                 819 
                 U41109 
                   
               
               
                 
                   elegans 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Caenorhabditis 
                 
                  23-66  (11) 
                 1614 
                 U64836/ 
                 Putative 
               
               
                 
                   elegans 
                 
                   
                   
                 AF016419 
                 Endochitinase 
               
               
                   
                  78-121 (21) 
                   
                   
                   
               
               
                   
                 143-186 (21) 
                   
                   
                   
               
               
                   
                 208-251 (19) 
                   
                   
                   
               
               
                   
                 271-314 (20) 
                   
                   
                   
               
               
                   
                 335-378 (23) 
                   
                   
                   
               
               
                   
                 402-445 (21) 
                   
                   
                   
               
               
                   
                 467-510 (37) 
                   
                   
                   
               
               
                   
                 548-591 (44) 
                   
                   
                   
               
               
                   
                 636-679 (66) 
                   
                   
                   
               
               
                   
                 746-786 (8) 
                   
                   
                   
               
               
                   
                 795-838 
                   
                   
                   
               
               
                   
               
               
                 
                   Caenorhabditis 
                 
                  23-66  (51) 
                 1484 
                 U70858 
                 Putative 
               
               
                 
                   elegans 
                 
                   
                   
                   
                 Endochitinase 
               
               
                   
                 118-161 (25) 
                   
                   
                   
               
               
                   
                 187-226 (9) 
                   
                   
                   
               
               
                   
                 236-279 
                   
                   
                   
               
               
                   
               
               
                 
                   Bacillus 
                 
                 191-136 
                 240 
                 L47648 
                   
               
               
                 
                   subtilis 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Citrobacter 
                 
                  65-113 
                 936 
                 Q07591 
                   
               
               
                 
                   fruendii 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Escherichia 
                 
                  65-113 
                 934 
                 P43261 
                 Necessary for close 
               
               
                 
                   coli 
                 
                   
                   
                   
                 (intimate) attachment 
               
               
                   
                   
                   
                   
                 of bacteria 
               
               
                   
               
               
                 
                   Micrococcus 
                 
                 171-218 
                 220 
                 Z96935 
                 Bacterial Cytokine 
               
               
                 
                   luteus 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Bacillus 
                 
                  40-90 
                 105 
                 Z73234 
                   
               
               
                 
                   subtilis 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Streptococcus 
                 
                 147-103 
                 393 
                 U09352 
                   
               
               
                 
                   pyogenes 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Bacillus 
                 
                 176-234 
                 235 
                 P54335 
                   
               
               
                 
                   subtilis 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Bacillus 
                 
                 177-234 
                 235 
                 G1225954 
                   
               
               
                 
                   subtilis 
                 
                   
                   
                   
                   
               
               
                   
               
               
                 
                   Bacillus 
                 
                 161-218 
                 219 
                 P45932 
                   
               
               
                 
                   subtilis 
                 
               
               
                   
               
             
          
           
               
                 Consensus 
                   Y x VK x GDTL xx IA xxxxxxxxx L xxx N xx L xxxxx I xx GQ x I x V x 
                 (SEQ ID NO: 163) 
               
               
                 repeat 
                 
                   H IR  ESV  LS         I      I     L     L I 
                 
                   
               
               
                   
                    L     I  V                       V     V L   
               
               
                   
               
               
                 a) Proteins listed were obtained by a homology search in the SWISSPROT, PIR, and Genbank databases with the repeats of AcmA using the BLAST program. 
               
               
                 b) *; genes encoding cell wall hydrolases. 
               
               
                 #; proteins containing repeats that are longer than the consensus sequence. 
               
               
                 c) The number of aa residues between the repeats is given between brackets. 
               
               
                 d) Number of aa of the primary translation product. 
               
               
                 e) Genbank accession number. 
               
             
          
         
       
     
     
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 4 
               
             
             
               
                   
               
               
                 Calculated pIs of individual repeat sequences of the AcmA and 
               
               
                 AcmD protein anchors. 
               
             
          
           
               
                   
                 AcmA anchor domain 
                   
                 AcmD anchor domain 
                   
               
             
          
           
               
                   
                 Repeat 
                 Calculated pI 
                 Repeat 
                 Calculated pI 
               
               
                   
                   
               
             
          
           
               
                   
                 A1 
                 9.75 
                 D1 
                 4.15 
               
               
                   
                 A2 
                 9.81 
                 D2 
                 3.78 
               
               
                   
                 A3 
                 10.02 
                 D3 
                 4.15 
               
               
                   
                 A1A2A3 
                 10.03 
                 D1D2D3 
                 3.85 
               
               
                   
                   
               
             
          
         
       
     
     
       
         
               
             
               
               
               
             
               
               
               
               
             
               
               
               
               
             
           
               
                 TABLE 5 
               
             
             
               
                   
               
               
                 Hybrid protein anchors composed of different AcmA and AcmD 
               
               
                 repeat sequences and their calculated pIs. 
               
             
          
           
               
                   
                 Composition of hybrids 
                   
               
             
          
           
               
                   
                 AcmA-repeat sequence 
                 AcmD-repeat sequence 
                 Calculated pI 
               
               
                   
                   
               
             
          
           
               
                   
                 A1A2A3 
                 — 
                 10.03 
               
               
                   
                 A1A2 
                 D1 
                 9.53 
               
               
                   
                 A1A2A3 
                 D1D2D3 
                 8.66 
               
               
                   
                 A1 
                 D2 
                 8.45 
               
               
                   
                 A3 
                 D1D2 
                 7.39 
               
               
                   
                 A1A2 
                 D1D2D3 
                 6.08 
               
               
                   
                 A3 
                 D1D2D3 
                 5.07 
               
               
                   
                 A1 
                 D1D2D3 
                 4.37 
               
               
                   
                 — 
                 D1D2D3 
                 3.85 
               
               
                   
                   
               
             
          
         
       
     
     REFERENCES 
     
         
         Bolotin et al. (2001)  Genome Res.  11: 731-753. 
         Buist et al. (1995)  J. Bacteriol.  177: 1554-1563. 
         Gasson (1983)  J. Bacteriol.  154: 1-9. 
         Kok et al. (1988)  Appl. Environ. Microbiol.  54: 231-238. 
         Kuipers et al. (1997)  Tibtech.  15: 135-140. 
         Morata de Ambrosini et al. (1998)  J. Food Prot.  61: 557-562. 
         Navarre and Schneewind (1994)  Mol. Microbiol.  14: 115-121. 
         Norton et al. (1994)  FEMS Microbiol. Lett.  120: 249-256. 
         Norton et al. (1996)  FEMS Immunol. Med. Microbiol.  14: 167-177. 
         Poquet et al. (2000)  Mol. Microbiol.  35: 1042-1051. 
         Ramasamy (1987)  Immunol. Cell Biol.  65: 419-424. 
         Ramasamy et al. (1999)  Parasite Immunol.  21: 397-407. 
         Robinson et al. (1997)  Nature Biotechnol.  15: 653-657. 
         Sauvé et al. (1995)  Anal. Biochem.  226: 382-283.