Attaching substances to microorganisms

[0001] This application is a divisional of U.S. Ser. No. 09/554,354, filed May 12, 2000, which is a national entry of PCT International Patent Application No. PCT/NL98/00655, filed on Nov. 12, 1998, (corresponding to PCT International Publication No. WO 99/25836, the contents of which is incorporated by this reference as is the sequence listing in U.S. Ser. No. 09/554,354).

[0002] The invention relates to surface display of proteins on microorganisms via the targeting and anchoring of heterologous proteins to the outer surface of cells such as yeast, fungi, mammalian, plant cells, and bacteria.

[0003] Heterologous surface display of proteins (Stahl and Uhlen, TIETECH May 1997, 15, 185-192) on recombinant microorganisms via the targeting and anchoring of heterologous proteins to the outer surface of host-cells such as yeast, fungi, mammalian and plant cells, and bacteria has been possible for several years. Display of heterologous proteins at these cells' surfaces has taken many forms, varying from 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 research in microbiology, molecular biology, vaccinology, and biotechnology, and several patent applications have been filed.

[0004] Another application of bacterial surface display has been developing live-bacterial-vaccine delivery systems. The cell-surface display of heterologous antigenic determinants has been advantageous for inducing antigen-specific immune responses when using live recombinant cells 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.

[0005] In general, one has used chimeric proteins consisting of an anchoring or targeting part specific and selective for the recombinant organism used and has combined this part with a part comprising a reactive group as described above. A well known anchoring part, for example, comprises the so-called LPXTG box that binds covalently to a Staphylococcus bacterial surface, i.e., in the form of a fully integrated membrane protein. In this way, chimeric proteins are composed of at least two (poly)peptides of different genetic origin joined by a normal peptide bond. For example, in PCT International Publication Number WO 94/18830 relating to the isolation of compounds from complex mixtures and the preparation of immobilized ligands (bioadsorbents), a method has been claimed for obtaining such a ligand which comprises anchoring a binding protein in or at the exterior of the cell wall of a recombinant cell. The binding protein is essentially a chimeric protein produced by the recombinant cell, and is composed of an N-terminal part, derived from, for example, an antibody, that is capable of binding to a specific compound joined with a C-terminal anchoring part, derived from an anchoring protein purposely selected for being functional in the specific cell chosen. In patent application WO 97/08553 a method has been claimed for the targeting of proteins selectively to the cell wall of Staphylococcus spp, using as anchoring proteins long stretches of at least 80-90 amino acid long amino acid cell wall-targeting signals derived from the lysostaphin gene or amidase gene of Staphylococcus which encode for proteins that selectively bind to Staphylococcus cell wall components.

[0006] Vaccine delivery or immunization via attenuated bacterial vector strains expressing distinct antigenic determinants against a wide variety of diseases is now commonly being developed. Recently, mucosal (for example nasal or oral) vaccination using such vectors has received a great deal of attention. For example, both systemic and mucosal antibody responses against an antigenic determinant of the hornet venom were detected in mice orally colonized with a genetically engineered human oral commensal Streptococcus gordonii expressing the antigenic determinant on its surface (Medaglini et al., PNAS 1995, 2; 6868-6872). Also, a protective immune response could be elicited by oral delivery of a recombinant bacterial vaccine wherein tetanus toxin fragment C was expressed constitutively in Lactococcus lactis (Robinson et al., Nature Biotechnology 1997, 15; 653-657). Especially mucosal immunization as a means of inducing IgG and secretory IgA antibodies directed against specific pathogens of mucosal surfaces is considered an effective route of vaccination. Immunogens expressed by bacterial vectors are presented in particulate form to the antigen-presenting cells (for example M-cells) of the immune system and should, therefore, be less likely to induce tolerance than soluble antigens. In addition, the existence of a common mucosal immune system permits immunization on one specific mucosal surface to induce secretion of antigen-specific IgA, and other specific immune responses at distant mucosal sites. A drawback to this approach is the potential of the bacterial strain to cause inflammation and disease in itself, potentially leading to fever and bacteraemia. An alternative approach avoids the use of attenuated bacterial strains that may become pathogenic themselves by choosing recombinant commensal bacteria as vaccine carriers, such as Streptococcus spp. and Lactococcus spp.

[0007] However, a potential problem with such recombinant organisms is that they may colonize the mucosal surfaces, thereby generating a long-term exposure to the target antigens expressed and released by these recombinant microorganisms. Such long term exposure can cause immune tolerance. In addition, the mere fact alone that such organisms are genetically modified and contain recombinant nucleic acid is meeting considerable opposition from the lay public as a whole, stemming from a low level of general acceptance for products containing recombinant DNA or RNA. Similar objections exist against the use of even-attenuated strains of a pathogenic nature or against proteins or parts of proteins derived from pathogenic strains. However, as explained above, present techniques of heterologous surface display of proteins in general entail the use of anchoring or targeting proteins that are specific and selective for a limited set of microorganisms which in general are of recombinant or pathogenic nature, thereby greatly restricting their potential applications.

[0008] The invention provides substances and methods to anchor or attach the substances to a cell wall or cell wall component of a wide range of microorganisms. A preferred embodiment of the invention provides substances and methods to attach the substances to non-recombinant microorganisms. The substances provided by the invention—are not limited to (chimeric) proteins alone, but can be fully or only partly of a peptide nature, whereby a peptide part is covalently joined to a non-peptide moiety. The invention provides a proteinaceous substance comprising at least one stretch of amino acids derived from a first microorganism which substance is capable of attaching to a cell wall of a second microorganism. The substance according to the invention is, for example, produced by a first microorganism (for example a microorganism from which the knowledge about the sequence of the stretch of amino acids originates, but another recombinant microorganism can produce the substance as well). After its production, the substance is harvested, optionally stored for future use, and then brought in contact with the second microorganism, where it attaches to its cell wall. Alternatively, the substance is produced synthetically by using established peptide synthesis technology. A preferred embodiment of the invention provides a substance wherein the second microorganism is a non-recombinant microorganism. With a substance provided by the invention, it is now possible to attach or anchor, for example, a heterologous or chimeric protein produced by a recombinant microorganism to an innocuous non-recombinant microorganism.

[0009] A preferred embodiment of the invention provides a proteinaceous substance wherein the stretch of amino acids has a sequence corresponding to a consensus sequence listed in FIG. 10 (SEQ ID NO:17 through SEQ ID NO:19), or wherein the stretch of amino acids (herein also called attaching peptide) has a sequence corresponding to a sequence selected from those listed in FIG. 11 (SEQ ID NO:20 through SEQ ID NO:110), or a homologous sequence derived from another species. The sequences listed in FIG. 11 (SEQ ID NO:20 through SEQ ID NO: 110), and sequences homologuous thereto, are found in a variety of species, both microorganisms and higher organisms, an example of such a higher organism is C. elegans. Preferably, the attaching peptide is derived from any one of the proteins listed in FIG. 11 (SEQ ID NO:20 through SEQ ID NO: 10), more preferably the attaching peptide comprises an amino acid sequence as shown in FIG. 10 (SEQ ID NO:14 through SEQ ID NO:19), or a sequence derived thereof. For example, the invention provides a proteinaceous substance wherein the attaching peptide is derived from the major peptidoglycan hydrolase of Lactococcus lactis (SEQ ID NO:14 through SEQ ID NO:22).

[0010] Yet another preferred embodiment of the invention provides a proteinaceous substance wherein the second microorganism is selected from any of the group of Gram-positive bacteria and Gram-negative bacteria. Examples are microorganisms, such as Bacillus subtilis (SEQ ID NO:75 through SEQ ID NO:78, SEQ ID NO:81 through SEQ ID NO:87, SEQ ID NO:104, SEQ ID NO:107, SEQ ID NO:109 and SEQ ID NO:110), Clostridium beijerinckii, Lactobacillus plantarum, Lb. buchneri, Listeria inocua, Streptococcus thermophilus, Enterococcus faecalis (SEQ ID NO:23 through SEQ ID NO:27), E. coli (SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:79, SEQ ID NO:106), and others.

[0011] The invention provides a proteinaceous substance which is additionally comprising a reactive group. For example, the invention provides a proteinaceous substance comprising a reactive group such as an antigenic determinant, heterologous enzyme, single-chain antibody or fragment thereof, polyhistidyl tag, fluorescing protein, luciferase, binding protein or peptide, or another substance such as an antibiotic, hormone, non-peptide antigenic determinant, carbohydrate, fatty acid, aromatic substance and reporter molecule, and an anchoring or targeting protein or part thereof (herein also called attaching peptide) useful in heterologous surface display which is both broadly reactive with cell wall components of a broad range of microorganisms.

[0012] For example, the invention provides a substance wherein the reactive group is a non-protein moiety, for example, is selected from the group of antibiotics, hormones, aromatic substances and reporter molecules. The substance is constructed by binding, for example, an antibiotic, such as penicillin or tetracycline, but various other antibiotics can be used, or a hormone, such as a steroid hormone, or any other compound to an attaching peptide provided by the invention. Such binding can be achieved by various techniques known in the art, and thereby can label or “flag” the attaching peptide. A preferred example is the binding of an attaching peptide to a reporter molecule such as FITC, or HRPO, whereby tools are generated that can be used in diagnostic assay whereby microorganisms having peptidoglycan are detected. Similarly, an attaching peptide with an antibiotic bound thereto can be used in vivo by, for example, parenteral administration into the bloodstream of humans or animals or in vitro to bind to such microorganisms having peptidoglycan, thereby increasing the concentration of antibiotic around the organism, which then gets killed by the antibiotic action.

[0013] The invention provides a substance wherein the reactive group is a protein moiety, for example, selected from the group of antigenic determinants, enzymes, single-chain antibodies or fragments thereof, polyhistidyl tags, fluorescing proteins, binding proteins or peptides. For example, the invention provides a protein which comprises as a reactive group a protein or polypeptide. Also, the invention provides a nucleic acid molecule encoding a protein provided by the invention. Such a nucleic acid molecule (being single- or double-stranded DNA, RNA or DNA/RNA) at least comprises nucleic acid sequences specifically encoding an attaching peptide as well as nucleic acid sequences specifically encoding the reactive group polypeptide, but can additionally also comprise other nucleic acid sequences, which, for example, encode a signal peptide, or comprise, for example, promoter and/or regulatory nucleic acid sequences. The invention also provides a vector comprising a nucleic acid molecule encoding a protein provided by the invention.

[0014] The invention provides a proteinaceous substance comprising a reactive group joined with or bound to at least one attaching peptide which comprises a stretch of amino acids corresponding to the consensus amino acid sequence listed in FIG. 10, the substance capable of attaching or anchoring or binding to a cell wall component of a microorganism.

[0015] “Corresponding to” is defined as having an amino acid sequence homologous to the consensus amino acid sequence listed in FIG. 10 or having an amino acid sequence derived from the sequence listed in FIG. 10 which comprises a functionally equivalent stretch of amino acids.

[0016] Preferably, the attaching peptide is derived from any one of the proteins listed in FIG. 11 or a protein having a repeat sequence related or homologous to the sequence listed in FIG. 10, more preferably, the attaching peptide comprises an amino acid sequence as shown in FIG. 10 or a sequence derived therefrom. Homology between the various amino acid sequences of related attaching peptides provided by the invention can, for instance, be determined by performing a homology search between amino acid sequences, such as can be found in a protein database, such as the SWISSPROT, PIR and Genbank databases, using a computer program such as the BLAST program that can determine homology between amino acid sequences. For example, the invention provides a proteinaceous substance wherein the attaching peptide is derived from the major peptidoglycan hydrolase of Lactococcus lactis. The invention provides a proteinaceous substance comprising a reactive compound wherein at least two stretches of amino acids corresponding to an attaching peptide sequence are located adjacent to each other, possibly separated by one or more amino acid residues. The stretches or repeats can be separated by a short distance, for example, 3-6 to 10-15 amino acids apart, or by a medium distance 15-100 amino acids apart, or by longer distances (>100 amino acid residues apart). Examples of such distances can be found in FIG. 11, but longer distances are also possible. The distances between the stretches or repeats can also be used for an additional reactive group, whereby a reactive group is inserted between repeats, thereby allowing an even better anchoring to a cell wall component. A preferred embodiment provided by the invention is a proteinaceous substance comprising a reactive group and at least one attaching peptide which comprises a stretch of amino acids having a sequence corresponding to the consensus amino acid sequence listed in FIG. 10, wherein the substance is capable of attaching to a cell wall component of a microorganism, such as can be found from among any of the groups of yeast, molds, gram-positive bacteria and gram-negative bacteria. Examples are microorganisms, such as Bacillus subtilis, Clostridium beijerinckii, Lactobacillus plantarum, Lb. buchneri, Listeria inocua, Streptococcus thermophilus, Enterococcus faecalis, E. coli, and others. A preferred embodiment provided by the invention is a proteinaceous substance which is capable of attaching to a cell wall component of a conventional non-recombinant microorganism. In this embodiment, the invention provides, for example, non-recombinant organisms displaying heterologous proteins. These may colonize the mucosal surfaces without causing problems such as immune tolerance since they do not generate a long-term exposure to the target antigens expressed. In addition, the mere fact alone that such organisms provided by the invention are not genetically modified and do not contain recombinant nucleic acid, will alleviate the opposition from the lay public as a whole against recombinant microorganisms, stemming from a low level of general acceptance for products containing recombinant DNA or RNA. Similar objections that exist against the use of (even attenuated) strains of a pathogenic nature or against proteins or parts of proteins derived from pathogenic strains are now also overcome by the invention, in that it is now possible to attach a proteinaceous substance to a non-recombinant, non-pathogenic microorganism, such as L. lactis which is generally considered as safe. The invention provides a proteinaceous substance comprising a reactive group such as an antigenic determinant, (heterologous) enzyme, (single-chain) antibody or fragment thereof, polyhistidyl tag, fluorescing protein, luciferase, binding protein or peptide, or another compound such as an antibiotic, hormone, non-peptide antigenic determinant, carbohydrate, fatty acid, aromatic compound and reporter molecule, and an anchoring or targeting protein or part thereof (herein also called attaching peptide), useful in heterologous surface display, which is both broadly reactive with cell wall components of a broad range of microorganisms. The attaching peptide is preferably derived from a microorganism which is generally recognized as safe (G.R.A.S.), thereby greatly enhancing the potential of applications of the heterologous surface display technique. Lactococcus lactis is a non-pathogenic, non-invasive, and non-colonizing gram-positive bacterium which is not adapted for growth in the body or even the gut; it does not belong to the commensal species of lactic acid bacteria. L. lactis has a history of safe use of several thousand years. The major cell wall hydrolase AcmA of the gram-positive bacterium Lactococcus lactis subsp. cremoris MG1363 is an N-acetylmuramidase which is required for cell separation and is responsible for cell lysis during the stationary phase. The protein consists of three separate domains (FIG. 9, Buist et al., J. Bacteriol. (1995) 177:1554-1563) of which the first 57 amino acids of the N-terminal domain encompasses the signal peptide needed for secretion. This domain is followed by the active site domain running from the Ala at position 58 to Ser-218. The active site domain was overproduced in and purified from Escherichia coli as a thioredoxin fusion protein. The AcmA part was released by proteolytic cleavage with enterokinase and shown to be active in vitro. Three homologous repeated regions or stretches of amino acids of 35-55 amino acid residues, more often 40-50 amino acid residues, are present in the C-terminus of, for example, AcmA which are separated by non-homologous sequences (FIG. 10). The repeat sequences of AcmA (cA) can be deleted and additional repeat sequences could be added without impairing cell wall hydrolyzing activity in vitro. The AcmA deletion derivatives lacking one or two repeat sequences and the protein containing at least one additional repeat were able to bind to lactococcal cells when added from the outside. The derivative lacking all three repeats did not bind to the cells nor did the purified active site domain. The invention provides an attaching peptide that comprises at least one repeat sequence as shown in FIG. 10 or a sequence that is similar to the sequence of FIG. 10, “similar” being defined as comprising at least a part of a consensus sequence as shown in FIG. 11. Also, attaching peptides are provided by the invention which comprise amino acid sequences derived from a sequence as shown in FIG. 11. “Derived herein” means, among others, by comparison with heterologous sequences, whereby a consensus sequence is obtained, or derived via conventional amino acid substitutions, whereby amino acids are substituted by like amino acids, or derived via substitutions, whereby functional amino acids are replaced by functionally alike or better amino acids, identified by methods such as PEPSCAN techniques or replacement mapping. The invention provides a proteinaceous substance comprising a reactive group and at least one attaching peptide which comprises a stretch of amino acids having a sequence corresponding to at least a part of the consensus amino acid sequence provided in FIG. 10. Repeats similar to those in AcmA were, for example, shown to be present in various cell wall hydrolases and other secreted proteins of gram-positive and gram-negative bacteria and other microorganisms and constitute a general cell wall-binding domain in these proteins. An attaching peptide comprising at least one AcmA repeat or an amino acid sequence similar to the AcmA repeat provided by the invention represents a general and broadly reactive tool to bind or attach reactive groups such as antigenic determinants, enzymes, antibodies, proteins or peptides to cell walls of microorganisms. The repeat comprises a peptide composed of a stretch of amino acids having a sequence corresponding to at least a part of the consensus amino acid sequence provided in FIG. 10. Furthermore, we also demonstrated that an attaching peptide provided by the invention bound or attached to cells of other, e.g., non-recombinant microorganisms, such as Bacillus subtilis, Clostridium beijerinckii, Lactobacillus plantarum, Lb. buchneri, Listeria inocua, Streptococcus thermophilus, Enterococcus faecalis, E. coli, and others. Binding of the attaching peptide and reactive group joined therewith, as provided by the invention, is stable at pH values ranging from 2-10. Moreover, the attaching peptide provided by the invention is, when attached to the cell wall, protected against proteolytic degradation. One embodiment of the invention is a protein wherein the attaching peptide is derived from any of the proteins listed in FIG. 11. An example of such an attaching peptide is provided in the experimental part of this description wherein an attaching peptide having a sequence as shown in FIG. 10 or a sequence similar thereto is used. Furthermore, the invention provides a protein which comprises, as a reactive group, a protein or polypeptide. Also, the invention provides a nucleic acid molecule encoding a protein provided by the invention. Such a nucleic acid molecule (being single- or double-stranded DNA, RNA or DNA/RNA) at least comprises nucleic acid sequences specifically encoding an attaching peptide as well as nucleic acid sequences specifically encoding the reactive group polypeptide, but can additionally also comprise other nucleic acid sequences which, for example, encode a signal peptide or comprise, for example, promoter and/or regulatory nucleic acid sequences. The invention also provides a vector comprising a nucleic acid molecule encoding a protein provided by the invention. Such a vector can, for example, be a plasmid, phage, or virus, and can now be constructed using a nucleic acid provided by the invention and routine skills of the art. Examples of such a vector can be found in the experimental part of the description. Other examples can, e.g., be a baculovirus vector, or comparable vector viruses through which a protein provided by the invention can be expressed or produced in insection cells. The invention also provides a host cell or expression system comprising a nucleic acid molecule or a vector. Such a host cell expressing a protein is provided by the invention as a microorganism to which a protein is attached. Such a host cell or expression system can, for example, be a gram-positive or gram-negative bacterium, a yeast cell, an insect cell, plant cell, or mammalian cell, or even a cell-free expression system, such as a reticulocyte lysate, and can now be constructed or obtained using a nucleic acid or vector provided by the invention and routine skills of the art. Examples of such a host cell or expression system can be found in the experimental part of the description. Other examples can be obtained using a nucleic acid or vector provided by the invention and routine skills of the art.

[0017] The invention provides a method for attaching a substance to the cell wall of a microorganism comprising the use of an attaching peptide which comprises a stretch of amino acids having a sequence corresponding to at least a part of the consensus amino acid sequence provided in FIG. 10. An example of the method provided by the invention is anchoring of recombinant (poly)peptides, being (chimeric) proteins fused to the cell wall-anchoring repeats of AcmA of Lactococcus lactis MG1363 or to the cell wall of gram-positive bacteria. The recombinant proteins are obtained by the expression of DNA sequences encoding these recombinant (poly)peptides in a suitable production strain (e.g. E. coli or L. lactis) and subsequent purification of the expression products. The recombinant proteins are then mixed, either in vitro or in vivo, with a non-recombinant target bacterium to obtain binding to the cell wall. Another example of the method provided by the invention is anchoring of recombinant (poly)peptides, being (chimeric) proteins fused to the cell wall anchoring repeats of AcmA of Lactococcus lactis, to the cell wall of the recombinant Lactococcus lactis which produces the protein itself. A preferred embodiment of the method provided by the invention, the binding of (purified) proteins to bacterial cells upon addition from the outside, is an excellent tool to anchor recombinant proteins or other substances to non-recombinant bacterial cells.

[0018] A preferred method according to the invention comprises the use of an attaching peptide which is derived from the major peptidoglycan hydrolase of Lactococcus lactis. Another method according to the invention is provided wherein the substance is a (poly)peptide or a protein, for example, being part of a protein provided by the invention. Since post-translational modifications occurring to such a polypeptide or protein are inherent to the host cell or expression system used, a post-translationally modified protein as provided by the invention is, therefore, also provided. However, yet another method according to the invention is provided wherein the compound is selected from the group composed of antibiotics, hormones, antigenic determinants, carbohydrate chains, fatty acids, aromatic compounds and reporter molecules. The substance is constructed by binding, for example, an antibiotic, such as penicillin or tetracycline (but various other antibiotics may be used), or a hormone, such as a steroid hormone, or any other compound to an attaching peptide provided by the invention. Such binding can be achieved by various techniques known in the art and thereby can label or “flag” the attaching peptide. A preferred example is the binding of an attaching peptide to a reporter molecule such as FITC or HRPO, whereby tools are generated that can be used in a diagnostic assay whereby microorganisms having peptidoglycan are detected. Similarly, an attaching peptide with an antibiotic bound thereto can be used in vivo by, for example, parenteral administration into the bloodstream of humans or animals or in vitro to bind to such microorganisms having peptidoglycan, thereby increasing the concentration of antibiotic around the organism, which than can get killed by the antibiotic action. The microorganism is preferably selected from any of the group of yeast, molds, gram-positive bacteria and gram-negative bacteria. For example, the experimental part of this description describes mixing of β-lactamase::cA fusion protein with lactococcal cells which resulted in binding to the cells whereas this was not the case when mature β-lactamase not joined with an attachment protein was added. Also, fusion of β-lactamase of E. coli and α-amylase of Bacillus licheniformis to the attaching peptide provided by the invention and subsequent production of these fusion proteins resulted in active, secreted proteins which were located (attached) in L. lactis cell walls. Binding of AcmA and the β-lactamase::cA fusion protein was also demonstrated to isolated lactococcal cell walls and SDS-washed cell walls (the major part of this fraction is peptidoglycan).

[0019] Anchoring of recombinant proteins to non-recombinant microorganisms such as lactococci or other, bacteria or fungi, is especially attractive if the use of recombinant bacteria is not desired, e.g., in food processes or as pharmaceuticals for medical use such as in vaccines or in antibacterial therapy. The invention provides, for example, vaccine delivery or immunization via microorganisms which are labeled with distinct antigenic determinants and which may be directed against a wide variety of diseases. A protective immune response can, for example, be elicited by oral delivery of a bacterial vaccine provided by the invention wherein tetanus toxin fragment C is attached via a protein provided by the invention to a non-recombinant Lactococcus lactis. Such immunogens expressed by microorganisms provided by the invention are presented in particulate form to the antigen-presenting cells (for example M-cells) of the immune system and are, therefore, less likely to induce tolerance than soluble antigens. In addition, the existence of a common mucosal immune system permits immunization on one specific mucosal surface to induce secretion of antigen-specific IgA and other specific immune responses at distant mucosal sites. The invention solves the drawback of earlier bacterial vaccines whereby the potential to flourish on mucosal surfaces of the attenuated or recombinant bacterial strain used can cause problems such as inflammation and disease in itself, potentially leading to fever and bacteraemia or to the induction of immune tolerance. Also, the invention avoids the potential risks that are involved when using recombinant DNA-containing bacterial vectors for vaccination. In yet another possible vaccine and vaccine use provided by the invention, certain (killed) micro-organisms with adjuvant properties (such as the mycobacteria used in BCG) are labeled or loaded with a protein or substance composed of an antigenic determinant and an attaching peptide. These microorganisms then function as adjuvant, thereby greatly enhancing the immune response directed against the specific antigenic determinant. Yet another use provided by the invention comprises anchoring proteins from the outside to a microorganism which provides a means to present proteins or peptides which normally cannot be overexpressed and/or secreted by the microorganism. For example, the subunit B of cholera toxin (CTB) can be overproduced in E. coli but expression in L. lactis has been unsuccessful until now. The adjuvant activity of CTB in experimental recombinant vaccines is well documented and the ability of CTB or part thereof to bind to GM1 ganglioside on eucaryotic cell surfaces is of interest with respect to the use of L. lactis or other gram-positives in vaccines which specifically require targeting to mucosal surfaces. Yet another medical use provided by the invention is the addition of purified antigen::cA fusion proteins in vivo by parenteral administration into the bloodstream of humans or animals to combat bacterial infections. In this case, the antigen::cA fusion protein is used as a “flag” for the immune system. The antigenic determinant of a protein provided by the invention being a subunit of a vaccine regularly used for the immunization of humans (preferably children) or animals, e.g. a subunit of the Rubella, Pertusis, Poliomyelitis, tetanus or measles vaccine. After delivery into the bloodstream, the “flag” will bind through the AcmA repeats to the pathogenic bacterium present in the blood. A “flag” protein provided by the invention will then activate a memory response, i.e., the response to the antigenic determinant present in the protein. The antibodies thus produced recognise the “flag”-labeled bacteria, which will then be neutralised by the immune system. In this way, the protein is used to stimulate a pre-existing memory immune response, non-related to the bacterial infection, to clear bacterial infections from the system. Yet another use (which alternatively may be considered medical use or food use) provided by the invention is the use wherein a protein provided by the invention has the ability to bind to cells, such as mucosal cells, e.g. of the gut. The reactive group of such a protein is in such a case, for example, partly or wholly derived from a fimbriae protein or another gut attachment protein as is present, for example, in various E. coli strains. Microorganisms to which such a protein is attached will specifically home or bind to certain areas of the gut, a property which, for example, is beneficial for certain bacterial strains (i.e., lactococcal or lactobacillar strains) used as a probiotic. In another food or use of food provided by the invention, the protein or substance is composed of a food additive (such as an enzyme or flavor compound) which affects quality, flavor, shelf-life, food value or texture, joined with an attaching peptide, and subsequently attached or anchored to a microorganism which is then mixed with the foodstuff. The anchoring of such proteins to a bacterial carrier offers the additional advantage that the additive can be targeted to a solid bacteria-containing matrix (e.g. curd) in a process for the preparation of food, e.g. cheese or tofu. Yet another use of a proteinaceous substance or microorganism provided by the invention is the use of bacterial surface display in generating whole-cell bioadsorbents or biofilters for environmental purposes, microbiocatalysts, and diagnostic tools.

[0020] The invention is further explained in the experimental part which cannot be seen as limiting the invention.

[0021] FIG. 1. Analysis of AcmA activity in supernatant fractions of end-exponential-phase cultures of MG1363 containing pGK13 (1) and MG1363acmAΔ1 containing either pGK13, not encoding AcmA (2), pGKAL1, encoding enzyme A3 (3), pGKAL3, encoding enzyme A2 (4), pGKAL4, encoding enzyme A1 (5), pGKAL5, encoding enzyme A0 (6), pGKAL6, encoding enzyme A1.5 (7), or pGKAL7, encoding enzyme A4 (8) in a renaturing SDS-(12.5%)PAA gel containing 0.15% M. lysodeikticus autoclaved cells. Molecular masses (in kilodaltons, kDa) of standard proteins (lane M) are shown in the left margin. Below the gel, the lower part of lanes 5, 6 and 7 of the same gel is shown after one week of renaturation. The right half of the figure gives a schematic representation of the various AcmA derivatives. SS (black), signal sequence; Rx (dark grey), repeats; light grey, Thr, Ser and Asn-rich intervening sequences (6); arrows, artificially duplicated region in the AcmA derivative containing four repeats. The active site domain is shown in white. MW, expected molecular sizes in kDa of the secreted forms of the AcmA derivatives. The numbers of the AcmA derivatives correspond with the lane numbers of the gel. Numbered arrowheads indicate the putative location of proteolytic cleavage sites.

[0022] FIGS. 2A-2B. Purification of the AcmA active site domain (nA). (FIG. 2A) SDS-(12.5%) PAGE of cell extract of 10 μl of E. coli BL21(DE3) (pETAcmA) (lane 3) induced for four hours with IPTG. Lane 2, 10 μl of purified fusion protein isolated from 25 μl of induced E. coli culture and lane 1, 10 μl of the enterokinase cleft protein. (FIG. 2B) Renaturing SDS-(12.5%) PAGE with 0.15% M. lysodeikticus autoclaved cells using the same amount of the samples 1 and 2 shown in part A. Molecular masses (in kilodaltons) of standard proteins are shown on the left of the gel. Before loading, the samples were mixed with an equal volume of 2× sample buffer (15).

[0023] FIG. 3. Schematic representation of plasmids pGBLR and pGALR carrying, respectively, C-terminal fusions of the repeats of AcmA to β-lactamase and α-amylase. α-amy, α-amylase gene of B. licheniformis; β-lac, β-lactamase gene of E. coli; acmA, 3-prime end of the N-acetylmuramidase gene of L. lactis MG1363 encoding the three repeats; EmR and CmR, erythromycin and chloramphenicol resistance genes; AL9 and BL1, protein secretion signals from L. lactis MG1363 (21); repA and ORI, gene for the replication protein and origin of replication of the lactococcal plasmid pWV01, respectively; Pspo2, B. subtilis phage Spo2 promoter. Black boxes indicate the PCR fragments used for the introduction of the restriction enzyme sites EcoRV and NdeI at the position of the stopcodons of the α-amylase and β-lactamase genes, respectively. The open box indicates the part which has been subcloned into pUK21 for construction work. The grey boxes show the fragment of pAL01 used to fuse the 3′-end of acmA to the α-amylase and β-lactamase genes. Only relevant restriction enzyme sites are shown.

[0024] FIG. 4. β-lactamase activity in L. lactis. Activity of wild-type β-lactamase and its AcmA fusion derivative (βcA) produced by cells of L. lactis MG1363 and MG1363acmAΔ1 containing pGK13, pGBL1 or pGBLR. The ½M17 agar plate was stained with iodine after overnight growth of the colonies according to the protocol of Smith et al. (29).

[0025] FIG. 5. α-amylase activity in the supernatant of L. lactis. Activity of wild-type α-amylase (α) and the αcA fusion protein in an SDS-(12.5%)PAA gel containing 1% starch. The proteins were renatured by washing the gel with Triton X-100 and subsequently stained with iodine (33). The equivalent of 40 μl of supernatant of ½M17 cultures of L. lactis MG1363 (M) and MG1363acmAΔ1 (Δ) containing pGAL9 or pGALR were loaded onto the gel. Molecular masses (in kDa) of standard proteins are shown in the left margin.

[0026] FIG. 6. Localization of β-lactamase in L. lactis. Western blot analysis of fractions of MG1363acmAΔ1 expressing β-lactamase (from PGBL1) or βcA fusion protein (encoded by pGBLR) using polyclonal antibodies directed against β-lactamase. Amount of samples loaded is equal to 200 μl of culture. Fractions: S, supernatant; CW, cell wall; CY, cytoplasm; MB, membrane-associated; and M, membrane.

[0027] FIG. 7. Analysis of the binding of AcmA derivatives nA and A1 by a renaturing SDS-(17.5%) PAGE with 0.15% M. lysodeikticus autoclaved cells. Cell (C) and supernatant (S) fractions of MG1363acmAΔ1 cells incubated with nA and A1 from the culture supernatant of MG1363acmAΔ1 containing pGKAL4. 60 μl of the samples were loaded. Molecular masses (in kDa) of standard proteins are shown in the left margin.

[0028] FIG. 8. Binding of the βcA fusion protein to L. lactis. The figure shows a Western blot using polyclonal antibodies against β-lactamase. Cell extracts (lanes 1, 3, 5) and supernatants (lanes 2, 4, 6) of mid-exponential phase MG1363acmAΔ1 (pGK13) cells incubated for five minutes with supernatants of MG1363acmAΔ1 containing pGK13 (lanes 1, 2), pGBLR (lanes 3, 4) or pGBL1 (lanes 5, 6), respectively. The positions of wild-type β-lactamase (β) and the βcA fusion protein are indicated on the right. Molecular masses (in kDa) of standard proteins are shown in the left margin. Twenty μl of samples were loaded onto an 12.5% PAA gel.

[0029] FIG. 9. Schematic representation of the AcmA protein. SS (black), signal sequence; R. (dark grey), repeats; shaded regions, intervening sequences. The active site domain is shown in white.

[0030] FIG. 10. Amino acid sequence alignment of the repeats of AcmA in L. lactis plus consensus sequence. Amino acid sequences SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18 and SEQ ID NO:19 are depicted.

[0031] FIGS. 11A and 11B. Amino acid sequence alignment of repeats in various species (SEQ ID NO:20 through SEQ ID NO:110), wherein:

SEQ ID NO:	Species and protein	Residue No.
SEQ ID NO: 20	Lactobacillus lactis acmA	245-287	(33)
SEQ ID NO: 21		321-363	(31)
SEQ ID NO: 22		395-437
SEQ ID NO: 23	Enterococcus faecalis autolysin	363-405	(25)
SEQ ID NO: 24		431-473	(25)
SEQ ID NO: 25		499-541	(25)
SEQ ID NO: 26		567-609	(19)
SEQ ID NO: 27		629-671
SEQ ID NO: 28	Enterococcus hirae mur2	257-299	(38)
SEQ ID NO: 29		338-380	(33)
SEQ ID NO: 30		414-456	(32)
SEQ ID NO: 31		489-531	(33)
SEQ ID NO: 32		565-607	(15)
SEQ ID NO: 33		623-665
SEQ ID NO: 34	Lactococcus øTuc2009 lys	332-375	(10)
SEQ ID NO: 35		386-428
SEQ ID NO: 36	Lactococcus ø-LC3 lysB	333-376	(10)
SEQ ID NO: 37		387-429
SEQ ID NO: 38	Bacillus øPBSX xy1A	161-204
SEQ ID NO: 39	Bacillus ø PZA orf15	163-207	(6)
SEQ ID NO: 40	(=ø-29)	214-258
SEQ ID NO: 41	Bacillus ø B103 orf15	165-209	(9)
SEQ ID NO: 42		219-263
SEQ ID NO: 43	Bacillus øgle lys	399-442
SEQ ID NO: 44	Bacillus sphaericus Pep I	3-46	(6)
SEQ ID NO: 45		53-96
SEQ ID NO: 46	Haemophilus influenzae amia	294-336
SEQ ID NO: 47		387-430
SEQ ID NO: 48	Listeria monocytogenes P60	30-72	(130)
SEQ ID NO: 49		203-245
SEQ ID NO: 50	Listeria innocua P60	30-72	(130)
SEQ ID NO: 51		201-243
SEQ ID NO: 52	Listeria ivanovii P60	30-72	(125)
SEQ ID NO: 53		198-240
SEQ ID NO: 54		314-356
SEQ ID NO: 55	Listeria seeligeri P60	30-72	(127)
SEQ ID NO: 56		200-242	(75)
SEQ ID NO: 57		320-362
SEQ ID NO: 58	Listeria welshimeri P60	30-72	(127)
SEQ ID NO: 59		198-240	(75)
SEQ ID NO: 60		316-358
SEQ ID NO: 61	Listeria grayi P60	30-72	(104)
SEQ ID NO: 62		177-219	(79)
SEQ ID NO: 63		299-342
SEQ ID NO: 64	Escherichia coli yebA	77-121
SEQ ID NO: 65	Haemophilus influenzae yebA	131-174
SEQ ID NO: 66	Escherichia coli nlpD	123-166
SEQ ID NO: 67	Haemophilus influenze lppB	147-190
SEQ ID NO: 68	Haemophilus somnus lppB	120-164
SEQ ID NO: 69	Pseudomonos aeruginosa lppB	69-113
SEQ ID NO: 70	Synechocystis nlpD	87-130
SEQ ID NO: 71	Sinohizobium meliloti nlpD	166-209
SEQ ID NO: 72	Escherichia coli dniR	113-155	(16)
SEQ ID NO: 73		172-213
SEQ ID NO: 74	Staphylococcus aureus ProtA	431-474
SEQ ID NO: 75	Bacillus subtilis papQ	28-70	(17)
SEQ ID NO: 76		88-130	(20)
SEQ ID NO: 77		151-193
SEQ ID NO: 78	Bacillus subtilis spoVID	525-568
SEQ ID NO: 79	Escherichia coli	50-93
SEQ ID NO: 80	Synechocystis	4-47
SEQ ID NO: 81	Bacillus subtilis yaaH	1-43	(5)
SEQ ID NO: 82		49-92
SEQ ID NO: 83	Bacillus subtilis yhdD	29-71
SEQ ID NO: 84		94-136	(29)
SEQ ID NO: 85		176-218	(23)
SEQ ID NO: 86		242-284	(24)
SEQ ID NO: 87		309-353
SEQ ID NO: 88	Caenorhabditis elegans	23-66	(11)
SEQ ID NO: 89		78-121	(21)
SEQ ID NO: 90		143-186	(21)
SEQ ID NO: 91		208-251	(19)
SEQ ID NO: 92		271-314	(20)
SEQ ID NO: 93		335-378	(23)
SEQ ID NO: 94		402-445	(21)
SEQ ID NO: 95		467-510	(37)
SEQ ID NO: 96		548-591	(44)
SEQ ID NO: 97		636-679	(66)
SEQ ID NO: 98		746-786	(8)
SEQ ID NO: 99		795-838
SEQ ID NO: 100	Caenorhabditis elegans	23-66	(51)
SEQ ID NO: 101		118-161	(25)
SEQ ID NO: 102		187-226	(9)
SEQ ID NO: 103		236-279
SEQ ID NO: 104	Bacillus subtilis	191-136
SEQ ID NO: 105	Citrobacter fruendii eae	65-113
SEQ ID NO: 106	Escherichia coli eae	65-113
SEQ ID NO: 107	Bacillus subtilis yneA	40-90
SEQ ID NO: 108	Streptococcus pyogenes	47-103
SEQ ID NO: 109	Bacillus subtilis yqbp	177-234
SEQ ID NO: 110	Bacillus subtilis	161-218
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 (1).
b) *; genes encoding cell wall hydrolases. #; proteins containing repeats that are longer than average
c) The number of amino acid residues between the repeats are given between brackets.
d) Number of amino acids of the primary translation product.
e) Genbank accession number.

Experimental Part

Introduction

[0032] The major autolysin AcmA of Lactococcus lactis subsp. cremoris MG1363 is an N-acetylmuramidase which is required for cell separation and is responsible for cell lysis during the stationary phase (5, 6). The 40.3-kDa secreted mature protein produces a number of activity bands in a zymogram of the supernatant of a lactococcal culture. Bands as small as that corresponding to a protein of 29 kDa were detected. As no clearing bands are produced by an L. lactis acmA deletion mutant, all bands represent products of AcmA (6). From experimental data and homology studies, it was inferred that AcmA likely consists of three domains: a signal sequence followed by an active site domain and a C-terminal region containing three highly homologous repeats of approximately 45 amino acids which are involved in cell wall binding. As the smallest active protein is 29 kDa, it was suggested that the protein undergoes proteolytic breakdown in the C-terminal portion (5, 6).

[0033] Cell wall hydrolases of various bacteria and bacteriophages contain repeats similar to those present in AcmA (4, 9, 10, 17). Partially purified muramidase-2 of Enterococcus hirae, a protein similar to AcmA, containing six similar repeats, binds to peptidoglycan fragments of the strain (11). The p60 protein of Listeria monocytogenes contains two such repeats and was shown to be associated with the cell surface (24). However, which parts of these enzymes contained the binding capacity was not assessed in any of these studies.

[0034] Nearly all cell wall hydrolases examined so far seem to consist of a catalytic domain and usually, although not always, a domain containing a number of specific amino acid repeats. In several studies it has been shown that only a part of some of the cell wall hydrolases is required for enzymatic activity (13, 14, 17, 19, 22, 34). Rashid et al. reported the cloning of the gene encoding a 90-kDa glucosaminidase of Bacillus subtilis of which the C-terminus shows significant similarity with the glucosaminidase domain of the S. aureus autolysin (23). The protein contains two repeated sequences in its N-terminus and two different repeats in the middle domain. A deletion derivative lacking the C-terminal 187 amino acids remained tightly bound to the cell walls, but no catalytic activity was observed when expressed in B. subtilis. By making deletions from the N-terminus it was shown that nearly two-thirds of the protein could be removed without complete loss of cell wall-hydrolyzing activity in E. coli, although loss of more than one repeat drastically reduced lytic activity.

[0035] The N-terminal domain of the major autolysin LytA of Streptococcus pneumonia provides the N-acetylmuramyl-L-alanine amidase catalytic function, whereas the C-terminal domain, which contains six repeated sequences, determines the specificity of binding to the cell wall (for review: see reference 18). The protein lacks a signal sequence and requires choline-containing teichoic acids to fully degrade pneumococcal cell walls. Furthermore, it was shown that at least four of the six repeats were needed for efficient recognition of the choline residues of pneumococcal cell walls and the retention of appreciable hydrolytic activity (7).

[0036] LytA, pneumococcal phage lysins, as well as clostridial and lactococcal cell wall hydrolases, have been used for the construction of active proteins, such that the activity domain and cell wall recognition domains were exchanged. The N-terminal half of the lactococcal phage enzyme was fused to the C-terminal domain of LytA (28). The chimeric enzyme exhibited a glycosidase activity capable of hydrolyzing choline-containing cell walls of S. pneumonia. This result showed that the lactococcal phage lysin consisted of at least two domains with a glucosidase activity contained in its N-terminus and two repeats similar to those in AcmA in the C-terminus (6). A tripartite pneumococcal peptidoglycan hydrolase has been constructed by fusing the N-terminal catalytic domain of the phage CPL1 lysozyme to HBL3, a protein with an amidase activity and a choline-binding domain (27). The three domains acquired the proper conformation as the fusion protein behaved as an amidase, a lysozyme and as a choline-dependent enzyme.

[0037] Also from nature, an enzyme is known as having two separate functional activity domains: the autolysin gene from Staphylococcus aureus encodes a protein that contains an amidase and an endo-β-N-acetylglucosaminidase domain separated by three highly similar repeats (20). This protein is processed posttranslationally into the two constituting activity domains.

[0038] The aim of the present study was to investigate the modular structure of AcmA. This was done by consecutively deleting the C-terminal repeats and by fusing the repeats to heterologous proteins. On the basis of cell fractionation and binding studies involving whole cells, it is concluded that the C-terminal repeats in AcmA bind the autolytic enzyme to the cell wall of L. lactis.

Materials and Methods

[0039] Bacterial strains, plasmids, and growth conditions. The strains and plasmids used in this study are listed in Table 1. Lactococcus lactis was grown at 30° C. in two-fold diluted M17 broth (Difco Laboratories, Detroit, Mich.) containing 0.5% glucose and 0.95% β-glycerophosphate (Sigma Chemical Co., St. Louis, Mo.) as standing cultures (½M17). Agar plates of the same medium contained 1.5% agar. Five μg/ml of erythromycin (Boehringer GmbH, Mannheim, Germany) was added when needed. Escherichia coli was grown at 37° C. with vigorous agitation in TY medium (Difco), or on TY medium solidified with 1.5% agar. When required, the media contained 100 μg of ampicillin (Sigma), 100 μg erythromycin or 50 μg kanamycin (both from Boehringer) per ml. Isopropyl-β-D-thiogalactopyranoside (IPTG) and 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-gal) (both from Sigma) were used at concentrations of 1 mM and 0.002%, respectively.

General DNA Techniques and Transformation.

[0040] Molecular cloning techniques were performed essentially as described by Sambrook et al. (25). Restriction enzymes, Klenow enzyme and T4 DNA ligase were obtained from Boehringer and were used according to the instructions of the supplier. Deoxynucleotides were obtained from Pharmacia (Pharmacia Biotech, Uppsala, Sweden). All chemicals used were of analytical grade and were from Merck (Darmstadt, Germany) or BDH (Poole, United Kingdom). Electrotransformation of E. coli and L. lactis was performed by using a gene pulser (Bio-Rad Laboratories, Richmond, Calif.), as described by Zabarovsky and Winberg (37) and Leenhouts and Venema (16), respectively. Plasmid DNA was isolated using the QIAGEN plasmid DNA isolation kit (QIAGEN GmbH, Hilden, Germany) or by CsCl-ethidiumbromide density gradient centrifugation and DNA fragments were isolated from agarose gels using the QIAGEN gel extraction kit and protocols from QIAGEN.

Primer Synthesis, PCR and DNA Sequencing.

[0041] Synthetic oligo deoxyribonucleotides were synthesized with an Applied Biosystems 392 DNA/RNA synthesizer (Applied Biosystems Inc., Foster City, Calif.). The sequences of the oligonucleotides used are listed in Table 2.

[0042] Polymerase chain reactions (PCR) were performed in a Bio-Med thermocycler 60 (Bio-Med GmbH, Theres, Germany) using super Taq DNA polymerase and the instructions of the manufacturer (HT Biotechnology Ltd., Cambridge, United Kingdom). PCR fragments were purified using the nucleotide removal kit and protocol of QIAGEN.

[0043] Nucleotide sequences of double-stranded plasmid templates were determined using the dideoxy chain termination method (26) with the T7 sequencing kit and protocol (Pharmacia) or the automated fluorescent DNA sequencer 725 of Vistra Systems (Amersham Life Science Inc., Buckinghamshire, United Kingdom).

[0044] Nucleotide and amino acid sequences were analyzed with the PC/GENE sequence analysis program (version 6.8, IntelliGenetics, Inc., Geneva, Switzerland). Protein homology searches in the SWISSPROT, PIR, and Genbank (release September 23, 1996) databases were carried out with the BLAST program (1).

Construction of AcmA Derivatives.

[0045] A stop codon and EcoRI restriction enzyme site were introduced in acmA at the end of nucleotide sequences encoding the repeats and at the end of the sequence specifying the active site domain by PCR using the primers REPDEL-1 (SEQ ID NO:1), REPDEL-2 (SEQ ID NO:2), and REPDEL-3 (SEQ ID NO:3) and plasmid pAL01 as a template. Primer ALA-4 (SEQ ID NO:4), annealing within the sequence encoding the signal peptide of AcmA, was used in all cases as the upstream primer. All three PCR products were digested with SacI and EcoRI and cloned into the corresponding sites of pBluescript SK+ leading to pDEL1, pDEL2, and pDEL3. Subsequently, the 1,1 87-bp PflmI-EcoRI fragment of pGKAL1 (5) was replaced by the 513, 282 and 76-bp PflmI-EcoRI fragments of the inserts of pDEL1, 2 and 3, respectively. The proper plasmids specifying proteins containing one, two or all three repeats (pGKAL5, 4, and 3, respectively) were obtained in L. lactis MG1363acmAΔ1. pGKAL1 was cut with SpeI. The sticky ends were flushed with Klenow enzyme and self-ligation introduced a UAG stop codon after the Ser 339 codon of acmA. The resulting plamid was named pGKAL6.

[0046] A DNA fragment encoding half of the first repeat until the SpeI site in the middle of the second repeat was synthesized by PCR using the primers REP-4 A (SEQ ID NO:5) and B (SEQ ID NO:6). The NheI and SpeI sites at the ends of the 250-bp PCR product were cut and the fragment was cloned into the unique SpeI site of pGKAL1 resulting in plasmid pGKAL7.

Overexpression and Isolation of the AcmA Active Site Domain.

[0047] A DNA fragment encoding the active site domain of AcmA was obtained using the primers ACMHIS (SEQ ID NO:7) and REPDEL-3 with plasmid pAL01 as a template. The 504-bp PCR fragment was digested with Bg/II and EcoRI and subcloned into the BamHI and EcoRI sites of pET32A (Novagen R&D Systems Europe Ltd, Abingdon, United Kingdom). The proper construct, pETAcmA, was obtained in E. coli BL21(DE3) (30). Expression of the thioredoxin/AcmA fusion protein was induced in this strain by adding IPTG (to 1 mM final concentration) at an OD₆₀₀ of 0.7. Four hours after induction, the cells from 1 ml of culture were collected by centrifugation and the fusion protein was purified over a Talon™ metal affinity resin (Clontech Laboratories Inc., Palo Alto, Calif.) using 8 M ureum-elution buffer and the protocol of the supplier. The eluate (200 μl) was dialyzed against a solution containing 50 mM NaCl and 20 mM Tris (pH 7) after which CaCl₂ was added to a final concentration of 2 mM. One unit of enterokinase (Novagen) was added and the mixture was incubated at room temperature for 20 hours. The protein mixture was dialyzed against several changes of demineralized water before SDS-PAGE analysis and cell binding studies.

Construction of β-lactamase and α-amylase Fusions to the AcmA Repeat Domain.

[0048] For the introduction of a unique NdeI site at the position of the stop codon of the E. coli TEM-β-lactamase, the oligonucleotides BETA-1 (SEQ ID NO:8) and BETA-2 (SEQ ID NO:9) were used in a PCR with plasmid pGBL1 (21) as a template. The 403-bp PCR fragment was cut with NdeI and PstI and cloned as a 311 -bp fragment into the same sites of pUK21. The resulting plasmid, pUKblac, was digested with NdeI, treated with Klenow enzyme and subsequently digested with XbaI. The β-lactamase encoding fragment was ligated to a 1,104-bp PvuII-XbaI DNA fragment from pAL01 containing the acmA part encoding the repeat region of AcmA. The resulting plasmid, pUKblacrep, was digested with PstI and DraI and the 1349-bp fragment was inserted into the PstI-SnaBI sites of pGBL1, leading to plasmid pGBLR. After digestion of pGAL9 (21) with ClaI and HindIII, the 1,049-bp fragment encompassing the 3′-end of the Bacillus licheniformis α-amylase gene was subcloned into corresponding sites of pUK21. According to the paper of Perez Martinez et al. (21), this fragment should be 1,402-bp, but after restriction enzyme analysis, it turned out to be approximately 350-bp smaller. The resulting plasmid was called pUKAL1. A unique EcoRV restriction enzyme site was introduced by PCR at the position of the stop codon of the B. licheniformis α-amylase gene using the oligonucleotides ALFA-A (SEQ ID NO:10) and ALFA-B (SEQ ID NO:11) with plasmid pGAL9 as a template. After restriction of the 514-bp PCR fragment with SalI and EcoRV, the 440-bp fragment was cloned into the same sites of pUKAL1 resulting in plasmid pUKAL2. The EcoRV and XbaI sites of this plasmid were used to clone the 1,104-bp PvuII-XbaI fragment of pAL01 encoding the repeats of AcmA. The 1,915-bp ClaI-HindIII fragment of the resulting plasmid pUKALR was used to replace the corresponding 1,049-bp fragment of pGAL9 (pGALR). All cloning steps described above were performed in E. coli NM522. The plasmids pGBL1, pGBLR, pGAL9 and pGALR were used to transform L. lactis MG1363 and MG1363acmAΔ1.

SDS-polyacrylamide Gel Electrophoresis (SDS-PAGE) and Detection of AcmA and α-amylase Activity.

[0049] Two ml of end exponential phase L. lactis cultures were subjected to centrifugation. 0.5 ml of the supernatant fractions were dialyzed against several changes of demineralized water, lyophilized, and dissolved in 0.25 ml of denaturation buffer (3). Cell pellets were washed with 2 ml of fresh ½M17 medium and resuspended in 1 ml of denaturation buffer. Cell extracts were prepared as described by van de Guchte et al. (32).

[0050] AcmA activity was detected by a zymogram staining technique using SDS-PAA (12.5% or 17.5%) gels containing 0.15% autoclaved, lyophilized Micrococcus lysodeikticus ATCC 4698 cells (Sigma) as described before (6). For the analysis of α-amylase activity, 1% starch was included into 12.5% PAA gels. After electrophoresis, proteins were renatured using the AcmA renaturation solution (3) and the gel was stained with an I₂/KI solution (at final concentrations of 12 and 18 mM, respectively) (33).

[0051] SDS-PAGE was carried out according to Laemmli (15) with the Protean II Minigel System (Bio-Rad) and gels were stained with Coomassie brilliant blue (Bio-Rad). The standard low range and prestained low and high range SDS-PAGE molecular weight markers of Bio-Rad were used as references.

[0052] Fractionation of mid- and end-exponential phase cultures of L. lactis was performed according to the protocol of Baankreis (2).

Binding of AcmA and its Derivatives to Lactococcal Cells.

[0053] The cells of 2 ml of exponential phase cultures of MG1363acmAΔ1 were gently resuspended in an equal volume of supernatant of similarly grown MG1363acmAΔ1 carrying either plasmid pGK13, pGKAL1, -3, -4, -5, -6 or -7 and incubated at 30° C. for 20 m Subsequently, the mixtures were centrifugated. The cell pellets were washed with 2 ml of ½M17 and cell extracts were prepared in 1 ml of denaturation buffer as described above, while 0.4 ml of the supernatants were dialyzed against demineralized water, lyophilized and dissolved in 0.2 ml of denaturation buffer.

[0054] To analyze competitive binding between AcmA derivatives containing 1 or 2 repeats, equal volumes of the supernatants of MG1363acmAΔ1 containing pGKAL3 or pGKAL4 were mixed prior to incubation with the MG1363acmAΔ1 cells. The samples were treated for SDS-PAGE as described above.

[0055] Three 500 μl samples of a mid-exponential phase culture of MG1363acmAΔ1 were centrifugated. From one sample, 50 μl of the supernatant were replaced by 50 μl of a solution containing the AcmA active site domain (see above). 100 μl of the supernatant of sample two were replaced by 50 μl demineralized water and 50 μl of the supernatant of a mid-exponential phase culture of MG1363acmAΔ1 (pGKAL4). Of the third sample, 100 μl of the supernatant were replaced by 50 μl of the solution containing the AcmA active site domain and 50 μl of the supernatant of MG1363acmAΔ1 (pGKAL4). Subsequently, the three samples were vortexed to resuspend the cells and incubated for 15 minutes at 30° C. After centrifugation, cell and supernatant fractions were prepared in 500 μl of denaturation buffer for analysis of AcmA activity in SDS-(1 7.5%)PAGE as described above.

[0056] Binding of the β-lactamase/AcmA fusion protein was studied by growing MG1363acmAΔ1 containing pGK13, pGBL1 or pGBLR until mid-exponential phase. The cells of 1 ml of MG1363acmAΔ1 (pGK13) culture were resuspended in an equal volume of supernatant of either of the other two cultures. The mixtures were prepared in duplo and one series was incubated at 30° C. for five minutes while the other was kept at that temperature for 15 minutes. Then, cell and supernatant fractions were treated as described for the AcmA-binding studies, resuspended in denaturation buffer in half of the original volume, and subjected to SDS-(12.5%)PAGE followed by Western blot analysis.

Western Blotting and Immunodetection.

[0057] Proteins were transferred from SDS-PAA gels to BA85 nitrocellulose membranes (Schleicher and Schuell, Dassel, Germany) as described before (31). α-amylase and β-lactamase antigen was detected with 2000-fold diluted rabbit polyclonal anti-ampicillinase antibodies (5 prime→3 prime, Inc., Boulder, Colo.), and alkaline phosphatase-conjugated goat anti-rabbit antibodies (Promega Corporation, Madison, Wis.) using the western-Light Chemiluminescent detection system and protocol (TROPIX Inc., Bedford, Mass.).

Enzyme Assays and Optical Density Measurements.

[0058] AcmA activity was visualized on ½M17 agar plates containing 0.2% autoclaved lyophilized M. lysodeikticus cells as halos around colonies after overnight growth at 30° C.

[0059] α-amylase activity was detected by spotting 10 μl of an overnight culture onto a ½M17 agar plate containing 1% of starch (Sigma). After 18 hours of incubation at 30° C., halos were visualized by staining with an iodine solution according to the protocol of Smith et al. (29). A similar method was used for the detection of β-lactamase activity (29).

[0060] X-prolyl dipeptidyl aminopeptidase (PepX) was measured using the chromogenic substrate Ala-Pro-p-nitroanilid (BACHEM Feinchemicalien AG, Bubendorf, Switzerland). After two minutes of centrifugation in an eppendorf microcentrifuge, 75 μl of a culture supernatant was added to 50 μl substrate (2 mM) and 75 μl Hepes buffer (pH 7). The mixture was pipetted into a microtiter plate well and color development was monitored in a THERMOmax microtiter plate reader (Molecular Devices Corporation, Menlo Oaks, Calif.) at 405 nm during 20 minutes at 37° C. Optical densities were measured in a Novaspec II spectrophotometer (Pharmacia) at 600 nm.

Results

Two of the Three Repeats in AcmA are Sufficient for Autolysis and Cell Separation.

[0061] Several mutant AcmA derivatives were constructed to investigate the function of the three repeats in the C-terminus of AcmA. A stop codon was introduced behind the codon for Thr-287 (pGKAL4) or Ser-363 (pGKAL3) (see FIG. 1). Plasmid pGKAL4-specified AcmA (A1) only contains the first (most N-terminal) of the three repeats, while pGKAL3 specifies an AcmA variant (A2) carrying the first two repeats. pGKAL5 specifies an AcmA derivative lacking repeats (A0) due to the introduction of a stop codon after Ser-21 8. AcmA specified by pGKAL6 contains one and a half repeat (A.1.5) due to the presence of a stop codon behind the Ser-339 codon. From pGKAL7, an AcmA mutant (A4) is produced which carries an additional (fourth) repeat as the result of duplication of the polypeptide from Ser-263 to Thr-338. All proteins were expressed from the acmA promoter in the AcmA-negative strain L. lactis MG1363acmAΔ1. The various deletions of AcmA were examined with respect to the following properties: (I) their effect on halo formation on plates containing cell wall fragments of M. lysodeikticus, (II) chain length of the cells expressing the mutant AcmAs, and sedimentation of the cells in a standing culture, (III) their enzymatic activity, both in the cell and supernatant fraction and (IV) autolysis.

[0062] Halo formation. On a ½M17 plate containing cell wall fragments of M. lysodeikticus, halos were absent when MG1363acmAΔ1 carried pGK13 or pGKAL5. All other strains produced a clear halo that differed in size. The halo size was clearly correlated with the number of full-length repeats present, although the addition of an extra repeat resulted in a reduced halo size (see Table 3). Apparently, for optimal cell wall lytic activity, a full complement of repeats is required.

[0063] Cell separation and sedimentation. The deletion of one and a half, two and all three repeats had a clear effect on the chain length and on sedimentation of the cells after overnight growth (see Table 3). Thus, efficient cell separation requires the presence of at least two repeats in AcmA.

[0064] Enzyme activity. Cells and supernatants of overnight cultures of all strains were analyzed for AcmA activity by SDS-PAGE. In the cell fractions, no activity was detected for A0, not even after one week of renaturation of the protein (Table 3). Of the other derivatives, two major activity bands were present in this fraction. In each case, their positions in the gel corresponded to proteins with the calculated molecular weights of the unprocessed and the processed form. (Table 3 and not shown.) As shown in FIG. 1, all AcmA derivatives were still active in the supernatant fractions. AcmA produced the characteristic breakdown pattern as determined before (FIG. 1, lanes 1 and 3; (6)). All AcmA derivatives except A0 and A1 also showed a distinct and highly reproducible degradation pattern. A4 showed two additional breakdown products after prolonged renaturation (results not shown). These data indicate that removal of the repeats does not destroy AcmA activity and suggests that one repeat is sufficient to keep the enzyme cell-associated.

[0065] Autolysis. To analyze the effect of the repeats on autolysis during the stationery phase, overnight cultures of all strains were diluted an hundred-fold and incubated at 30° C. for six days. The decrease of optical density (OD₆₀₀) was followed. All cultures exhibited similar growth rates, reached the same maximal optical densities and did not lyse during the exponential phase of growth. After approximately 60 hours of incubation, maximal reduction in OD₆₀₀ was reached in all cases. The results are presented in Table 3 and show that the reduction in OD₆₀₀ is correlated with the reduction of the number of AcmA repeats. To investigate whether the decrease in OD₆₀₀ really reflected autolysis, the activity of the intracellular enzyme PepX was measured. After 60 hours of incubation, PepX activity in the culture medium was also maximal in all samples, decreasing in all cases upon further incubation. Hardly any PepX activity was detected in the supernatant of the acmAΔ1 mutant and in cultures producing A0, A1 or A.1.5. In contrast, a considerable quantity of PepX had released into the supernatant of cultures producing A2 and A3. Thus, two repeats in AcmA are sufficient for autolysis of L. lactis. A2 or A4 production led to reduced lysis of the producer cells. Taken together, these results indicate that the repeats in AcmA function in efficient autolysis and are required for cell separation.

The Active Site Domain of AcmA Resides in the N-terminal Part.

[0066] To examine whether the active site is located in the N-terminal domain of AcmA, a DNA fragment starting at codon 58 until codon 218 of acmA was synthesized by PCR and fused to the thioredoxin gene in plasmid pET32A. The fusion protein comprises 326 amino acids. A protein with the expected molecular mass (35 kDa) was isolated from a culture of E. coli BL21(DE3) (pETAcmA) (FIG. 2, lane A2). By cleavage with enterokinase, the protein was split into a thioredoxin part of 17 kDa and an AcmA domain (nA) of 18 kDa (FIG. 2, lane A1). The zymogram (FIG. 2B) shows that the fusion protein did not have appreciable cell wall hydrolytic activity, while the released domain of AcmA was active (FIG. 2, lanes B1 and B2), indicating that the active site domain was in the N-terminal part of AcmA.

Fusion of the Repeats of AcmA to α-amylase and β-lactamase Yields Active Enzymes.

[0067] The three C-terminal repeats of AcmA (cA) were fused C-terminally to B. licheniformis α-amylase and E. coli TEM β-lactamase as described in Material and Methods and shown in FIG. 3. The hybrid proteins were fused to the lactococcal signal sequences AL9 and BL1, respectively (21). Both fusion proteins were active in plate assays, as is only shown for the β-lactamase/AcmA fusion protein (βcA) (FIG. 4). The halos around colonies producing the fusion proteins were smaller than those produced by the wild-type enzymes, which could either be caused by reduced intrinsic enzyme activities due to the presence of repeats or by increased susceptibility to proteolytic degradation. However, the smaller halos produced by the chimeric proteins might also be caused by hampered diffusion due to cell wall binding (see below).

[0068] The activities of α-amylase and the αcA fusion protein were also detected in a renaturing SDS-(12.5%)PAA gel containing 1% starch. The primary translation product of the α-amylase gene is a protein of 522 amino acid residues which contains a signal sequence of 37 amino acids (21). It is secreted as a 55-kDa protein. αcA consists of 741 amino acids and, if processed and secreted, would give rise to a 78-kDa protein. Cell and supernatant fractions of L. lactis MG1363 and MG1363acmAΔ1 carrying pGAL9 or pGALR were analyzed after overnight growth of the strains. The results are presented in FIG. 5 and show that the clearing bands are present at the position expected for both mature proteins. Apparently, αcA is active. Clearly, smaller products are present in the supernatants of the cells producing the fusion protein, the smallest being approximately of the size of wild-type mature α-amylase (FIG. 5 and not shown).

The β-lactamase Fusion Protein is Predominantly Present in the Cell Wall.

[0069] To examine whether the presence of the C-terminal domain of AcmA resulted in binding of βcA to the cell wall, mid-exponential phase cultures of L. lactis MG1363acmAΔ1 containing pGBL1, encoding β-lactamase or pGBLR specifying βcA were fractionated and subjected to Western blot analysis (FIG. 6). From pGBL1, β-lactamase is expressed as a protein of 322 amino acids containing a signal sequence of 47 amino acids. The secreted protein is 30 kDa. βcA consists of 540 amino acids and is secreted as a protein with a molecular mass of 52 kDa. FIG. 6 shows that most of the wild-type β-lactamase is present in the culture supernatant and none in the cytoplasm. Slightly larger bands, likely representing the unprocessed form, are found in the membrane fractions of this strain. In contrast, βcA is predominantly retained in the cell wall fraction, although a considerable amount resides in the cytoplasm, strongly suggesting that the AcmA repeats anchored the hybrid enzyme to the cell wall. The smaller band present in both cytoplasmic fractions is caused bycross-hybridization of the antibodies to an unspecified lactococcal protein (unpublished observation). In the supernatant fraction of cells producing βcA, only little full-length protein was observed. Several distinct smaller products are present in this fraction which were also detectable in very low amounts in the cell wall fraction after prolonged exposure of the film (not shown) but were absent from the other fractions.

The C-Terminal Repeats in AcmA are Required for Cell Wall Binding.

[0070] Although the results presented in the previous section strongly suggest that the C-terminal repeats are required for the retention of protein in the cell wall, definite proof was obtained by mixing the supernatant fractions of end-exponential phase cultures containing AcmA, or one of its deletion derivatives (see FIG. 1), with the cells from an equal volume of a culture of MG1363acmAΔ1 (pGK13). After incubation, cell and supernatant fractions were examined for the presence of AcmA. Except for A0, all proteins were capable of binding to the MG1363acmAΔ1 cells (Table 3). Also, all degradation products of AcmA and its derivatives were capable of binding. The finding that A0 was unable to bind was corroborated by adding the mixture of enterokinase-released nA and thioredoxin to supernatant containing A1. When incubated with AcmA-minus cells, only A1 bound to the lactococcal cells FIG. 7) as only this protein was detectable in the cell fraction. nA was only detected in the supernatant. This was also the case when the experiment was repeated with nA alone (not shown).

Binding of AcmA or βcA to Lactococcal Cells at Different pHs.

[0071] The supernatant fraction of a mid-exponential phase L. lactis MG1363acmAΔ1 culture was replaced by the supernatant of a mid-exponential phase L. lactis MG1363 culture. This mixture was incubated at 30° C. for five minutes. Thereafter the supernatant was removed by centrifugation and the cell pellet was washed with M17. The cell pellets were dissolved in M17 with pHs ranging from 2 to 10 and incubated at 30° C. for 30 minutes. The cell and supernatant fractions were separated and treated as described before and analyzed for the presence of AcmA activity. A similar experiment was executed with mid-exponential phase L. lactis MG1363acmAΔ1 cells with the supernatant of an L. lactis MG1363acmAΔ1 (pGBLR) culture. The presence of βcA was analyzed by western blotting and immunodetection as described.

[0072] At all different pHs, ACmA and βcA was found to be bound to the lactococcal cells. The binding of both AcmA and βcA was better at low pH as judged from the activity in a zymogram and the visual presence of the amount of βcA fusion protein in the cell extracts after immunodetection.

Proteolytic Breakdown of AcmA by Pronase and Trypsin.

[0073] The supernatant fraction of a mid-exponential phase MG1363acmAΔ1 culture was replaced by the supernatant of a mid-exponential phase MG1363 culture. This mixture was incubated at 30° C. for 15 minutes. Thereafter, the supernatant and the cell fractions were separated and the cell pellet was dissolved in an identical volume of M17. To both fractions, Pronase and Trypsin (1 mg/ml) dissolved in 10 mM NaPi buffer (pH=7) was added to an end concentration of (10 μg/ml) and the mixtures were incubated at 30° C. Samples were taken after 5 and 30 minutes and two hours of incubation. The cell and supernatant fractions of each sample were separated and prepared for zymographic analysis as described above.

[0074] A complete hydrolysis of AcmA by pronase was observed in the supernatant fraction after two hours of incubation while activity was still present in the cell extract at this time point. The hydrolysis of AcmA by trypsin was slower and activity was still present in the supernatant after two hours of incubation. In time, the portion of activity present in the cell extracts was always higher than that observed in the supernatant. These results indicate that the ACmA protein is protected when it is bound to the cell.

Binding of AcmA to Different Types of Bacterial Cells.

[0075] The strains Bacillus subtilis DB104, Lactobacillus plantarum 80, Streptococcus faecalis JH2-2, Streptococcus thermophilus ATCC 19258, Listeria P, Lactobacillus buchneeri L4, Clostridium beijerinckii CNRZ 530 and Escherichia coli NM522 were grown overnight in GM17. Two fractions of each overnight culture were centrifuged and the supernatants were replaced by the supernatant of an overnight-culture of L. lactis MG1363acmAΔ1 (pGKAL1) or MG1363acmAΔ1 (pGK13). The mixtures were incubated at 30° C. for 15 minutes. Subsequently, the cell and supernatant fractions were separated and the cells were washed once with M17 and were prepared for SDS-PAGE as described before and analyzed for AcmA activity.

[0076] In all cell extracts AcmA activity was present while such an activity was absent in extracts of cells which had been incubated with the supernatant of MG1363acmAΔ1 (pGK13) which lacks the presence of AcmA.

[0077] To investigate the effect of repeat numbers on binding, equal volumes of the supernatants of cultures of MG1363acmAΔ1 (pGKAL3, encoding A2) and MG1363acmAΔ1 (pGKAL4, specifying A1) were mixed. The undiluted and a ten-fold diluted mixture were incubated with the AcmA-free cells. Analysis of zymograms of serial dilutions showed that the two activities were equally distributed over the cell and supernatant fractions, indicating that both proteins bind equally well (results not shown).

[0078] To examine whether the C-terminal repeat sequences of AcmA had the capacity to bind a heterologous, extracellular enzyme to lactococcal cells, binding of βcA was assessed by incubation of AcmA-minus L. lactis cells with culture supernatants containing either secreted wild-type β-lactamase or βcA. As FIG. 8 shows, wild-type β-lactamase was exclusively present in the supernatant fraction, whereas βcA fractionated with the lactococcal cells and, thus, had bound to these cells.

Discussion

[0079] The results presented in this work indicate that the mature form of the N-acetylmuramidase AcmA of L. lactis consists of two separate domains. The overproduced and purified N-terminus, from amino acid residue 58 to 218 in the pre-protein, is active on M. lysodeikticus cell walls and, thus, contains the active site of the enzyme. This is in agreement with the finding that the repeat-less AcmA mutant A0 can still hydrolyze M. lysodeikticus cell walls, albeit with severely reduced efficiency. Prolonged renaturation was needed to detect the activity of the enzyme in vitro while colonies producing the protein did not form a halo. Enzymes A1 and A2 had in vitro activities which were nearly the same as that of the wild-type protein, although in the plate assay A1 produced a smaller halo than A2 which, in turn, was smaller than the wild-type halo. A strain producing A1 grew in longer chains than cells expressing A2 and, in contrast to A2-producing cells, sedimented and did not autolyze. Taken together, these results indicate that, although the N-terminus of AcmA contains the active site, the presence of at least one complete repeat is needed for the enzyme to retain appreciable activity. Second, only cultures producing AcmAs containing two or more full-length repeats are subject to autolysis and produce wild-type chain lengths. It is tempting to speculate that this apparent increase in catalytic efficiency of AcmA is caused by the repeat domain by allowing the enzyme to bind to its substrate, the peptidoglycan of the cell wall. As was postulated by Knowles et al. (12) for the cellulase-binding domains in cellobiohydrolases, such binding would increase the local concentration of the enzyme. The repeats could be involved in binding alone or could be important for proper positioning of the catalytic domain towards its substrate. The increase in AcmA activity with an increasing number of repeats to up to 3 in the wild-type enzyme, suggests an evolutionary process of repeat amplification to reach an optimum for proper enzyme functioning. The binding of A1, A1.5 and A4 was comparable with that of wild-type AcmA, but these enzyme varieties caused only little or no autolysis. These observations seem to support the idea that three repeats are optimal for proper functioning of AcmA. The presence of five and six repeats in the very similar enzymes of E. faecalis and E. hirae, respectively, may reflect slight differences in cell wall structure and/or the catalytic domain, requiring the recruitment by these autolysins of extra repeats for optimal enzyme activity.

[0080] The hypothesis that the C-terminal domain of AcmA is involved in cell binding (6) was corroborated in this study. First of all, it was shown that AcmA is indeed capable of cell binding. AcmA and its derivatives A1, A1.5, A2 and A4 all bound to cells of L. lactis when added from the outside. To prove that it was the C-terminus of AcmA that facilitated binding and not some intrinsic cell wall-binding capacity of the N-terminal domain, the repeat domain was fused to two heterologous proteins which do not normally associate with the cell wall. The smaller halos produced by αcA and , βcA compared to the wild-type proteins and the presence of most of βcA in the cell wall fraction are indicative of cell binding of the fusion proteins via the AcmA-specific repeats.

[0081] The βcA-binding studies clearly show that it is the AcmA repeat domain that specifies cell wall-binding capacity: whereas wild-type β-lactamase (and, for that matter, repeat-less AcmA) did not bind to lactococcal cells, βcA did bind to these cells when added from the outside. The results obtained with A1 in the binding assay show that only one repeat is sufficient to allow efficient binding of AcmA. In a separate study (5), it was shown that AcmA can operate intercellularly: AcmA-free lactococcal cells can be lyzed when grown together with cells producing AcmA. Combining this observation with the results presented above, it was concluded that AcmA does not only bind when confronting a cell from the outside but, indeed, is capable of hydrolyzing the cell wall with concomitant lysis of the cell.

[0082] AcmA-like repeats were found to be present at different locations in more than 30 proteins after a comparison of the amino acid sequences of the repeats in AcmA with the protein sequences of the Genbank database (release 23). Not all of these proteins with repeats varying from one to six are cell wall hydrolases. Alignment of the amino acid sequences of all the repeats yielded a consensus sequence similar to that postulated by Birkeland and Hourdou et al. (4, 9). Interestingly, if a limited number of modifications are allowed in the consensus repeat, the repeat is also present 12 and 4 times, respectively, in two proteins of Caenorhabditis elegans, which both show homology with endochitinases (Gene accession numbers U64836 and U70858) (36). Possibly, these repeats anchor these enzymes to fungi ingested by this organism. The presence of similar repeats in proteins of different bacterial species strongly suggests that they recognize and bind to a general unit of the peptidoglycan. An interesting goal for the future will be to elucidate the unit to which they bind and the nature of the binding.

[0083] As has been reported earlier for intact AcmA (5) and as shown here for its C-terminal deletion derivatives, the enzyme is subject to proteolytic degradation. None of the degradation products were present in cell extracts of whole cells indicating that they are not formed inside the cell (data not shown). The degradation pattern of each AcmA derivative is specific and very reproducible. Based on the sizes of the degradation products, a number of the proteolytic cleavage sites probably residing in the intervening sequences. One such site (1 in FIG. 1) is present between repeat 1 and 2. Cleavage at this position would result in an active protein of approximately 28 kDa, which is indeed seen in the supernatants of all strains producing AcmA with 1.5 or more repeats. A second cleavage site is probably located between the second and third repeat (2 in FIG. 1). Cleavage at this site is either rather infrequent or the resulting degradation product is not very active which, in both cases, would lead to the faint bands of activity observed in lanes 1 and 3 of the zymogram presented in FIG. 1. The presence of cleavage sites in between the AcmA repeats is further suggested by the presence of specific degradation products observed in αcA and βcA; their sizes are in accord with the location of the cleavage sites postulated in AcmA. In addition, as also bands of the size of the wild-type α-amylase and β-lactamase are observed, an additional cleavage site seems to be present around the fusion point of these enzymes and the cell wall-binding domain of AcmA.

[0084] All degradation products of AcmA and those of the two fusion proteins are mainly present in the supernatant and, to some extent, in the cell wall fraction but not in the cells. As none of the L. lactis strains used produced the cell wall-anchored proteinase PrtP, this enzyme cannot be held responsible for the specific degradation of AcmA or the fusion proteins. Apparently, an extracellular proteinase exists in L. lactis that is capable of removing the repeats, which may represent a mechanism for the regulation of AcmA activity.

TABLE 1
Bacterial strains and plasmids used in this study.
Strain or	Relevant phenotype(s) or	Source or
plasmid	genotype(s)	reference
Strains
L. lactis subsp.
cremoris
MG1363	Plasmid-free strain	(8)
MG1363acmAΔ1	Derivative of MG1363 carrying a	(6)
	701-bp SacI-SpeI deletion in acmA
E. coli
NM522	supE thi Δ (lac-proAB) Δhsd5	Stratagene
	(rk−, mk−) [F′ proAB lacIqZM15]
BL21 (DE3)	ompT rB−mB− int; bacteriophage	(30)
	DE3 lysogen carrying the T7 RNA
	polymerase gene controlled by the
	lacUV5 promoter
Plasmids
pET32A	Apr, vector for high level	Novagen
	expression of thioredoxin
	fusion proteins
pUK21	Kmr, general cloning vector	(35)
pBluescript SK+	Apr, general cloning vector	Stratagene
pAL01	Apr, pUC19 carrying a 4,137-bp	(6)
	lactococcal chromosomal DNA
	insert with acmA gene
pDEL1	Apr, pBluescript SK+ with 785-bp	This work
	SacI-EcoRI fragment of acmA
	obtained by PCR with primers ALA-4
	and REPDEL-1
pDEL2	Apr, pBluescript SK+ with 554-bp	This work
	SacI-EcoRI fragment of acmA
	obtained by PCR with primers ALA-4
	and REPDEL-2
pDEL3	Apr, pBluescript SK+ with 348-bp	This work
	SacI-EcoRI fragment of acmA
	obtained by PCR with primers ALA-4
	and REPDEL-3
pGKAL1	Emr, Cmr, pGK13 containing acmA	(5)
	under control of its own promoter
	on a 1,942-bp SspI-BamHI insert
pGKAL3	Emr, Cmr, pGKAL1 derivative	This work
	expressing A2
pGKAL4	Emr, Cmr, pGKAL1 derivative	This work
	expressing A1
pGKAL5	Emr, Cmr, pGKAL1 derivative	This work
	expressing A0
pGKAL6	Emr, Cmr, pGKAL1 derivative	This work
	expressing A1.5
pGKAL7	Emr, Cmr, pGKAL1 derivative	This work
	expressing A4
pETAcmA	Apr, pET32A expressing active	This work
	site domain of AcmA from residues
	58 to 218 fused to thioredoxin
pGBL1	Emr, pWV01 derivative expressing	(21)
	E. coli TEM-β-lactamase fused
	to export element BL1 of L. lactis
pGAL9	Emr, pWV01 derivative expressing	(21)
	B. licheniformis α-amylase fused
	to export element AL9 of L. lactis
pUKAL1	Kmr, pUK21 with ±1,050-bp	This work
	ClaI-HindIII fragment of pGAL9
pUKAL2	Kmr, pUKAL1 in which the ±650-bp	This work
	SalI-EcoRV fragment is replaced
	by the 440-bp SalI-EcoRV
	fragment of the PCR fragment
	obtained with primers ALFA-A and -B
pUKALR	Kmr, pUKAL2 with 1,104-bp	This work
	PvuII-XbaI fragment of pAL01
	in EcoRV and XbaI sites
pUKblac	Kmr, pUK21 with 311-bp PstI-NdeI	This work
	PCR fragment obtained with
	primers BETA-1 and -2
pUKblacR	Kmr, pUKblac carrying 1,104-bp	This work
	PvuII-XbaI fragment of pAL01
	in NdeI and XbaI sites
pGBLR	Emr, pGBL1 expressing the	This work
	β-lactamase/AcmA fusion protein
pGALR	Emr, pGAL9 expressing the	This work
	α-amylase/AcmA fusion protein

[0085]

TABLE 2
Oligonucleotides used in this studya)
Name	Nucleotide sequence (5′ → 3′)	R/E site
REPDEL-1	CGCGAATTCAGATTATGAAACAATAAG	(SEQ ID NO:1)	EcoRI
REPDEL-2	CGCGAATTCTTATGTCAGTACAAGTTTTTG	(SEQ ID NO:2)	EcoRI
REPDEL-3	CGCGAATTCCTTATGAAGAAGCTCCGTC	(SEQ ID NO:3)	EcoRI
ALA-4	CTTCAACAGACAAGTCC	(SEQ ID NO:4)
REP-4A	AGCAATACTAGTTTTATA	(SEQ ID NO:5)	SpeI
REP-4B	CGCGAATTCGCTAGCGTCGCTCAAATTCAAAGTGCG	(SEQ ID NO:6)	NheI
ACMHIS	AGGAGATCTGCGACTAACTCATCAGAGG	(SEQ ID NO:7)	BglII
BETA-1	GGATCATGTAACTCGCC	(SEQ ID NO:8)
BETA-2	GGAATTCCATATGCTTAATCAGTGAGG	(SEQ ID NO:9)	NdeI
ALFA-A	GCATCCGTTGAAAGCGG	(SEQ ID NO:10)
ALFA-B	GAATTCGATATCTTTGAACATAAATTG	(SEQ ID NO:11)	EcoRV
ALA-14	GATAAATGATTCCAAGC	(SEQ ID NO:12)
ALA-22	CTCAAATTCAAAGTGCG	(SEQ ID NO:13)
a)The indicated restriction enzyme (R/E) sites are underlined while stopcodons are shown in italic.

[0086]

TABLE 3
Properties of L. lactis expressing AcmA derivatives.
								AcmA
	Strain	AcmA	% Reduction	PepX	Chain		Sedimen-	activityi)	Cell
Numbera)	(plasmid)b)	variantc)	in OD600d)	activitye)	lengthf)	Halog)	tationh)	sup	ce	bindingj)
1	MG pGK13	A3	32.6	16.9	A	3.1	−	+	+	+
2	Δ1 pGK13	—	15.2	0.3	C	0	+	−	−	−
3	Δ1 pGKAL1	A3	36.7	19.8	A	5.0	−	+	+	+
4	Δ1 pGKAL3	A2	29.3	13.3	A	4.6	−	+	+	+
5	Δ1 pGKAL4	A1	18.8	0.4	B	3.9	+	+	+	+
6	Δ1 pGKAL5	A0	15.6	0.3	C	0	+	+	−	−
7	Δ1 pGKAL6	A1.5	18.6	1.6	B	2.2	±	+	+	+
8	Δ1 pGKAL7	A4	21.1	4.9	A	4.0	−	+	+	+
a)The number corresponds to the AcmA derivative produced, as schematized in FIG. 1.
b)MG: L. lactis MG1363, Δ1: L. lactis MG1363acmAΔ1.
c)—: no AcmA produced; Ax: AcmA with x repeats.
d)The OD600 reduction was calculated using the following formula: [(ODmax. − OD60 hours)/ODmax.] * 100%.
e)Activity is in arbitrary units measured as the increase of absorption at 405 nm in time.
f)End exponential phase ½M17 cultures were subjected to light microscopic analysis.
A: mainly single cells and some chains up to 5 cells
B: some single cells but mainly chains longer than 5 cells
C: no single cells, only very long chains
g)The sizes of the halo's were measured in millimeters from the border of the colony after 45 h of incubation at 30° C.
h)Analyzed by visual inspection of standing ½M17 cultures after overnight growth in test tubes.
i)Judged from zymograms of samples from end-exponential phase ½M17 cultures; sup: supernatant fraction, ce: cell-extract.
j)Binding of AcmA derivatives in supernatants of end-exponential phase ½M17 cultures to end-exponential phase cells of L. lactis MG1363acmAΔ1 after 20 min of incubation at 30° C. (see text for details).

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