# Patent

## Title
Bioinformatic method for identifying surface-anchored proteins from gram-positive bacteria and proteins obtained thereby

## Abstract

A bioinformatic method is provided for identifying and isolating proteins with MSCRAMM®—like characteristics from Gram positive bacteria, such as Enterococcus, Staphylococcus, Streptococcus and Bacillus bacteria, which can then be utilized in methods to prevent and treat infections caused by Gram-positive bacteria. The method involves identifying from sequence information those proteins with a putative C-terminal LPXTG (SEQ ID NO:1) cell wall sorting signal and other structural similarities to MSCRAMM® proteins having the LPXTG-anchored cell wall proteins. The MSCRAMM® proteins and immunogenic regions therein that are identified and isolated using the present invention may be used to generate antibodies useful in the diagnosis, treatment or prevention of Gram positive bacterial infections.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
The present application claims the benefit of U.S. provisional application Ser. No. 60/410,303, filed Sep. 13, 2002.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This Invention was made with Government support under Contracts 7R01-AR44415-04 and 2R01-A120624-17 awarded by NIH. The government has certain rights in this invention.


FIELD OF THE INVENTION
The present invention relates to the fields of microbiology, molecular biology, and immunology and more particularly relates to surface-anchored proteins known as MSCRAMM®s, and to a bioinformatic method of identifying putative MSCRAMM® proteins, i.e., proteins that can bind to extracellular matrix molecules, from Gram positive bacteria having a recognizable cell wall sorting signal and the genes encoding those proteins through detecting structural features from potential proteins including immunoglobulin(Ig)—like fold regions. In addition, the invention relates to antibodies which recognize such proteins, including polyclonal and monoclonal antibodies as well as host cells transformed with nucleic acids encoding monoclonal antibodies, and the use of such antibodies in the diagnosis, treatment or prevention of Gram positive bacterial infections in humans and animals.
BACKGROUND OF THE INVENTION
There are numerous Gram positive bacteria which have been of interest in the fields of medicine and epidemiology because of their potential to cause a myriad of infectious diseases in humans and animals. One such Gram positive bacterium, Enterococcus faecalis, belongs to the commensal flora in mammalian intestines. It has also long been known as a major causative agent of bacterial endocarditis (Murray, 1990). During the last decades, E. faecalis has increasingly emerged as an opportunistic nosocomial pathogen, typically causing infections in hospitalized patients receiving antibiotic therapy. Clinical strains of this bacterium frequently harbor a multitude of acquired and intrinsically evolved resistance mechanisms toward the most commonly used antibiotics, which has complicated the treatment of enterococcal infections (Murray, 1990, 1999) (Tailor, 1993) (Huycke, 1998). Many of the antibiotic resistance genes are located in mobile genetic elements, e.g., small plasmids and transposons (Paulsen, 2003) This has raised fears for genetic transfer of resistance determinants from this organism to other bacterial species, e.g., the recently documented transfer of vancomycin resistance to Staphylococcus aureus (CDC, 2002). Still other Gram positive bacteria are known which commonly cause infections which are hard to control, including other bacteria from the Enterococcus genus, including Enterococcus faecium, as well as bacteria from species Streptococcus, such as Streptococcus mutans and pneumoniae, Staphylococcus, such as Staphylococcus aureus and epidermidis, and Bacillus, such as Bacillus anthracis. 
The ability to adhere to mammalian tissue is a critical step in the colonization and onset of microbial infections. However, in light of the many unknown factors regarding microbial adherence, it remains a challenge to study and utilize information obtained regarding relatively little known adhesion mechanisms of Gram positive bacteria so as to provide a means for developing alternative antibacterial therapies. One such inroad into developing such therapies is the presence of the human extracellular matrix underneath epithelial and endothelial cells which is a complex, dynamic and multifunctional structure consisting mainly of collagens and other glycoproteins. As one of the outermost layers to external environment, it is a major adhesion target and entry point for pathogenic bacteria (Foster and Hook, 1998) (Westerlund and Korhonen, 1993). Numerous bacterial adhesins that specifically bind to ECM components have been characterized at the molecular level. A group of related cell surface proteins from Gram-positive bacteria, collectively designated MSCRAMM® proteins (microbial surface components recognizing adhesive matrix molecules) bind to major components of the ECM, such as collagens, fibronectin, laminin, fibrinogen, keratin, vitronectin and bone sialoprotein (Patti, 1994) (Foster and Hook, 1998) (Tung, 2000) (O'Brien, 2002). MSCRAMM® proteins are mosaic proteins that typically consist of an N-terminal signal sequence for Sec-dependent transport across the cytoplasmic membrane, followed by an N-terminal A domain which exhibits the binding activity in most cases and repetitive B domains that confer fibronectin binding in a group of fibronectin binding MSCRAMM® protein (Joh et al., 1994). Covalent attachment to the bacterial cell wall is mediated through a C-terminally located LPxTG motif preceded by a cell wall spanning domain and followed by a hydrophobic trans-membrane region and, finally, a cytosolic tail composed of a short sequence of positively charged amino acid residues (Schneewind et al., 1995) (Mazmanian et al., 2001).
In any event, it remains a distinct problem in the field of infectious diseases to develop new means of countering a wide range of bacterial infections in an efficient and effective manner without the potential of increasing the development of antibiotic-resistant bacterial strains. Moreover, in light of the potential problems that are caused by bacterial strains in general and antibiotic-resistant strains in general, particularly in hospitalized patients, it is increasingly important to develop methods to counteract such infections without utilizing antibiotics and without increasing the likelihood that antibiotic-resistant strains will develop. It is thus highly desirable to develop new means for identifying, treating and preventing infectious diseases caused by Gram positive bacteria, and to develop means for identifying and isolating new MSCRAMM® proteins from such bacteria which will allow the generation of antibodies thereto which will lead to new methods for treating and preventing the spread of infections from Gram-positive bacteria.
SUMMARY OF THE INVENTION
Accordingly, it is an object of the present invention to provide a bioinformatic method of identifying and isolating MSCRAMM® proteins from Gram-positive bacteria which can be utilized in methods of treating or preventing infectious diseases arising from Gram-positive bacteria.
It is another object of the present invention to identify and isolate proteins obtained using the bioinformatic method of the present invention, and to identify therein effective antigenic domains such as the A domain, and to utilize these antigenic domains in methods of treating or preventing infectious diseases arising from Gram-positive bacteria.
It is further an object of the present invention to utilize the proteins and antigenic domains isolated and identified using the bioinformatic method of the present invention to generate antibodies which can recognize these proteins and antigenic regions which can thus be useful in diagnosing, treating or preventing diseases and infections caused by Gram positive bacteria
It is still further an object of the present invention to provide vaccines, kits and other therapeutic methods which utilize the proteins and antigenic domains identified and isolated using the bioinformatic method of the present invention which can be used as an alternative to conventional antibiotic therapy and can thus provide safe and effective modes of treating or preventing infections caused by Gram-positive bacteria.
These and other objects are provided by virtue of the present invention which utilizes a bioinformatic approach to identify proteins with MSCRAMM®—like characteristics among Gram positive bacteria, such as bacteria from Enterococcus, Staphylococcus, Streptococcus and Bacillus, among many others, which can then be utilized in methods to prevent and treat infections caused by Gram-positive bacteria. In particular, the method involves looking for proteins with a putative C-terminal LPXTG (SEQ ID NO:1) cell wall sorting signal and structural similarities to MSCRAMM® proteins having the LPXTG-anchored cell wall proteins. In particular, the present invention provides a method for identifying and isolating MSCRAMM® proteins, i.e., proteins that can bind to extracellular matrix molecules, such as by locating regions that adopt an immunoglobulin—like fold, and includes the recombinant production of these proteins from nucleic acids identified in the present process which code for those proteins. These Ig fold-containing regions consist of several consecutive and overlapping matches to solved crystal structures ( ̃150-500 aa) of the immunoglobulin superfamily (IgSF), which consist of one to four domains of equal size and Ig-type fold. The homologous Ig-fold regions are indicative of a “beads-in-a-string” arrangement of consecutive modules such like the ones found in fibronectin and other IgSF proteins (Leahy, 1996)(Sharma, 1999)(Hamburger, 1999)(Luo, 2000). For example, a tandem repeat of Ig folded subdomains (N2 and N3) is found in the crystal structure of the fibrinogen-binding domain of ClfA. The full-length A domains of ClfA and the similarly structured ClfB consist of an additional N-terminal subdomain, N1 (Deivanayagam, 2002)(Perkins, 2001). Based on sequence and secondary structure similarities, an analogous subdomain organization is also expected in other MSCRAMM® proteins including FnbpA, FnbpB, Ace and the Sdr proteins. The solved crystal structure of CNA minimum collagen-binding domain is made of a single Ig-type subdomain (N2) (Symersky, 1997) and the C-terminal repeat domains B1 and B2 each consist of a tandem repeat of Ig-folded subdomains (Deivanayagam, 2000). A similar modular structure is expected in the B3 and B4 repeats.
In accordance with the invention, novel MSCRAMM®—like protein surface-anchored proteins which can bind to major extracellular matrix proteins are obtained from Gram-positive bacteria such as those from the genera Enterococcus, Streptococcus, Staphylococcus and Bacillus, and such proteins are characterized in that they are (i) structurally homologous to the solved Ig-folded crystal structures of ClfA and CNA as well as to the predicted tertiary structures of other MSCRAMM® proteins, (ii) share a similar β-sheet rich secondary structure as is found in Ig-folded proteins and (iii) have a similar organization with a secretion signal, a non-repeated domain followed by repeats as well as a C-terminal cell wall anchor domain. Moreover, the binding of proteins identified by the present method has confirmed that they target and bind to various extracellular matrix (ECM) molecules including proteins and other components. For example, three of the isolated proteins bind to major ECM proteins; two to fibrinogen and at least one to collagen and laminin. The proteins of the present invention have also been shown to be present in most isolates and are expressed in vivo during infection.
Thus, in accordance with the present invention, a method is provided for identifying and isolating a module structure of multiple Ig-folded units which appears to be a general characteristic in the MSCRAMM® protein family. The length of the N-subdomains of MSCRAMM® proteins is typically  ̃150 aa, and the proteins identified by the present invention including those set forth below may accommodate more than three Ig-folded subdomains in their A domains.
These embodiments and other alternatives and modifications within the spirit and scope of the disclosed invention will become readily apparent to those skilled in the art from reading the present specification and/or the references cited herein, all of which are incorporated by reference.



BRIEF DESCRIPTION OF THE DRAWING FIGURES
FIG. 1 is a schematic representation of MSCRAMM® proteins identified in accordance with the present invention illustrating the different regions of the proteins and their immunoglobulin—like fold regions
FIG. 2 illustrates a Coomassie stained SDS-PAGE of the E coli-expressed and purified A domains of the LPXTG-containing proteins of the present invention.



DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
In accordance with the present invention, there is provided a bioinformatic method for identifying and isolating proteins from Gram-positive bacteria, for example bacteria from genera such as Enterococcus, Staphylococcus, Streptococcus and Bacillus, in particular proteins which have MSCRAMM®—like characteristics, and utilizing the identified and isolated proteins to generate antibodies and diagnose, treat or prevent infections caused by Gram-positive bacteria. In general, the method involves looking for proteins with a putative C-terminal LPXTG (SEQ ID NO:1) cell wall sorting signal and/or other structural similarities to MSCRAMM® proteins (Microbial Surface Components Recognizing Adhesive Matrix Molecules) having LPXTG-containing cell wall-anchored proteins. In the preferred embodiment, the present invention provides a method for identifying and isolating MSCRAMM® proteins, i.e., surface proteins that bind to extracellular matrix molecules, such as proteins, carbohydrates and other components, of host cells, wherein those located proteins contain regions that adopt an immunoglobulin—like fold. These Ig fold-containing regions consist of several consecutive and overlapping matches to solved crystal structures ( ̃150-500 aa) of the immunoglobulin superfamily (IgSF), which consist of one to four domains of equal size and Ig-type fold. The homologous Ig-fold regions are indicative of a “beads-in-a-string” arrangement of consecutive modules such like the ones found in fibronectin and other IgSF proteins (Leahy, 1996)(Sharma, 1 999)(Hamburger, 1999)(Luo, 2000). For example, a tandem repeat of Ig folded subdomains (N2 and N3) is found in the crystal structure of the fibrinogen-binding domain of ClfA. The full-length A domains of ClfA and the similarly structured ClfB consist of an additional N-terminal subdomain, N1 (Deivanayagam, 2002)(Perkins, 2001). Based on sequence and secondary structure similarities, an analogous subdomain organization is also expected in other MSCRAMM® proteins including FnbpA, FnbpB, Ace and the Sdr proteins. The solved crystal structure of CNA minimum collagen-binding domain is made of a single Ig-type subdomain (N2) (Symersky, 1997) and the C-terminal repeat domains B1 and B2 each consist of a tandem repeat of Ig-folded subdomains (Deivanayagam, 2000). A similar modular structure is expected in the B3 and B4 repeats.
In accordance with the invention novel MSCRAMM®—like protein surface-anchored proteins are obtained from Gram-positive bacteria such as those from the genera Enterococcus, Streptococcus, Staphylococcus and Bacillus, and such proteins are characterized in that they are (i) structurally homologous to the solved Ig-folded crystal structures of ClfA and CNA as well as to the predicted tertiary structures of other MSCRAMM® proteins, (ii) share a similar β-sheet rich secondary structure as is found in Ig-folded proteins and (iii) have a similar organization with a secretion signal, a non-repeated domain followed by repeats as well as a C-terminal cell wall anchor domain. Moreover, the binding of proteins identified by the present method has confirmed that they target and bind to various extracellular matrix molecules. For example, three of the isolated proteins bind to major ECM proteins; two to fibrinogen and at least one to collagen and laminin. The proteins of the present invention have also been shown to be present in most isolates and are expressed in vivo during infection.
In accordance with the present invention, a method is provided for identifying and isolating a module structure of multiple Ig-folded units which have the general characteristics of the MSCRAMM® protein family. The length of the N-subdomains of MSCRAMM® proteins is typically  ̃150 aa, and the proteins identified by the present invention including those set forth below may accommodate more than three Ig-folded subdomains in their A domains. The isolation and use of the MSCRAMM® proteins of the present invention or their A domains in the generation of antibodies that can bind thereto or in methods of diagnosing, treating or preventing disease will be similar to that as described with other MSCRAMM® proteins such as in U.S. Pat. Nos. 6,288,214; 6,177,084; 6,008,241; 6,086,895; 5,980,908; 5,866,541; 5,851,794; 5,840,846; 5,789,549; 5,770,702, 5,652,217; 5,648,240; 5,571,514; 5,440,014; 5,416,021 and 5,320,951; and WO 00/68242; all of said references incorporated herein by reference.
In accordance with the present invention, a series of steps is undertaken in order to identify and isolate the characteristic module structure of one or more surface-anchored MSCRAMM® protein family of Gram positive bacteria, including the step of locating immunoglobulin—like (or Ig—like) folds in the putative LPXTG-containing proteins. This method can be used with any presently known database containing sequence information from Gram positive bacterial species, e.g., amino acid and/or nucleic acid sequences, and involves the steps of locating proteins with the LPXTG (SEQ ID NO:1) motif, and then reviewing and analyzing the sequence information so as to screen for proteins having particular structural similarities to MSCRAMM® as set forth below.
In the general process of the invention, the first part of the process is to search a database containing sequence information on one or more Gram positive bacteria so as to locate those proteins which contain the LPXTG (SEQ ID NO:1) motif contained in cell wall anchored proteins in annotated genomes of Gram-positive bacteria. This is done by initially obtaining the entire genome of amino acids sequences from one or more Gram positive bacteria of interest, such as from any of a number of web sites of sequencing centers, e.g., TIGR, NCBI, etc. In the preferred method, these sequences can be downloaded and stored in electronic memory before carrying out the identifying steps, such as in a local Silicon Graphics machine (SGI) or other suitable computer system. In the preferred method, this stored information is used to prepare a local searchable database, such as by using the program form “atdb” obtained from NCBI, and such a searchable database is installed locally on the SGI.
The LPXTG-motif is identified from the stored sequence information by any of a number of suitable programs. For example, these LPXTG-motif containing proteins can be identified using PHI-blast, which is obtained from NCBI and once again can be installed and stored locally on the SGI or other suitable computer system. The PHI-blast search uses a degenerate LPXTG pattern L-P-X-[TSA]-[GANS](SEQ ID NO:25), X being any amino acid. The exact templates for PHI-blast can vary depending on the particular organism, but in any case, the present system includes methods of identifying the LPXTG motif. For each organism, it is preferred to use at least two known cell wall anchored proteins of S. aureus with no sequence homology as well as known cell wall anchored proteins from the target organism if available.
Once LPXTG-containing proteins are identified obtained using a suitable system such as PHI-blast, these proteins are further analyzed so as to select for those that contain typical features of LPXTG-motif containing cell wall anchored proteins which have the properties of MSCRAMM®S. In the preferred process, these features will generally include a signal peptide at the N-terminus, the LPXTG-motif being close to the C-terminus, followed by a hydrophobic transmembrane segment, and several positively charged residues at the C-terminus. These are done as described below:
The signal peptides may be identified using any suitable identification method such as that method described in “Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites”. Henrik Nielsen, Jacob Engelbrecht, Søren Brunak and Gunnar von Heijne, Protein Engineering 10, 1-6 (1997), incorporated herein by reference. In the present process, a preferred system is to use the SignalP prediction server at cbs.dtu.dk/services/SipnalP, but other similar methods for identifying the signal peptide may also be used. Location of LPXTG-motif and the determination of positively charged amino acids residues at the C terminus are accomplished using visual examination of the sequence, although databases may also be used to determine the presence of these features.
In the preferred embodiment, the hydrophobic transmembrane segment after the LPXTG-motif may also be located using a conventional program which can predict the presence of such regions. An example of one such system is the TMHMM server available on the Internet at cbs.dtu.dk/services/TMHMM-2.0/ which can be used for the prediction of transmembrane segments. However, a number of other suitable prediction servers are available either on the Internet or in stored computer programs, including the TMpred available at ch.embnet.org/software/TMPRED form.html the DAS system available at www.sbc.su.se/ ̃miklos/DAS/, and the HMMTOP at www.enzim.hu/hmmtop.
By following the procedures set forth above, putative LPXTG-containing sequences that contain the above features can be selected as highly likely to be MSCRAMM® proteins, i.e., to have the ability to bind extracellular matrix components. Following these initial steps, it is contemplated that the LPXTG-containing proteins identified in this matter will turn out be MSCRAMM® proteins at least about 90% of the time, as confirmed by expressing the putative protein or its A domain and determining if that protein or it's a domain binds to extracellular matrix components. This can be done by simple binding assays which are routine in the art and which would be well within the abilities of one skilled in the art.
Additionally, the LPXTG-containing sequences as initially located, or as further selected using the signal peptide/C terminal/transmembrane identifying characteristics as described above, can be further analyzed as indicated below to confirm the presence of immunoglobulin—like folds characteristic of MSCRAMM® proteins from Gram positive bacteria.
Similarly, in such a method, LPXTG-containing cell wall proteins may also be located using an annotated genomic nucleotide database such as the one located at the TIGR website (comprehensive microbial resource) at tigr.org/tigrscripts/CMR2/CMRHomePage.spl http://www.tigr.org/tigrscripts/CMR2/CMRHomePage.spl. With these databases, the term “LPXTG” or “cell wall” may be used to search for such proteins that are annotated as cell wall anchored proteins in the genome of interest.
Finally, LPXTG-motif containing cell wall anchored proteins may also be identified in un-annotated nucleotide genomes of Gram-positive bacteria. In this case, genome sequences are obtained from the web sites of sequencing centers, and the sequences may be stored as appropriate in computer memory such as a local Silicon Graphics machine (SGI). Gene prediction may be carried out using the program such as Glimmer 2.0 from TIGR, and this can be facilitated by UNIX C shell scripts which may be modified as desired to suit particular organisms or features. In the preferred process, the predicted genes are translated into amino acid sequences using a suitable translation program, preferably one that is capable of translating large batches of sequences. Finally, the translated amino acid sequences are formatted into a searchable database locally as described above, and subject to further analysis as described below.
In the preferred process of the present invention, steps are carried out by which the Immunoglobulin—like (Ig—like) fold in putative LPXTG-motif containing cell wall anchored proteins can be predicted and identified. In accordance with the invention, the amino acid sequences of putative LPXTG-motif containing cell wall anchored proteins are then analyzed to determine the presence of Ig—like folds which are characteristic of MSCRAMM® proteins. This can be done in a number of ways, such as by processing the putative MSCRAMM® using fold-recognition software, such as available using the web server 3D-PSSM available at sbg.bio.ic.ac.uk/ ̃3dpssm/ Additional methods of fold prediction are discussed in Kelley LA, MacCallum RM & Steinberg MJE. Enhanced Genome Annotation using Structural Profiles in the Program 3D-PSSM. J MoI Biol. 2000 June 2;299(2):499-520, incorporated herein by reference. Using this method, the output of 3D-PSSM gives a probability E value indicating the likelihood of the submitted sequence adopting a similar 3D structure as the known and published MSCRAMM®s. In accordance with the invention, proteins that have an E value <0.25 to a published Ig—like fold structure, are considered to contain the predicted Ig—like folds, and such proteins are identified as useful MSCRAMM® proteins in accordance with the invention, i.e., proteins that recognize adhesin molecules on the extracellular matrix of host cells.
The present invention has thus been carried out so as to identify and produce proteins and A domains therefrom which have MSCRAMM®—like characteristics from such Gram positive bacteria, such as Enterococcus, Streptococcus, Staphylococcus and Bacillus. In the preferred process, proteins identified as set forth above or their antigenic A domains may be expressed, purified and characterized as set forth herein.
Accordingly, in accordance with the present invention, a bioinformatic approach was used to identify proteins with MSCRAMM®—like characteristics among Gram positive bacteria, and those predicted proteins have been shown to have MSCRAMM—like characteristics. In one such case using Enterococcus faecalis, forty-two proteins with a putative C-terminal LPxTG cell wall sorting signal were identified in the E. faecalis genome. In accordance with the present method, these proteins were analyzed to determine the presence of Ig—like folds in the manner set forth above. Based on the present method, nine proteins were found to contain regions that adopt an immunoglobulin—like fold. The Ig fold-containing regions for these nine proteins are shown in FIG. 1 and consist of several consecutive and overlapping matches to solved crystal structures ( ̃150-500 aa) of the immunoglobulin superfamily (IgSF), which consist of one to four domains of equal size and Ig-type fold. The homologous Ig-fold regions cover most of the enterococcal proteins and may indicate a similar “beads-in-a-string” arrangement of consecutive modules that are found in fibronectin and other IgSF proteins.
Further expression, purification and analysis of the A domains of these proteins was carried out. As shown in FIG. 2, the A regions of eight proteins expressed as N-terminal His6-tag fusion proteins migrated as expected in SDS-PAGE gels, while EF1091 showed a band approx. 160 kDa in size; a larger-size molecule than the expected 113 kDa. Some degradation was observed in proteins EF1091, EF1824, EF0089 and EF3023, possibly due to their relatively large sizes. They were nevertheless estimated to be >95% pure. The putative glucosyl hydrolase domain of EF1824 (amino acids 42-819), which was cloned and expressed separately from the rest of the protein, (FIG. 1) was found in the insoluble fraction of E. coli cytoplasm. Hence, purification by metal affinity chromatography under native, non-denaturing conditions employed for the other expressed proteins was not feasible. The purified proteins were further characterized with Maldi-TOF mass spectrometry. All nine proteins, including EF1091 with aberrant migration in SDS-PAGE, gave peaks that were in good agreement with the molecular weights calculated from amino acid sequences (Table 1), and thus indicated that full-size proteins had been produced with no post-translational processing.
Secondary structure predictions and CD-measurements (Table 2) support finding of Ig-folded module-structures in the enterococcal proteins. Both methods show a similar high proportion of β-sheet ( ̃50%) and coil and a minor quantity of α-helix, an identical situation as seen in MSCRAMM® proteins and in IgSF in general. The higher amount of α-helix in EF1824 and EF3023 probably reflects their relatively short predicted regions with Ig-folds and suggests the remainder of the proteins is structurally more distant to MSCRAMM® proteins.







TABLE 1







Molecular size analysis










Molecular mass (Da)













Sequence
Mass



Protein
prediction
spectrometry















EF1091
113,021
113,025



EF1824
111,893
111,901



EF0089
122,853
122,857



EF3023
113,338
113,323



EF1092
47,291
47,295



EF2224
82,194
82,199



EF1269
64,776
64,776



EF1099
39,281
39,293



EF1093
62,363
62,366

















TABLE 2







Summary of secondary structure components












Protein
α-Helix
β-Sheet
Other











Sequence prediction












EF1091
0.10 ± 0.05
0.33 ± 0.08
0.53 ± 0.06



EF1824
0.45 ± 0.04
0.16 ± 0.04
0.39 ± 0.08



EF0089
0.07 ± 0.07
0.44 ± 0.14
0.49 ± 0.08



EF3023
0.24 ± 0.09
0.29 ± 0.10
0.47 ± 0.12



EF1092
0.15 ± 0.05
0.36 ± 0.06
0.49 ± 0.10



EF2224
0.15 ± 0.10
0.32 ± 0.05
0.54 ± 0.10



EF1269
0.09 ± 0.10
0.42 ± 0.12
0.49 ± 0.10



EF1099
0.04 ± 0.07
0.47 ± 0.07
0.49 ± 0.07



EF1093
0.09 ± 0.06
0.41 ± 0.11
0.51 ± 0.11







CD measurement












EF1091
0.14 ± 0.05
0.41 ± 0.11
0.45 ± 0.10



EF1824
0.29 ± 0.04
0.29 ± 0.17
0.44 ± 0.17



EF0089
0.08 ± 0.04
0.49 ± 0.13
0.43 ± 0.12



EF3023
0.33 ± 0.05
0.16 ± 0.05
0.51 ± 0.03



EF1092
0.05 ± 0.04
0.50 ± 0.12
0.45 ± 0.14



EF2224
0.16 ± 0.03
0.36 ± 0.10
0.48 ± 0.09



EF1269
0.03 ± 0.04
0.55 ± 0.14
0.42 ± 0.12



EF1099
0.07 ± 0.03
0.49 ± 0.13
0.44 ± 0.14



EF1093
0.06 ± 0.05
0.57 ± 0.18
0.37 ± 0.17










In addition to EF1099 (Ace), the primary sequence of EF1269 is clearly related to the MSCRAMM® protein family. Similarly to Ace, it has homologous N2 and N3 subdomains including the conserved TYTDYVD-motif and a connecting tyrosine residue between the two subdomains. The absence of N1 further resembles Ace. However, the rest of their sequences share little homology. Although the A domain of EF1269 is made of similar N2 and N3 subdomains as the fibrinogen-binding ClfA, ClfB, SdrG, and to a lesser extent, FnbpA and FnbpB, it failed to bind fibrinogen. In this respect, EF1269 resembles SdrD and SdrE, which contain N2 and N3 subdomains, but for which the ligand is yet to be found. This is strengthened by our finding that the highest similarity of the EF1269 N2 and N3 domains is to the corresponding region in SdrE (identity 26%). Further, two putative repeats (95 and 109 aa) with lower conservation (identity 20%), which make up the rest of the C-terminal EF1269 sequence, show relatedness to the B repeats of SdrE (25% identity over 375 to 531 aa of EF1269). Proteins EF1091, EF0089, EF1092, EF2224 and EF1093 are not simply orthologs of previously described MSCRAMM® proteins, since they lack high sequence identity to streptococcal and staphylococcal adhesins. Yet, they share similar structural organization and an abundance of β-sheet rich secondary structures with similar predicted folding as MSCRAMM® proteins. The two remaining proteins, EF1824 and EF3023, have large regions related to known enzymes, glucosyl hydrolases and hyaluronan lyases, respectively, which sets these regions apart from MSCRAMM® proteins. Hyaluronidase activity could be significant for bacterial entry and spreading in hyaluronan-containing tissues during infection and/or potentially contribute to bacterial nutrition during commensal life in the human intestine. The large putative catalytic domains of EF1824 and EF3023 agree well with the above-discussed structural unrelatedness in these regions to MSCRAMM® proteins.
When screening binding to major ECM proteins, we found ligands for five of the MSCRAMM® proteins EF0089, EF1091, EF1092, EF1093, and EF2224. The presence of more than one fibrinogen-binding MSCRAMM® proteins in E. faecalis is consistent to findings in the related S. aureus in which four fibrinogen-binding MSCRAMM® proteins, ClfA, ClfB, FnbpA and FnbpB, have been described (McDevitt et al., 1994) (Ni Eidhin et al., 1998) (Wann et al., 2000) (Davis et al., 2001; Hartford et al., 2001). EF0089 and EF2224 have strong structural resemblance to MSCRAMM® proteins throughout their lengths: similar primary organization and homologous β-sheet rich secondary structure expected to form modular Ig-folded subdomains. Relatively low sequence identity to known fibrinogen binding adhesins may mean novel adaptations for ligand binding. Our initial results suggest EF2224 binds to the α- and β-chains of fibrinogen and thus resembles ClfB (Ni Eidhin et al., 1998). Mammalian tissue surfaces express a multitude of possible ligands for bacterial adherence. Here, we assessed binding to type I, III and IV collagens, laminin, fibronectin, fibrinogen and vitronectin.
In accordance with the invention, a PCR process may be used to amplify A domains from proteins identified and isolated using the present invention. Using PCR oligonucleotides such as those in Table 3, below, the A domains from EF0089, EF1091, EF1092, EF1093, EF1099, EF1269, EF1824, EF2224, and EF3023 were amplified from E. faecalis V583 or E. faecalis EF1 (EF1099) genomic DNA and subcloned into the E. coli expression vector PQE-30 (Qiagen). One liter culture of E. coli M15(pREP4) cultures harboring appropriate pQE-30 based constructs were grown to OD600=0.6 with an initial 2% inoculation from overnight cultures. After 2-3 h induction with 0.4 mM isopropyl-beta-d-thiogalactoside (IPTG), cells were collected with centrifugation, resuspended in 10 mM Tris-Cl, 100 mM NaCl, pH 7.9 and stored at −80 C.
To lyse the cells and release the expressed protein, cells were passed twice through French Press with a gauge pressure setting at 1200 PSI to give an estimated internal cell pressure of 20,000 PSI. The lysate was centrifuged at RCFmax of 165,000×g and the supernatant was filtered through a 0.45 □m filter. The volume was adjusted to 15 ml with 10 mM Tris-Cl, 100 mM NaCl, pH 7.9 and 0.2 M imidazole in the same buffer was added to increase the imidazole concentration to 6.5 mM in order to minimize non-specific binding. The sample was loaded to a nickel affinity chromatography column (HiTrap chelating, Pharmacia) connected to an FPLC system (Pharmacia) and previously equilibrated with 10 mM Tris-Cl, 100 mM NaCl, pH 7.9. Bound protein was eluted with a linear gradient of 0-100 mM imidazole in 10 mM Tris-Cl, 100 mM NaCl, pH 7.9 over 100-200 ml. Protein-containing fractions were analyzed in SDS-PAGE (FIG. 2) and dialyzed against 25 mM Tris-Cl, 1 mM EDTA, pH 6.5-9 (depending on pI of protein purified) before applying the samples to an ion-exchange column (HiTrap Q, Pharmacia) for further purification. Bound protein was eluted with a linear gradient of 0-0.5 M NaCl in 25 mM Tris-Cl, 1 mM EDTA, pH 6.5-9 over 100 ml. Finally, protein samples were dialyzed extensively against PBS and stored at +4° C.
Alternatively EF1091, EF1092, and EF1093 were expressed in shake flasks or in bioreactors, the cells were harvested by centrifugation and the cell paste frozen at −80° C. Cells were lysed in 1×PBS (10 mL of buffer/1 g of cell paste) using 2 passes through a microfluidizer at 10,000 psi. Lysed cells were spun down at 17,000 rpm for 30 minutes to remove cell debris. Supernatant was passed over a 5-mL HiTrap Chelating (Pharmacia) column charged with 0.1M NiCl2. After loading, the column was washed with 5 column volumes of 10 mM Tris, pH 8.0, 100 mM NaCl (Buffer A). Protein was eluted using a 0-100% gradient of 10 mM Tris, pH 8.0, 100 mM NaCl, 500 mM imidazole (Buffer B). Protein containing fractions were dialyzed in 1×PBS.
The nine enterococcal genes encoding the MSCRAMM® are ubiquitous among E. faecalis strains as summarized in Table 3. Seven of the nine genes were 100% preserved in all strains. The two genes, EF1824 and EF3023, with predicted encoded protein catalytic domains and relatively low proportion of MSCRAMM®—like protein characteristics, were present in 16/30 and 23/30 strains, respectively. Nine enterococcal proteins encoded by their respective gene showed elevated titers in infected individuals suggesting expression in vivo during an E. faecalis infection. Although these proteins have a high distribution in strains, there were clear differences in induced antigenic responses; proteins EF1091, EF1092, EF1093 and EF2224 exhibited the highest titers. This may be due to different expression levels in physiological conditions or to highly immunogenic surface epitopes and, hence, a strong immune response. Interestingly, the three proteins (EF1091, EF1092 and EF1093) with the highest titers are organized as a putative operon in the E. faecalis genome. The operon is preceded by two promoter consensus regions and a ribosome binding site and thus, these proteins are likely co-transcribed. The next gene downstream, EF1094, codes for a putative LPxTG transpeptidase sortase and EF1099 (Ace) is closely linked. It remains to be seen what role this cluster of MCSRAMM®—like proteins and a putative sortase may have in the infection process.







TABLE 3







Synthetic oligonucleotides used in this study(SEQ ID NO: 26-43)













Location
Cloning



Oligonucleotide

(aa)
site
Oligonucleotide














EF1091A  
Fw
102
SphI
5′-CCGCATGCCAAGAGCAAACAGCAAAAGAAG-3′



Rev
1107
SalI
5′-CCGTCGACTTAAGTACCAGAAGTGGTGGTTTTC-3′


 


EF1824AI 
Fw
42
SphI
5′-CCGCATGCCAAGAGCAAACAGCAAAAGAAG-3′



Rev
819
SalI
5′-GGGTCGACTTATTGTTTCAAGGTTACTTCTGTC


 


EF1824AII
Fw
819
BamHI
5′-CCGGATCCGCAGCTAATAAAGAAGAATTTTTAG



Rev
1829
SalI
5′-CCGTCGACTTAAGTACCAGAAGTGGTGGTTTTC-3′


 


EF0089A  
Fw
35
SacI
5′-CCGAGCTCGAAGAGGTTAACAGCGATGG-3′



Rev
1143
PstI
5′-CCCTGCAGTTACCCACCAAATGTGATAACCC-3′


 


EF3023A  
Fw
25
BamHI
5′-CCGGATCCGAAGAAATAACTGATTTATTTTTAC-3′



Rev
1024
SacI
5′-CCGAGCTCTTATTGTTCCTGAATTAATTTTTCTAAC-3′


 


EF1092A  
Fw
27
SphI
5′-CCGCATGCTCGCAAGCAAGCGTTCAAG-3′



Rev
438
PstI
5′-CCCTGCAGTTAGAAGCCTGACTCTTTTACTTTT-3′


 


EF2224A  
Fw
30
BamHI
5′-CCGGATCCCAAGAAGTAACAAGTGATGCTG-3′



Rev
771
SacI
5′-CCGAGCTCTTAAGTTACTTGTTCGTCCGCAAT-3′


 


EF1269A  
Fw
26
BamHI
5′-CCGGATCCGAAACAGGATATGCGCAAAC-3′



Rev
596
SacI
5′-CCGAGCTCTTATTCCTTATTTACGAATCGCCTG-3′


 


EF1093A  
Fw
32
BamHI
5′-GCGGGATCCGAAGAAAATGGGGAGAGCGC-3′



Rev
590
SacI
5′-GCGGAGCTCTTAGGTACCTTTGTGTTTGTTTGG-3′





5′ overhang cloning site in each oligonucleotide sequence is marked in bold, stop codon in italic


Fw, oligonucleotide primer in forward direction;


Rev, in reverse direction






The presence of several MSCRAMM®—like proteins in E. faecalis including two that bind fibrinogen and the previously described collagen and laminin binding Ace, suggests that E. faecalis resembles S. aureus and other Gram-positive cocci by having an armory of ECM-binding adhesins. Since the introduction of antibiotic therapy, E. faecalis has shown an increasing tendency to emerge as an opportunistic pathogen capable of crossing the thin line from a harmless commensal to being able to invade host tissues and cause infections. A repertoire of adhesins may enhance its adaptability for colonizing and spreading in various human tissue types of susceptible human hosts.
Accordingly, the present invention allows for the identification and ultimate production of novel MSCRAMM®—like protein surface-anchored proteins from Gram positive bacteria which (i) are structurally homologous to the solved Ig-folded crystal structures of ClfA and CNA as well as to the predicted tertiary structures of other MSCRAMM® proteins, (ii) can share a similar β-sheet rich secondary structure as is found in Ig-folded proteins and (iii) have a similar organization with a secretion signal, a non-repeated domain followed by repeats as well as a C-terminal cell wall anchor domain. Further, these proteins may bind to major ECM proteins such as fibrinogen, collagen and laminin, and due to the similarities in proteins from different Gram positive bacterial species, these proteins may provide antibodies which are cross-reactive and can bind to similar proteins found in different Gram positive bacterial species. Such antibodies, as described further below, may thus be useful in diagnosing or fighting a variety of different infections at the same time.
In addition to proteins identified and isolated using the present method, particular, the present invention contemplates the generation of antibodies from the MSCRAMM®—like proteins obtained using the present method, or from antigenic regions such as the A domains from these proteins. By “antibody” is meant any intact antibody molecule or fragments thereof that recognize antigen (e.g. Fab or F(ab′)2 fragments) and can be of polyclonal or monoclonal type, and the antibodies in accordance with the invention will be capable of recognizing the MSCRAMM® proteins of the invention and/or the specific antigenic epitopes from said proteins including their A domains. These antibodies will thus be effective in methods of diagnosing, monitoring, treating or preventing infection from Gram positive bacteria. By “epitope” is meant any antigenic determinant responsible for immunochemical binding with an antibody molecule. Epitopes usually reside within chemically active surface groupings of protein molecules (including amino acids and often also sugar side-chains) and have specific three-dimensional structural characteristics and specific charge characteristics. With reference to the proteins of the invention, or epitopes and peptides as described herein, it is understood that such terms also include those proteins and peptides which differ from a naturally occurring or recombinant protein by the substitution, deletion and/or addition of one or more amino acids but which retains the ability to be recognized by an antibody raised against the entire protein. An example is a carrier/antigen fusion polypeptide of the whole antigen or an immunoreactive fragment thereof, where the antigen or fragment can be embedded within the carrier polypeptide or linked to the carrier polypeptide at either end.
Accordingly, in accordance with the present invention, isolated and/or purified antibodies can be generated from the Gram-positive MSCRAMM® proteins of the present invention, or from particular epitopes such as those epitopic peptide sequences from the A domains from those proteins as described herein. These antibodies may be monoclonal or polyclonal and may be generated using any suitable method to raise such antibodies such as would be well known in this art. The antibodies in accordance with the invention will be particularly useful in inhibiting the binding of Gram positive bacteria to extracellular matrix components of the host cells and in diagnosing, treating or preventing infections of Gram positive bacteria.
For example, with regard to polyclonal antibodies, these may be generated using a number of suitable methods generally involving the injection of the isolated and/or purified or recombinantly produced proteins (or their immunogenic active peptides or epitopes) into a suitable host in order to generate the polyclonal antibodies which can then be recovered from the host. For example, in accordance with the invention, an isolated and purified MSCRAMM® protein or its A domain may be injected into rabbits in order to generate polyclonal antisera recognizing this protein.
In addition, monoclonal antibodies in accordance with the invention may be generated using a suitable hybridoma as would be readily understood by those of ordinary skill in the art. In the preferred process, a protein in accordance with the invention is first identified and isolated using the bioinformatic method as described above. Next, the protein is isolated and/or purified in any of a number of suitable ways commonly known in the art, or after the protein is sequenced, the protein used in the monoclonal process may be produced by recombinant means as would be commonly used in the art and then purified for use. In one suitable purification process, the cell wall proteins of the invention are isolated and examined using polyacrylamide gel electrophoresis (PAGE) and Western-blot techniques, and other conventional techniques including those discussed herein. In one suitable process, monoclonal antibodies were generated from proteins isolated and purified as described above by mixing the protein with an adjuvant, and injecting the mixture into BALB/c mice.
Immunization protocols consisted of a first injection (using complete Freund's adjuvant), two subsequent booster injections (with incomplete Freund's adjuvant) at three-week intervals, and one final booster injection without adjuvant three days prior to fusion (all injections were subcutaneous). For hybridoma production, mice were sacrificed and their spleen removed aseptically. Antibody secreting cells isolated and mixed with myeloma cells (NS1) using drop-wise addition of polyethylene glycol. After the fusion, cells were diluted in selective medium (vitamin-supplemented DMEM/HAT) and plated at low densities in multiwell tissue culture dishes. Tissue supernatants from the resulting fusion were screened by both ELISA (using the total 2-ME extract to coat the wells of a microtiter plate) and immunoblot techniques. Cells from these positive wells were grown and single cell cloned by limiting dilution, and supernatants subjected to one more round of screening by both ELISA and immunoblot. Positive clones were identified, and monoclonal antibodies collected as hybridoma supernatants.
In accordance with the invention, antibodies are thus produced which are capable of recognizing and binding proteins obtained using the bioinformatic method of the present invention and/or its epitopes and active regions such as the A domain, and such antibodies can be utilized in many diagnostic and therapeutic applications such as the ones described in more detail below.
Vaccines, Humanized Antibodies and Adjuvants
The isolated antibodies of the present invention, or the isolated proteins or epitopes as described above, may also be utilized in the development of vaccines for active and passive immunization against bacterial infections, as described further below. In the case of active vaccines, said vaccines are prepared by providing an immunogenic amount of the proteins of the invention or their active regions or epitopes as set forth above, and the active vaccine in accordance with the invention will thus comprise an immunogenic amount of the protein or peptide and will be administered to a human or animal in need of such a vaccine. The vaccine may also comprise a suitable, pharmaceutically acceptable vehicle, excipient or carrier which will be those known and commonly used in the vaccine arts. As referred to above, an “immunogenic amount” of the antigen to be used in accordance with the invention is intended to mean a nontoxic but sufficient amount of the agent, such that an immunogenic response will be elicited in the host so that the desired prophylactic or therapeutic effect is produced. Accordingly, the exact amount of the antigen that is required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the condition being treated, the particular carrier or adjuvant being used and its mode of administration, and the like. Similarly, the “immunogenic amount” of any such antigenic vaccine composition will vary based on the particular circumstances, and an appropriate immunogenic amount may be determined in each case of application by one of ordinary skill in the art using only routine experimentation. The dose should be adjusted to suit the individual to whom the composition is administered and will vary with age, weight and metabolism of the individual.
Further, when administered as pharmaceutical composition to a patient or used to coat medical devices or polymeric biomaterials in vitro and in vivo, the antibodies of the present invention may also be useful because these antibodies may be able to interfere with the ability of Gram positive bacteria to adhere to host cells and limit the extent and spread of the infection.
In addition, the antibody may be modified as necessary so that, in certain instances, it is less immunogenic in the patient to whom it is administered. For example, if the patient is a human, the antibody may be “humanized” by transplanting the complimentarity determining regions of the hybridoma-derived antibody into a human monoclonal antibody as described, e.g., by Jones et al., Nature 321:522-525 (1986) or Tempest et al. Biotechnology 9:266-273 (1991) or “veneered” by changing the surface exposed murine framework residues in the immunoglobulin variable regions to mimic a homologous human framework counterpart as described, e.g., by Padlan, Molecular Imm. 28:489-498 (1991), these references incorporated herein by reference. Even further, under certain circumstances, it may be desirable to combine the monoclonal antibodies of the present invention with a suitable antibiotic when administered so as to further enhance the ability of the present compositions to fight or prevent infections.
In a preferred embodiment, the antibodies may also be used as a passive vaccine which will be useful in providing suitable antibodies to treat or prevent a Gram-positive bacterial infection. As would be recognized by one skilled in this art, a vaccine may be packaged for administration in a number of suitable ways, such as by parenteral (i.e., intramuscular, intradermal or subcutaneous) administration or nasopharyngeal (i.e., intranasal) administration. One such mode is where the vaccine is injected intramuscularly, e.g., into the deltoid muscle, however, the particular mode of administration will depend on the nature of the bacterial infection to be dealt with and the condition of the patient. The vaccine is preferably combined with a pharmaceutically acceptable vehicle, carrier or excipient to facilitate administration, and the carrier is usually water or a buffered saline, with or without a preservative. The vaccine may be lyophilized for resuspension at the time of administration or in solution.
The preferred dose for administration of an antibody composition in accordance with the present invention is that amount will be effective in preventing of treating a bacterial infection, and one would readily recognize that this amount will vary greatly depending on the nature of the infection and the condition of a patient. An “effective amount” of antibody or pharmaceutical agent to be used in accordance with the invention is intended to mean a nontoxic but sufficient amount of the agent, such that the desired prophylactic or therapeutic effect is produced. Accordingly, the exact amount of the antibody or a particular agent that is required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the condition being treated, the particular carrier or adjuvant being used and its mode of administration, and the like. Accordingly, the “effective amount” of any particular antibody composition will vary based on the particular circumstances, and an appropriate effective amount may be determined in each case of application by one of ordinary skill in the art using only routine experimentation. The dose should be adjusted to suit the individual to whom the composition is administered and will vary with age, weight and metabolism of the individual. The compositions may additionally contain stabilizers or pharmaceutically acceptable preservatives, such as thimerosal (ethyl(2-mercaptobenzoate-S)mercury sodium salt) (Sigma Chemical Company, St. Louis, Mo.).
In addition, the antibody compositions of the present invention and the vaccines as described above may also be administered with a suitable adjuvant in an amount effective to enhance the immunogenic response against the conjugate. For example, suitable adjuvants may include alum (aluminum phosphate or aluminum hydroxide), which is used widely in humans, and other adjuvants such as saponin and its purified component Quil A, Freund's complete adjuvant, and other adjuvants used in research and veterinary applications. Still other chemically defined preparations such as muramyl dipeptide, monophosphoryl lipid A, phospholipid conjugates such as those described by Goodman-Snitkoff et al. J. Immunol. 147:410-415 (1991) and incorporated by reference herein, encapsulation of the conjugate within a proteoliposome as described by Miller et al., J. Exp. Med. 176:1739-1744 (1992) and incorporated by reference herein, and encapsulation of the protein in lipid vesicles such as NovasomeTM lipid vesicles (Micro Vescular Systems, Inc., Nashua, N.H.) may also be useful.
Pharmaceutical Compositions
As would be recognized by one skilled in the art, the identified and isolated proteins or the invention, and the antibodies thereto capable of recognizing and binding to said proteins may also be formed into suitable pharmaceutical compositions for administration to a human or animal patient in order to treat or prevent a Gram-positive bacterial infection, such as those caused by Enterococcus, Streptococcus, Staphylococcus, etc. Pharmaceutical compositions containing the proteins or antibodies of the present invention as defined and described above may be formulated in combination with any suitable pharmaceutical vehicle, excipient or carrier that would commonly be used in this art, including such as saline, dextrose, water, glycerol, ethanol, other therapeutic compounds, and combinations thereof. As one skilled in this art would recognize, the particular vehicle, excipient or carrier used will vary depending on the patient and the patient's condition, and a variety of modes of administration would be suitable for the compositions of the invention, as would be recognized by one of ordinary skill in this art. Suitable methods of administration of any pharmaceutical composition disclosed in this application include, but are not limited to, topical, oral, anal, vaginal, intravenous, intraperitoneal, intramuscular, subcutaneous, intranasal and intradermal administration.
For topical administration, the composition may be formulated in the form of an ointment, cream, gel, lotion, drops (such as eye drops and ear drops), or solution (such as mouthwash). Wound or surgical dressings, sutures and aerosols may be impregnated with the composition. The composition may contain conventional additives, such as preservatives, solvents to promote penetration, and emollients. Topical formulations may also contain conventional carriers such as cream or ointment bases, ethanol, or oleyl alcohol.
Additional forms of compositions, and other information concerning compositions, methods and applications with regard to other microbial surface proteins and peptides of the present invention and antibodies thereto, will be found in other patent references relating to MSCRAMM®s, including, for example, in U.S. Pat. No. 6,288,214 (Hook et al.), incorporated herein by reference.
The compositions which are generated in accordance with the present invention may also be administered with a suitable adjuvant in an amount effective to enhance the immunogenic response in a patient. For example, suitable adjuvants may include alum (aluminum phosphate or aluminum hydroxide), which is used widely in humans, and other adjuvants such as saponin and its purified component Quil A, Freund's complete adjuvant, RIBI adjuvant, and other adjuvants used in research and veterinary applications. Still other chemically defined preparations such as muramyl dipeptide, monophosphoryl lipid A, phospholipid conjugates such as those described by Goodman-Snitkoff et al. J. Immunol. 147:410-415 (1991) and incorporated by reference herein, encapsulation of the conjugate within a proteoliposome as described by Miller et al., J. Exp. Med. 176:1739-1744 (1992) and incorporated by reference herein, and encapsulation of the protein in lipid vesicles such as NovasomeTM lipid vesicles (Micro Vescular Systems, Inc., Nashua, N.H.) may also be useful.
In any event, the compositions of the present invention will thus be useful for interfering with, modulating, or inhibiting binding interactions by Gram positive bacteria. Accordingly, the present invention will have particular applicability in developing compositions and methods of preventing or treating Gram positive bacterial infections, and in inhibiting binding and spreading of bacteria to host cells.
Methods:
Detecting and Diagnosing Infections
In accordance with the present invention, methods are provided for identifying and diagnosing infection from Gram positive bacteria through the use of the proteins, epitopes and peptides obtained by the bioinformatic method of the invention as described above and antibodies that recognize such proteins, epitopes and/or peptides. In accordance with the present invention, the antibodies of the invention as set forth above may be used in kits to diagnose such infections, and such kits may be of the type generally known in the art and commonly used to detect an antigen or microorganism of interest which will bind to the antibodies of the invention. These diagnostic kits will generally include the antibodies of the invention along with suitable means for detecting binding by that antibody such as would be readily understood by one skilled in this art. For example, the means for detecting binding of the antibody may comprise a detectable label that is linked to said antibody. These kits can then be used in diagnostic methods to detect the presence of a Gram positive bacterial infection wherein one obtains a sample suspected of being infected by one or more Gram positive bacteria, such as a sample taken from an individual, for example, from one's blood, saliva, urine, cerebrospinal fluid, genitourinary tract, tissues, bone, muscle, cartilage, or skin, and introduces to the sample one or more of the antibodies as set forth herein. After introduction of the antibodies, it is then determined through conventional means whether there has been binding by the antigens or microorganisms in the sample, such as through suitable labeling, or assays wherein the antibodies are bound to solid supports, and this binding is reflective of the presence of the target antigens or microorganisms in the sample.
Methods for Monitoring Levels of Antibodies or Antigens
In accordance with the present invention, it is also contemplated that another use of the invention may be in monitoring the level of Gram positive bacterial antigens, or antibodies recognizing said antigens in a human or animal patients suspected of containing said antigens or antibodies. In the preferred process, this may be carried out by first obtaining a biological sample from the human or animal patient, and this would include any suitable sample routinely monitored for infection, such as for example, from one's blood, serum, saliva, tissues, bone, muscle, cartilage, or skin. Next, one would introduce into the sample either (1) when monitoring levels of one's antibodies to Gram positive bacteria, a determinable level of a protein or its A domain to which such antibodies will bind; or (2), when monitoring levels of bacterial infestation is desired, introducing into said sample a measurable level of an antibody to a protein as set forth above. The next step in the process is, after allowing sufficient time and conditions so that the antigens and antibodies in the sample can achieve binding, then determining the level of antigen-antibody binding which will be reflective of the amount or level of the Gram positive bacteria, or antibodies thereto, which are located in the sample. In the desired process, levels may be monitored at regular time periods (e.g., hourly, daily, etc.) so as to track the progression/remission of a Gram positive bacterial infection such as during the period of hospitalization or treatment.
Assays for Detecting and Diagnosing Infections
In accordance with the present invention, the detection of Gram positive bacteria present in a biological fluid (e.g. blood, serum, plasma, saliva, urine, cerebrospinal fluid, genitourinary tract) or other biological material (e.g., tissues, bone, muscle, cartilage, or skin) can constitute a method for the diagnosis of acute or chronic infections caused by Gram positive bacteria. Because the antibodies as set forth above can recognize the epitopes found in several Gram positive bacteria, these antibodies can be used in assays to allow the diagnosis of a wide variety of Gram positive bacteria and disease conditions. Either monoclonal antibodies or polyclonal antibodies could be used in the assay, and in the case of the monoclonals such as those referred to above. The detected antigens identified by use of the present assays can be detected by a number of conventional means, including Western immunoblot and other similar tests.
With regard to the assays of the present invention, these assays may use the antibodies of the invention in labeled form, and all well-known methods of labeling antibodies are contemplated, including without limitation enzymatic conjugates, direct labeling with dye, radioisotopes, fluorescence, or particulate labels, such as liposome, latex, polystyrene, and colloid metals or nonmetals. Multiple antibody assay systems, such as antigen capture sandwich assays, are also within the scope of this invention. Further, competitive immunoassays involving labeled protein or assays using the labeled protein to detect serum antibodies are also contemplated forms of the diagnostic assays of the present invention. Beyond diagnostic assays which occur in solution, assays which involve immobilized antibody or protein are also considered within the scope of the invention. (See, for example, Miles et al., Lancet 2:492, 1968; Berry et al., J. Virol. Met. 34:91-100, 1991; Engvall et al., G. Immunochemistry, 8:871, 1971, Tom, Liposomes and Immunology, Elsevier/North Holland, New York, N.Y., 1980; Gribnau et al., J. of Chromatogr. 376:175-89, 1986 and all references cited therein). Examples of the types of labels which can be used in the present invention include, but are not limited to, enzymes, radioisotopes, fluorescent compounds, chemiluminescent compounds, bioluminescent compounds, particulates, and metal chelates. Those of ordinary skill in the art will know of other suitable labels for binding to the monoclonal or polyclonal antibody (or to an antigen) or will be able to ascertain the same by the use of routine experimentation. Furthermore, the binding of these labels to the monoclonal or polyclonal antibody (or antigen) can be accomplished using standard techniques commonly known to those of ordinary skill in the art.
One of the ways in which an assay reagent (generally, a monoclonal antibody, polyclonal antibody or antigen) of the present invention can be detectably labeled is by linking the monoclonal antibody, polyclonal antibody, or antigen to an enzyme. This enzyme, in turn, when later exposed to its substrate, will react with the substrate in such a manner as to produce a chemical moiety which can be detected as, for example, by spectrophotometric or fluorometric means. Examples of enzymes which can be used to detectably label the reagents of the present invention include malate dehydrogenase, staphylococcal nuclease, delta-V-steroid isomerase, yeast alcohol dehydrogenase, alpha-glycerophosphate dehydrogenase, triose phosphate isomerase, horseradish peroxidase, alkaline phosphatase, asparaginase, glucose oxidase, beta-galactosidase, ribonuclease, urease, catalase, glucose-VI-phosphate dehydrogenase, glucoamylase and acetylcholine esterase.
The presence of the detectably labeled reagent of the present invention can also be detected by labeling the reagent with a radioactive isotope which can then be determined by such means as the use of a gamma counter or a scintillation counter. Isotopes which are particularly useful for the purpose of the present invention are .sup.3 H, .sup.125 I, .sup.32 P, .sup.35 S, .sup.14 C, .sup.51 Cr, .sup.36 Cl, .sup.57 Co, .sup.58 Co, .sup.59 Fe and .sup.75 Se. It is also possible to detect the binding of the detectably labeled reagent of the present invention by labeling the monoclonal or polyclonal antibody with a fluorescent compound. When the fluorescently labeled reagent is exposed to light of the proper wave length, its presence can then be detected due to the fluorescence of the dye. Among the most commonly used fluorescent labeling compounds are fluorescein isothiocyanate, rhodamine, phycoerythrin, phycocyanin, allophycocyanin, o-phthaldehyde and fluorescamine. The reagents of the present invention also can be detectably labeled by coupling it to a chemiluminescent compound. The presence of the chemiluminescent-tagged reagent is then determined by detecting the presence of luminescence that arises during the course of the chemical reaction. Examples of particularly useful chemiluminescent labeling compounds are luminol, isoluminol, theromatic acridinium ester, imidazole, acridinium salt and oxalate ester. Likewise, a bioluminescent compound may be used to label the reagent of the present invention. Bioluminescence is a type of chemiluminescence found in biological systems in which a catalytic protein increases the efficiency of the chemiluminescent reaction. The presence of a bioluminescent reagent is determined by detecting the presence of luminescence. Important bioluminescent compounds for purposes of labeling are luciferin, luciferase and aequorin.
Another technique which may also result in greater sensitivity when used in conjunction with the present invention consists of coupling the monoclonal or polyclonal antibody of the present invention to low molecular weight haptens. The haptens can then be specifically detected by means of a second reaction. For example, it is common to use such haptens as biotin (reacting with avidin) or dinitrophenol, pyridoxal and fluorescamine (reacting with specific antihapten antibodies) in this manner. Any biological sample containing the detectable yet unknown amount of a Gram positive antigen can be used in the assay. Normally, the sample is preferably a liquid, such as, for example, urine, saliva, cerebrospinal fluid, blood, serum and the like, or a solid or semi-solid, such as, for example, tissue, feces and the like.
The diagnostic assay of the present invention includes kit forms of such an assay. This kit would include antibodies as described above (raised against whole proteins or active immunoreactive fragments such as the A domain or immunogenic analogs thereof) which can be optionally immobilized, as well as any necessary reagents and equipment to prepare the biological sample for and to conduct analysis, e.g. preservatives, reaction media such as nontoxic buffers, microtiter plates, micropipettes, etc. The reagent (Abs and/or antigens) can be lyophilized or cryopreserved. As described above, depending on the assay format, the antibodies can be labeled, or the kit can further comprise labeled proteins, fragments or analogs thereof containing the relevant epitopes so as to enable the detection of antibodies to Gram positive bacteria in biological fluids and tissues. By analog is meant a protein or peptide which may differs from its naturally occurring or recombinant counterpart by the substitution, deletion and/or addition of one or more amino acids but which retains the ability to be recognized by an antibody raised against the entire protein. An example is a carrier/antigen fusion polypeptide of the whole antigen or an immunoreactive fragment thereof, where the antigen or fragment can be embedded within the carrier polypeptide or linked to the carrier polypeptide at either end. Accordingly, antibodies in accordance with the invention may also recognize such analogs. The types of immunoassays which can be incorporated in kit form are many. Typical examples of some of the immunoassays which can utilize the antibodies of the invention are radioimmunoassays (RIA) and immunometric, or sandwich, immunoassays.
By “immunometric assay” or “sandwich immunoassay”, in meant to include simultaneous sandwich, forward sandwich and reverse sandwich immunoassays. These terms are well understood by those skilled in the art. Those of skill will also appreciate that the monoclonal antibodies, polyclonal antibodies and/or antigens of the present invention will be useful in other variations and forms of immunoassays which are presently known or which may be developed in the future. These are intended to be included within the scope of the present invention. In a forward sandwich immunoassay, a sample is first incubated with a solid phase immunoadsorbent containing monoclonal or polyclonal antibody(ies) against the antigen. Incubation is continued for a period of time sufficient to allow the antigen in the sample to bind to the immobilized antibody in the solid phase. After the first incubation, the solid phase immunoadsorbent is separated from the incubation mixture and washed to remove excess antigen and other interfering substances, such as non-specific binding proteins, which also may be present in the sample. Solid phase immunoadsorbent containing antigen bound to the immobilized antibody is subsequently incubated for a second time with soluble labeled antibody or antibodies. After the second incubation, another wash is performed to remove unbound labeled antibody(ies) from the solid phase immunoadsorbent and removing non-specifically bound labeled antibody(ies). Labeled antibody(ies) bound to the solid phase immunoadsorbent is then detected and the amount of labeled antibody detected serves as a direct measure of the amount of antigen present in the original sample.
Alternatively, labeled antibody which is not associated with the immunoadsorbent complex can also be detected, in which case the measure is in inverse proportion to the amount of antigen present in the sample. Forward sandwich assays are described, for example, in U.S. Pat. Nos. 3,867,517; 4,012,294 and 4,376,110, incorporated herein by reference. In carrying out forward immunometric assays, the process may comprise, in more detail: (a) first forming a mixture of the sample with the solid phase bound antibody(ies) and incubating the mixture for a time and under conditions sufficient to allow antigen in the sample to bind to the solid phase bound antibody(ies), (b) adding to the mixture after said incubation of step (a) the detectably labeled antibody or antibodies and incubating the new resulting mixture for a time and under conditions sufficient to allow the labeled antibody to bind to the antigen-antibody complex on the solid phase immunoadsorbent; (c) separating the solid phase immunoadsorbent from the mixture after the incubation in step (b); and (d) detecting either the labeled antibody or antibodies bound to the antigen-antibody complex on the solid phase immunoadsorbent or detecting the antibody not associated therewith.
In a reverse sandwich assay, the sample is initially incubated with labeled antibody(ies), after which the solid phase immunoadsorbent containing multiple immobilized antibodies is added thereto, and a second incubation is carried out. The initial washing step of a forward sandwich assay is not required, although a wash is performed after the second incubation. Reverse sandwich assays have been described, for example, in U.S. Pat. Nos. 4,098,876 and 4,376,110. In carrying out reverse immunometric assays, the process may comprise, in more detail; (a) first forming a mixture of the sample with the soluble detectably labeled antibody for a time and under conditions sufficient to allow antigen in the sample to bind to the labeled antibody; (b) adding to the mixture after the incubation of step (a) the solid phase bound antibodies and incubating the new resulting mixture for a time and under conditions sufficient to allow antigen bound to the labeled antibody to bind to the solid phase antibodies; (c) separating the solid phase immunoadsorbent from the incubating mixture after the incubation in step (b); and (d) detecting either the labeled antibody bound to the solid phase immunoadsorbent or detecting the labeled antibody not associated therewith.
In a simultaneous sandwich assay, the sample, the immunoadsorbent having multiple immobilized antibodies thereon and labeled soluble antibody or antibodies are incubated simultaneously in one incubation step. The simultaneous assay requires only a single incubation and does not include washing steps. The use of a simultaneous assay is by far the preferred one. This type of assay brings about ease of handling, homogeneity, reproducibility, and linearity of the assays and high precision. The sample containing antigen, solid phase immunoadsorbent with immobilized antibodies and labeled soluble antibody or antibodies is incubated under conditions and for a period of time sufficient to allow antigen to bind to the immobilized antibodies and to the soluble antibody(ies). In general, it is desirable to provide incubation conditions sufficient to bind as much antigen as possible, since this maximizes the binding of labeled antibody to the solid phase, thereby increasing the signal. Typical conditions of time and temperature are two hours at 45 degrees C., or twelve hours at 37 degrees C. Antigen typically binds to labeled antibody more rapidly than to immobilized antibody, since the former is in solution whereas the latter is bound to the solid phase support. Because of this, labeled antibody may be employed in a lower concentration than immobilized antibody, and it is also preferable to employ a high specific activity for labeled antibody. For example, labeled antibody might be employed at a concentration of about 1-50 ng per assay, whereas immobilized antibody might have a concentration of 10-500 ng per assay per antibody. The labeled antibody might have a specific activity with, for instance, one radioiodine per molecule, or as high as two or more radioiodines per molecule of antibody.
Of course, the specific concentrations of labeled and immobilized antibodies, the temperature and time of incubation as well as other assay conditions can be varied, depending on various factors including the concentration of antigen in the sample, the nature of the sample and the like. Those skilled in the art will be able to determine operative and optimal assay conditions for each determination by employing routine experimentation.
In carrying out the simultaneous immunometric assay on a sample containing a multivalent antigen, the process may comprise, in more detail: (a) simultaneously forming a mixture comprising the sample, together with the solid phase bound antibody and the soluble labeled antibody or antibodies; (b) incubating the mixture formed in step (a) for a time and under conditions sufficient to allow antigen in the sample to bind to both immobilized and labeled antibodies;(c) separating the solid phase immunoadsorbent from the incubation mixture after the incubation; and(d) detecting either labeled antibody bound to the solid phase immunoadsorbent or detecting labeled antibody not associated therewith. Other such steps as washing, stirring, shaking filtering and the like may of course be added to the assays, as is the custom or necessity for any particular situation.
There are many solid phase immunoadsorbents which have been employed and which can be used in the present invention. Well-known immunoadsorbents include nitrocellulose, glass, polystyrene, polypropylene, dextran, nylon and other materials; tubes, beads, and microtiter plates formed from or coated with such materials, and the like. The immobilized antibodies can be either covalently or physically bound to the solid phase immunoadsorbent, by techniques such as covalent bonding via an amide or ester linkage, or by absorption. Those skilled in the art will know many other suitable solid phase immunoadsorbents and methods for immobilizing antibodies thereon, or will be able to ascertain such, using no more than routine experimentation.
Kits
As indicated above, in accordance with the present invention, the antibodies of the invention as set forth above may be used in kits to diagnose a Gram positive infection. Such diagnostic kits are well known in the art and will generally be prepared so as to be suitable for determining the presence of epitopes or proteins that will bind to the antibodies of the invention. These diagnostic kits will generally include the antibodies of the invention along with suitable means for detecting binding by that antibody such as would be readily understood by one skilled in this art. For example, the means for detecting binding of the antibody may comprise a detectable label that is linked to said antibody. These kits can then be used in diagnostic methods to detect the presence of a bacterial infection wherein one obtains a biological sample suspected of having such an infection, such as a sample taken from an individual, for example, from one's blood, saliva, urine, cerebrospinal fluid, genitourinary tract, tissues, bone, muscle, cartilage, or skin, introduces to the sample one or more of the antibodies as set forth herein, and then determines if the antibodies bind to the sample which would indicated the presence of such microorganisms in the sample.
In addition, as set forth above, these kits can also be useful in methods of monitoring the level of antibodies or bacterial antigens in the serum of a human or animal patient. If monitoring the level of antigen is desired, the kit will include an antibody in accordance with the present invention as described above along with a means of determining the level of binding to that antibody. When it is desired to measure the level of antibodies to Gram positive bacteria in a sample, the kit will preferably include an isolated protein or epitope (e.g., the A domain) such as described above, along with means for detecting binding of those antigens to antibodies present in the sample.
Treating or Protecting Against Infections
In accordance with the present invention, methods are provided for preventing or treating an infection caused by Gram positive bacteria which comprise administering an effective amount of the antibodies as described above to a human or animal patient in need of such treatment in amounts effective to treat or prevent the infection. Accordingly, in accordance with the invention, administration of an effective amount of the antibodies of the present invention in any of the conventional ways described above (e.g., topical, parenteral, intramuscular, etc.), and will thus provide an extremely useful method of treating or preventing bacterial infections in human or animal patients. As indicated above, by effective amount is meant that level of use, such as of an antibody titer, that will be sufficient to either prevent adherence of the bacteria, or to inhibit binding and colonization of such organisms to host cells and thus be useful in the treatment or prevention such infections. In addition, these antibodies also exhibit protective effects by a number of other mechanisms, including direct killing of the infectious microorganisms, increased opsonization, inhibition of morphological transition, etc., and thus an effective amount of antibodies will also include that amount by which any of the means to achieve a protective effect is obtained. As would be recognized by one of ordinary skill in this art, the level of antibody titer needed to be effective in treating or preventing infections will vary depending on the nature and condition of the patient, and/or the severity of the pre-existing infection.
Eliciting an Immune Response
In accordance with the present invention, a method is provided for eliciting an immunogenic reaction in a human or animal comprising administering to the human or animal an immunologically effective amount of a protein isolated using the bioinformatic method as described above, or a recombinantly produced version of such a protein, or an immunogenic fragment, region or epitope as described above so as to elicit an immunogenic response. As indicated above, an “immunogenic amount” of the antigen to be used in accordance with the invention to obtain an immunogenic reaction is intended to mean a nontoxic but sufficient amount of the agent, such that an immunogenic response will be elicited in the host so that the desired prophylactic or therapeutic effect is produced. Accordingly, the exact amount of the isolated protein that is required to elicit such a response will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the condition being treated, the particular carrier or adjuvant being used and its mode of administration, and the like. The invention also contemplates methods of generating antibodies which recognize the proteins and epitopes as described above, and suitable methods of generating monoclonal and polyclonal antibodies are described in more detail above.
Coating Devices
In accordance with the invention, the antibodies and compositions as described above may also be utilized to treat or protect against outbreaks of bacterial infections on certain medical devices and other implanted materials such as prosthetic devices. Medical devices or polymeric biomaterials that may be advantageously coated with the antibodies and/or compositions described herein include, but are not limited to, staples, sutures, replacement heart valves, cardiac assist devices, hard and soft contact lenses, intraocular lens implants (anterior chamber or posterior chamber), other implants such as corneal inlays, kerato-prostheses, vascular stents, epikeratophalia devices, glaucoma shunts, retinal staples, scleral buckles, dental prostheses, thyroplastic devices, laryngoplastic devices, vascular grafts, soft and hard tissue prostheses including, but not limited to, pumps, electrical devices including stimulators and recorders, auditory prostheses, pacemakers, artificial larynx, dental implants, mammary implants, penile implants, cranio/facial tendons, artificial joints, tendons, ligaments, menisci, and disks, artificial bones, artificial organs including artificial pancreas, artificial hearts, artificial limbs, and heart valves; stents, wires, guide wires, intravenous and central venous catheters, laser and balloon angioplasty devices, vascular and heart devices (tubes, catheters, balloons), ventricular assists, blood dialysis components, blood oxygenators, urethral/ureteral/urinary devices (Foley catheters, stents, tubes and balloons), airway catheters (endotracheal and tracheostomy tubes and cuffs), enteral feeding tubes (including nasogastric, intragastric and jejunal tubes), wound drainage tubes, tubes used to drain the body cavities such as the pleural, peritoneal, cranial, and pericardial cavities, blood bags, test tubes, blood collection tubes, vacutainers, syringes, needles, pipettes, pipette tips, and blood tubing.
It will be understood by those skilled in the art that the term “coated” or “coating”, as used herein, means to apply the antibody or composition as defined above to a surface of the device, preferably an outer surface that would be exposed to an infection such as those caused by Gram positive bacteria. The surface of the device need not be entirely covered by the protein, antibody or active fragment.
As indicated above, the antibodies of the present invention, or active portions or fragments thereof, may also be useful for interfering with the physical interaction between bacteria responsible for infection and a mammalian host, and may also be useful in interfering with the ability of the bacteria to adhere to extracellular matrix proteins such as fibrinogen, collagen, laminin, etc. Accordingly, the antibodies of the invention may be useful both in treating patients and in preventing or reducing bacterial infections, or for reducing or eliminating infection and infestation of such organisms in-dwelling medical devices and prosthetics to make them safer for use.
In short, the antibodies of the present invention as described above can be extremely useful in detecting, treating or preventing infections by Gram positive bacteria in human and animal patients, or in preventing or reducing infection of medical devices and prosthesis that can be caused by such organisms. In particular, the present invention will be of importance in the treatment or prevention of such infections in highly susceptible groups such as premature newborns, AIDS and debilitated cancer patients, and are particularly frequent and severe after bone marrow transplantation.
EXAMPLES
The following examples are provided which exemplify aspects of the preferred embodiments of the present invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventors to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.
EXAMPLES
Example 1
Method to Identify MSCRAMM® Proteins from Gram Positive Bacteria and Expression and Purification of Their A Domains
A. Searching for LPXTG-motif containing cell wall anchored proteins in annotated genomes of Gram-positive bacteria.


    1. Obtain the amino acid sequences of the entire genome of interest from web sites of sequencing centers. These sequences are stored in a local Silicon Graphics machine (SGI).
    2. A local searchable database is established using the program format db obtained from NCBI and installed locally on the SGI.
    3. LPXTG-motif containing proteins are identified using PHI-blast, which is obtained from NCBI and installed locally on the SGI. The PHI-blast search uses a degenerate LPXTG pattern L-P-X-[TSA]-[GANS], X being any amino acid. The templates for PHI-blast vary depend on the particular organism. For each organism, two known cell wall anchored proteins of S. aureus with no sequence homology were used as well as known cell wall anchored proteins from that particular organism if available.
    4. The LPXTG-containing proteins obtained from PHI-blast were analyzed to select for those that contain typical features of LPXTG-motif containing cell wall anchored proteins: a signal peptide at the N-terminus, the LPXTG-motif being close to the C-terminus followed by a hydrophobic transmembrane segment, and several positively charged residues at the C-terminus. These are done as described below:


Signal peptide: we use the SignalP prediction server. The method has been described in “Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites” . Henrik Nielsen, Jacob Engelbrecht, Søren Brunak and Gunnar von Heijne, Protein Engineering 10, 1-6 (1997).
Location of LPXTG-motif: visual examination of the sequence.
A hydrophobic transmembrane segment after the LPXTG-motif: we use the TMHMM server for the prediction of transmembrane segments. Several other prediction web servers can also be used, among which are TMpred, DAS, and HMMTOP.
Positively charged residues at C-terminus: visual examination.


    5. Sequences that contain the above features are putative LPXTG-motif containing cell wall anchored proteins.
    6. The term “LPXTG” or “cell wall” are used to search for proteins that are annotated as cell wall anchored proteins in the genome of interest at TIGR website (comprehensive microbial resource, http://www.tigr.org/tigrscripts/CMR2/CMRHomePage.spl).

B. Searching for LPXTG-motif containing cell wall anchored proteins in unannotated genomes of Gram-positive bacteria.

    1. Obtain genome sequences from the web sites of sequencing centers. These sequences are stored in a local Silicon Graphics machine (SGI).
    2. Gene prediction using the program Glimmer 2.0 from TIGR. This is facilitated by UNIX C shell scripts written in house.
    3. The predicted genes are translated into amino acid sequences using a translation program written in house. This program is capable of translating large batch of sequences.
    4. The translated amino acid sequences are formatted into a searchable database locally as in Section A.2. Subsequent analysis is as described in Section A.3-5.

C. Prediction of Immunoglobulin—like (Ig—like) fold in putative LPXTG-motif containing cell wall anchored proteins.



The amino acid sequences of putative LPXTG-motif containing cell wall anchored proteins are submitted to a Fold recognition web server 3D-PSSM. The method of prediction is described in Kelley LA, MacCallum RM & Steinberg MJE. Enhanced Genome Annotation using Structural Profiles in the Program 3D-PSSM. J Mol Biol. 2000 June 2;299(2):499-520
The output of 3D-PSSM gives a probability E value indicating the likelihood of the submitted sequence adopting a similar 3D structure as a published structure.
Proteins that have E value <0.25 to a published Ig—like fold structure, are considered containing predicted Ig—like folds. These should be considered MSCRAMM® proteins.
Accordingly, in accordance with the present invention, a bioinformatic approach was used to identify proteins with MSCRAMM®—like characteristics among Gram positive bacteria, particularly Enterococcus faecalis. Forty-two proteins with a putative C-terminal LPxTG cell wall sorting signal were identified in the E. faecalis genome. We then looked for structural similarities to MSCRAMM® proteins among LPxTG-anchored enterococcal proteins. Nine proteins were predicted to contain regions that adopt an immunoglobulin—like fold. The Ig fold-containing regions in FIG. 1 consist of several consecutive and overlapping matches to solved crystal structures ( ̃150-500 aa) of the immunoglobulin superfamily (IgSF), which consist of one to four domains of equal size and Ig-type fold. The homologous Ig-fold regions cover most of the enterococcal proteins and may indicate a similar “beads-in-a-string” arrangement of consecutive modules that are found in fibronectin and other IgSF proteins (Leahy, 1996)(Sharma, 1999)(Hamburger, 1999)(Luo, 2000). A tandem repeat of Ig folded subdomains (N2 and N3) is found in the crystal structure of the fibrinogen-binding domain of ClfA. The full-length A domains of ClfA and the similarly structured ClfB consist of an additional N-terminal subdomain, N1 (Deivanayagam, 2002)(Perkins, 2001). Based on sequence and secondary structure similarities, an analogous subdomain organization is also expected in other MSCRAMM® proteins including FnbpA, FnbpB, Ace and the Sdr proteins. The solved crystal structure of CNA minimum collagen-binding domain is made of a single Ig-type subdomain (N2) (Symersky, 1997) and the C-terminal repeat domains B1 and B2 each consist of a tandem repeat of Ig-folded subdomains (Deivanayagam, 2000). A similar modular structure is expected in the B3 and B4 repeats. Thus, a module structure of multiple Ig-folded units seems a general characteristic in the MSCRAMM® protein family. The length of the N-subdomains of MSCRAMM® proteins is typically  ̃150 aa suggesting that the large size of the A domains of EF1091 and EF0089 could accommodate more than three Ig-folded subdomains in their A domains.
Example 3
Expression and Purification of Recombinant Enterococcal MSCRAMM® Protein Fragments
To further characterize the utility of this invention, the A-domains of EF1091, EF1092 and EF1093 proteins from E. faecalis as well as Efae 2926, Efae 2925 and Efae 2924 proteins from E. faecium were cloned, expressed and purified. In addition, EF1824 was cloned in two segments, EF1824AI (aa 43-819) and EF1824AII (aa 820-1829) because of the large size of the protein. EF1824AI was insoluble in E. coli cytoplasm and excluded from the assays. Bolded and underlined sequence represents the putative A-domains that were cloned.








EF1824A1: amino acid residues 43-819



QEQTAKEDVADSATSVGAIVSIEKAEKNFVITYASGKKAQISILNDHLFRYHLDP
(SEQ ID NO: 2)


TGKFEEYPTPNDPKHVAKITAKTMADYGTQAFEQTNVTDSGNQFILENNGLKI


MFEKESALMKVLDKKKNQVILEETAPLSFKNDKATQTLKQSSQENYFGGGTQ


NGRFTHKGTAIQIVNTNNWVDGGVASPNPFYWSTAGYGVVRNTWKPGNYDF


GSHDPQKTTTTHEGTDFDAFYFFNDSSAGILKDYYELTGKPALMPEYGFYEAH


LNAYNRDYWVKVAEGTAGAVKFEDGNFYKEYQPGDLGNLNGTLESLNGEKE


NYQFSARAVIDRYKKNDMPLGWFLPNDGYGAGYGQTDSLDGDVQNLKEFTEY


AQANGVEVGLWTQSNLHPADPKNPKKGERDIAKEVSVAGVKALKTDVAWVG


YGYSFGLNGVEDAANVFVKETDGAVRPMIVSLDGWAGTQRHAGIWTGDQTG


GQWEYIRFHIPTYIGTSLSGQPNVGSDMDGIFGGKNKEINIRDFQWKTFTPVQL


NMDGWGSNPKTPFAFDQEATDLNRAYLKLKSMMMPYNYSIAKESVDGLPMV


RAMALEFPNEGTAYTKDSQYQYMWGPNLLVAPIYNGNQDEAGNSIRDGIYLPD


EKQVWVDLFTGEKYQGGRVLNGVKTPLWKVPVFVKDGSIIPMTNPNNNPKEI


QRDQRSFLIYPNGTTSFNMYEDDGISTSYEAGQSATTKINSQGPKSNEKGDLT


VTIEPTKGSYKDFVDERSTTLDLLASEAPESVTAMVGGTEVTLKQ


 


EF1824A1: amino acid residues 820-1829


AANKEEFLAGTNLYYFDKEFQVNQYLSEASGEKLNQSALSVKLAKQSVTAKDVQITVK
(SEQ ID NO: 3)


GFINKGTVDGGNTTVDDQLTIPANVAINEEKTTPSSLTLQWDQVTEATSYEVERDGTVF


GNIQTNTATFDGFSFLSEHTFRVRAVGKNGVSEWSEPIKGKTQDDPYKETINQVKATS


NLPEQPGAELKKLTDKDLSTGWHTNWSTGIANPSDGNFLSLKFDLGAEYQMDKIEYL


PRDNAGNGNILQLQYRTSKDGANWTEFSEPINWKQDALTKTIETKDQAYRFVEMKVL


KSVGNFGSGREMLFYKQPGTEGILHGDITNDGTIDENDAMSYRNYTGLESVDSDFNGY


VEKGDLNKNGVIDAYDISYVLRQLDGGIEIPDVEEIAGGLSLAVVNENGKDTYLPGDTLT


FILKGQDLKNINALSTKMSFDSSKFELVGQPATTNNTQQMENYSKYRKHSNDVENLYL


VLSNQGNKQLLNGSMDLVTFKVKVKETTRVKRATTVEQPLQFDMSQGLLVGQGFQQ


ATLSDFSVTVKPTELVDKELLQALITLNQARVEKEYTPETWAIFKPILDEAVAVLANEQA


TQTDVSAAAENLEKAASQLEKMPDVANKADLEKAIQEGLAKKPSDGQEFTEETKKVL


EESLAAAQKVFAQEKVTQEEIDQATKTLREAIAQLKEQPVAVDKETLKEQIAQARGRK


PEEGYQFTKETEKQLQEAIQAAEAIVAKETATKEEVSEALNALETAMAQLKEVPLVNK


DQLQEWKRAQQVTPSEGHQFTASSLQELQKALLAAKNTLKNPAANQKMIDEAVAEL


TSAIDGLQEEVLVTDKKALEAMIAKAKAIKPSAGKEFTSESKARLTEAIDQAEGILADKN


ARQEQIDIAEKNVKTALDSLEEQVLQTDKTKLKELLQKAETLKPKAGKQFTKASQEAL


AEAIKQAKALVEDPNATQEAVDKCLSILSQAIEAMAEEPISSNSTGNNGNHSTVSGTGG


VTSQGKGTATGGTTTKTTTSGT


 


EF0089A: amino acid residues 36-1143


EEVNSDGQLTLGEVKQTSQQEMTLALQGKAQPVTQEVVVHYSANVSIKAAHWAAPN
(SEQ ID NO: 4)


NTRKIQVDDQKKQIQIELNQQALADTLVLTLNPTATEDVTFSYGQQQRALTLKTGTDPT


ESTAITSSPAASANEGSTEEASTNSSVPRSSEETVASTTKAIESKTTESTTVKPRVAGPT


DISDYFTGDETTIIDNFEDPIYLNPDGTPATPPYKEDVTIHWNFNWSIPEDVREQMKAGD


YFEFQLPGNLKPNKPGSGDLVDAEGNVYGTYTISEDGTVRFTFNERITSESDIHGDFSL


DTHLNDSDGRGPGDWVIDIPTQEDLPPVVIPIVPDTEQQIDKQGHFDRTPNPSAITWTV


DINQAMKDQTNPVTETWPTGNTFKSVKVYELVMNLDGTIKEVGRELSPDEYTVDKNG


NVTIKGDTNKAYRLEYQTTIDEAVIPDGGGDVPFKNHATLTSDNNPNGLDAEATVTATY


GKMLDKRNIDYDEANQEFTWEINYNYGEQTIPKDQAVITDTMGDNLTFEPDSLHLYSVT


FDDKGNEVVGAELVEGKDYKVVINGDGSFAIDFLHDVTGAVKIDYKTKVDGIVEGDVAV


NNRVDVGTGQHSEDDGTASQQNIIKNTGAVDYQNSTIGWTLAVNQNNYLMENAVITDT


YEPVPGLTMVPNSLVVKDTTTGAQLTLGKDFMVEITRNADGETGFKVSFIGAYAKTSD


AFHITYTTFFDVTELDANNPALDHYRNTAAIDWTDEAGNNHHSEDSKPFKPLPAFDLNA


QKSGVYNAVTKEITWTIAVNLSNNRLVDAFLTDPILTNQTYLAGSLKVYEGNTKPDGSV


EKVKPTQPLTDITMEEPSEKNQNTWRVDFPNDSRTYVIEFKTSVDEKVIEGSASYDNTA


SYTNQGSSRDVTGKVSIQHGGESVKKGGEYHKDDPDHVYWHVMINGAQSVLDDVVIT


DTPSPNQVLDPESLVIYGTNVTEDGTITPDKSVILEEGKDYTLEVTTDNETGQQKIVVKM


AHIEAPYYMEYRSLVTSSAAGSTDTVSNQVSITGNGSEVVHGDDNGDVVVDIDHSGGH


ATGTKGKIQLKKTAMDETTILAGAHFQIWDQAKTQVLREGTVDATGVITFGG


 


EF3023A: amino acid residues 26-1024


EEITDLFLQKEVTYSGVEGGKIGENWKYPQFVGEKAVDGDETTRWSADKQDEQWLIV
(SEQ ID NO: 5)


DLGEVKNIGELVLQLHAESPVYEILVSTDGESYQSIFKEENGKGGQPTKKYIDGNNVQA


RFVKYQQMKMWQHTNKQFYSSSIISFEAYEKKRLPEAIKLLTENLTISEKRKQQLAFEV


SPAGVDITEDQIEWSSSDPTIVTVDQTGNLTAVKSGEAKVTVKIKGTEISDTIPVTVVAEN


KQYAEMRAKWKMRLLGTTQYDNDADVQQYRAQIATESLALWQTLNQAADREYLWER


KPSDTVSADYTTQFTNIKKLALGYYEPSSELFEKPEVYDAIVKGIEFMIDTKKYNGTYYT


GNWWDWQIGSAQPLTDTLILLHDDLLNTDAEKLNKFTAPLMLYAKDPNIQWPIYRATG


ANLTDISITVLGTGLLLEDNQRLVQVQEAVPSVLKSVSSGDGLYPDGSLIQHGYFPYNG


SYGNELLKGFGRIQTILQGSDWEMNDPNISNLFNVVDKGYLQLMVNGKMPSMVSGRS


ISRAPETNPFTTEFESGKETIANLTLIAKFAPENLRNDIYTSIQTWLQQSGSYYHFFKKP


RDFEALIDLKNVVNSASPAQATPMQSLNVYGSMDRVLQKNNEYAVGISMYSQRVGNY


EFGNTENKKGWHTADGMLYLYNQDFAQFDEGYWATIDPYRLPGTTVDTRELANGAYT


GKRSPQSWVGGSNNGQVASIGMFLDKSNEGMNLVAKKSWFLLDGQIINLGSGITGTT


DASIETILDNRMIHPQEVKLNQGSDKDNSWISLSAANPLNNIGYVFPNSMNTLDVQIEE


RSGRYGDINEYFVNDKTYTNTFAKISKNYGKTVENGTYEYLTVVGKTNEEIAALSKNKG


YTVLENTANLQAIEAGNYVMMNTWNNDQEIAGLYAYDPMSVISEKIDNGVYRLTLANPL


QNNASVSIEFDKGILEVVAADPEISVDQNIITLNSAGLNGSSRSIIVKTTPEVTKEALEKLI


QEQ


 


EF2224A: amino acid residues 31-771


QEVTSDAEKTVEKDGLKVIGKIEDTSSQEDIKTVTYEVTNTRDVPIKDLILKQKNTNDSPI
(SEQ ID NO: 6)


KFVLDTLSEERGPTSLEEQAKVETNEKDQTTDIKLLNLQPNSTRKITINGQITTKASNKL


LVSVLIEDNEKGTLVIDLPSKDILADKESVSKEKQETSETKVENQANETASSTNEMTATT


SNETKPEAGKAIESIQETALTQATESPEQPPLKAQPTGPLVPPTPGRGFNTPIYQSVHK


GELFSTGNTNLKIANENTAAAQTFLNTRGASSGYAINNFPLEFADVDNDPNTYNSSRAY


IDLNGAKEIAWAGLFWSASRYKGPAYGTNLSDEEISAPVQFTTPNGTVQRVSPQRYHR


IDQDATNPGQRFGYNNTGFSNYADVTSILQGDKSATGSYTLADIPMTSSLNGQYQYYN


FSGWSLFVVTKDQASKSRAFSIYYGARGNAAGTNNEFTMSNFLTAKQGNLDPIVTWFT


VQGDKYWTGDNAQIKNSAGTWVNISNTLNPVNNAMNATVTDNDEHMVDKYPGKFAP


DHPNFLDIDIDRMAIPEGVLNAGQNQINFRTTSSGDDYSTNAIGFAVNAETPEFEIKKEIV


EPKETYKVGETITYRVSLKNTKADSEAINSVSKDALDGRLNYLPGSLKIISGPNSGEKTD


ASGDDQAEYDETNKQIIVRVGNGATATQGGSYKADTAETIYEFKARINERAKANELVPN


SATVEAVDILTSAKVNETSNIVEAKIADEQVT


 


EF1269A: amino acid residues 27-596


ETGYAQTEPTSTSETNQISATPNVVPRKQVGNIVTAIQLTDKEGNPLGTINQYTDIYLRIE
(SEQ ID NO: 7)


FNLPDNTVNSGDTSVITLPEELRLEKNMTFNVVDDTGTVVAIAQTDVANKTVTLTYTDY


VENHANISGSLYFTSLIDFENVENESKIPIYVTVEGEKIFAGDLDYQGEGDDVNEKFSKY


SWFIEDDPTEIYNVLRINPTGQTYTDLEVEDVLKTESLSYMKDTMKIERGQWTLDGNAI


WQFTPEEDITDQLAVQYGPDDRNFSVHFGNIGTNEYRITYKTKIDHLPEKGETFTNYAK


LTENQTVVEEVEVSRVSQTGGGEANGEQYVVEIHKEDEAGQRLAGAEFELIRNSTNQT


VAKITTDQNGTAIVKGLLKDNYTLVETKAPTGYQLSQNKIPITPEDFGKNLVALKTVVNH


KISYQPVAASFLAGKVLLGKPLKDAEFQFELLDEKGTVLETVSNDTLGKIQFSPLTFET


PGNYQYTIREVNTQQTGVSYDTHNLQVQVTVEALLGNLVATTQYDGGQVFTNHYTPE


KPIESTTPPTSGTTDTTTNSTTETTSITIEKQAIRNKE


 


EF1091: Nucleotide Sequence


===0===ATGATAACAG=ATGAGAATGA=TAAAACGAAT=ATTAATATCG=AGTTAAATCT
(SEQ ID NO: 8)


==50===TCTCAACCAA=ACAGAGCAGC=CATTACAACG=AGAAATTCAA=TTGAAAAATG


=100===CACAGTTCAT=GGATACTGCT=GTAATTGAAA=AAGACGGATA=TTCTTACCAA


=150===GTGACTAATG=GTACGCTTTA=TCTGACTTTG=GACGCACAAG=TAAAAAAGCC


=200===GGTACAGCTT=TCGTTAGCTG=TTGAGCAAAG=TTCGCTTCAA=ACAGCTCAGC


=250===CACCTAAGTT=ATTGTATGAA=AACAACGAAT=ATGATGTTTC=AGTTACTTCT


=300===GAAAAAATAA=CAGTAGAGGA=TTCTGCTAAA=GAATCAACTG=AACCAGAAAA


=350===AATAACTGTA=CCAGAAAATA=CGAAAGAAAC=TAACAAAAAT=GATTCGGCTC


=400===CAGAAAAAAC=AGAACAGCCG=ACCGCAACAG=AAGAGGTAAC=CAATCCATTT


=450===GCAGAAGCAA=GAATGGCGCC=AGCTACTTTG=AGAGCGAATC=TGGCACTGCC


=500===TTTAATTGCA=CCACAATACA=CGACGGATAA=TTCTGGGACT=TATCCGACAG


=550===CTAATTGGCA=GCCCACAGGC=AATCAAAATG=TGTTAAACCA=TCAAGGGAAT


=600===AAAGACGGTA=GTGCACAATG=GGACGGCCAA=ACGAGTTGGA=ATGGGGACCC


=650===TACTAATCGC=ACAAATTCTT=ATATTGAGTA=TGGCGGTACA=GGAGACCAAG


=700===CCGATTATGC=CATCCGAAAA=TATGCTAGAG=AAACAACAAC=ACCAGGGCTT


=750===TTTGATGTAT=ATCTTAATGT=GCGTGGGAAT=GTTCAGAAAG=AAATCACGCC


=800===ATTGGATTTG=GTCTTAGTCG=TTGACTGGTC=CGGTAGTATG=AATGAAAACA


=850===ATCGGATTGG=TGAAGTTCAA=AAAGGAGTGA=ACCGTTTTGT=TGATACATTG


=900===GCAGATAGCG=GTATTACCAA=TAACATCAAC=ATGGGCTATG=TTGGCTACTC


=950===AAGTGACGGT=TATAATAACA=ACGCCATTCA=AATGGGGCCG=TTTGATACAG


1000===TCAAAAATCC=AATTAAAAAT=ATTACGCCAA=GTAGCACTAG=AGGAGGAACT


1050===TTCACTCAAA=AAGCATTAAG=AGATGCTGGT=GATATGTTAG=CAACGCCAAA


1100===TGGACATAAG=AAAGTCATTG=TACTTTTAAC=GGATGGCGTC=CCAACCTTCT


1150===CTTATAAAGT=GAGTCGAGTT=CAAACAGAGG=CGGATGGTCG=CTTTTACGGG


1200===ACACAATTTA=CGAATCGACA=AGATCAACCA=GGTAGCACTT=CTTATATCTC


1250===TGGTAGCTAT=AATGCGCCAG=ATCAAAACAA=TATCAATAAA=CGGATTAACA


1300===GTACGTTTAT=CGCCACGATA=GGTGAGGCAA=TGGTCTTAAA=ACAACGTGGG


1350===ATTGAAATAC=ATGGATTGGG=CATTCAATTG=CAAAGCGATC=CACGAGCTAA


1400===TTTATCTAAA=CAACAAGTTG=AAGATAAAAT=GCGTGAGATG=GTGTCAGCCG


1450===ATGAAAATGG=AGACCTTTAT=TATGAATCCG=CGGATTATGC=ACCAGACATT


1500===TCTGATTATT=TAGCGAAAAA=AGCCGTTCAG=ATTTCAGGAA=CGGTTGTAAA


1550===CGGAAAAGTA=GTTGATCCAA=TTGCTGAACC=TTTTAAATAC=GAGCCAAATA


1600===CATTATCAAT=GAAAAGTGTG=GGTCCTGTTC=AGGTTCAAAC=ATTACCAGAA


1650===GTGTCGCTAA=CAGGCGCTAC=AATTAATAGT=AATGAGATTT=ATTTGGGTAA


1700===AGGGCAAGAA=ATTCAAATTC=ATTATCAAGT=ACGTATTCAA=ACAGAGTCAG


1750===AAAACTTCAA=ACCTGATTTT=TGGTATCAAA=TGAATGGTCG=GACAACGTTT


1800===CAGCCATTAG=CCACGGCCCC=TGAAAAAGTT=GATTTTGGGG=TTCCTTCGGG


1850===AAAAGCACCT=GGCGTGAAGT=TAAACGTGAA=AAAAATCTGG=GAAGAGTATG


1900===ATCAAGACCC=GACAAGTCGG=CCAGATAATG=TGATTTATGA=AATTAGTAGA


1950===AAGCAAGTAA=CTGACACAGC=CAACTGGCAA=ACTGGGTATA=TTAAATTATC


2000===AAAACCAGAA=AATGATACCA=GCAATAGTTG=GGAGCGCAAA=AATGTAACCC


2050===AACTTTCCAA=AACCGCGGAT=GAAAGCTATC=AAGAAGTTCT=TGGGCTTCCC


2100===CAATACAACA=ATCAAGGACA=AGCTTTCAAT=TATCAAACAA=CCCGTGAATT


2150===AGCAGTTCCT=GGTTACAGTC=AAGAAAAAAT=CGACGATACT=ACTTGGAAAA


2200===ACACGAAGCA=GTTCAAGCCA=TTAGATTTAA=AAGTAATCAA=AAATTCTTCC


2250===TCAGGTGAGA=AAAACTTAGT=GGGAGCCGTC=TTTGAATTGA=GTGGTAAAAA


2300===TGTTCAAACA=ACATTAGTGG=ACAATAAAGA=TGGTAGCTAT=TCCTTGCCAA


2350===AAGATGTGCG=CCTACAAAAA=GGGGAACGCT=ATACATTAAC=TGAAGTAAAA


2400===GCACCTGCAG=GACATGAGTT=AGGCAAGAAA=ACGACTTGGC=AAATTGAGGT


2450===GAGTGAGCAA=GGCAAAGTAA=GCATCGATGG=ACAAGAAGTG=ACCACCACAA


2500===ATCAAGTTAT=TCCATTGGAA=ATTGAAAATA=AATTTTCTTC=TTTGCCAATC


2550===AGAATTAGAA=AATACACCAT=GCAAAATGGC=AAACAAGTGA=ACTTAGCAGA


2600===GGCGACTTTT=GCGTTGCAAA=GAAAAAATGC=TCAAGGAAGT=TACCAAACTG


2650===TGGCAACTCA=AAAAACAGAT=ACTACAGGAT=TGAGCTATTT=TAAAATTAGT


2700===GAACCTGGTG=AGTATCGAAT=GGTGGAACAA=TCAGGACCAT=TAGGCTACGA


2750===CACTCTTGCT=GGAAATTATG=AATTTACTGT=TGATAAATAT=GGGAAAATTC


2800===ACTATGCAGG=CAAAAATATT=GAAGAAAATG=CGCCAGAATG=GACACTGACA


2850===CATCAAAATA=ATTTGAAACC=TTTTGACTTA=ACAGTTAATA=AAAAAGCCGA


2900===TAATCAGACG=CCACTTAAAG=GAGCGAAATT=CCGTTTAACA=GGACCAGATA


2950===CGGATATTGA=ATTACCAAAA=GATGGCAAAG=AAACGGATAC=TTTTGTTTTT


3000===GAAAACTTAA=AACCAGGGAA=ATATGTTCTA=ACAGAAACCT=TTACGCCAGA


3050===AGGATATCAG=GGGTTAAAAG=AACCAATCGA=ATTAATAATT=CGTGAAGATG


3100===GTTCAGTCAC=GATAGATGGG=GAAAAAGTAG=CAGATGTTTT=AATTTCTGGA


3150===GAGAAGAATA=ATCAAATTAC=TTTAGACGTT=ACGAACCAAG=CAAAGGTTCC


3200===TTTACCTGAA=ACTGGTGGCA=TAGGACGCTT=GTGGTTTTAC=TTGATAGCGA


3250===TTAGTACATT=CGTGATAGCG=GGTGTTTATC=TCTTTATTAG=ACGACCAGAA


3300===GGGAGTGTG


 


EF1091 amino acid residues 63-1067


===0===MITDENDKTN=INIELNLLNQ=TEQPLQREIQ=LKNAQFMDTA=VIEKDGYSYQ
(SEQ ID NO: 9)


==50===VTNGTLYLTL=DAQVKKPVQL=SLAVEQSSLQ=TAQPPKLLYE=NNEYDVSVTS


=100===EKITVEDSAK=ESTEPEKITV=PENTKETNKN=DSAPEKTEQP=TATEEVTNPF


=150===AEARMAPATL=RANLALPLIA=PQYTTDNSGT=YPTANWQPTG=NQNVLNHQGN


=200===KDGSAQWDGQ=TSWNGDPTNR=TNSYIEYGGT=GDQADYAIRK=YARETTTPGL


=250===FDVYLNVRGN=VQKEITPLDL=VLVVDWSGSM=NENNRIGEVQ=KGVNRFVDTL


=300===ADSGITNNIN=MGYVGYSSDG=YNNNAIQMGP=FDTVKNPIKN=ITPSSTRGGT


=350===FTQKALRDAG=DMLATPNGHK=KVIVLLTDGV=PTFSYKVSRV=QTEADGRFYG


=400===TQFTNRQDQP=GSTSYISGSY=NAPDQNNINK=RINSTFIATI=GEAMVLKQRG


=450===IEIHGLGIQL=QSDPRANLSK=QQVEDKMREM=VSADENGDLY=YESADYAPDI


=500===SDYLAKKAVQ=ISGTVVNGKV=VDPIAEPFKY=EPNTLSMKSV=GPVQVQTLPE


=550===VSLTGATINS=NEIYLGKGQE=IQIHYQVRIQ=TESENFKPDF=WYQMNGRTTF


=600===QPLATAPEKV=DFGVPSGKAP=GVKLNVKKIW=EEYDQDPTSR=PDNVIYEISR


=650===KQVTDTANWQ=TGYIKLSKPE=NDTSNSWERK=NVTQLSKTAD=ESYQEVLGLP


=700===QYNNQGQAFN=YQTTRELAVP=GYSQEKIDDT=TWKNTKQFKP=LDLKVIKNSS


=750===SGEKNLVGAV=FELSGKNVQT=TLVDNKDGSY=SLPKDVRLQK=GERYTLTEVK


=800===APAGHELGKK=TTWQIEVSEQ=GKVSIDGQEV=TTTNQVIPLE=IENKFSSLPI


=850===RIRKYTMQNG=KQVNLAEATF=ALQRKNAQGS=YQTVATQKTD=TTGLSYFKIS


=900===EPGEYRMVEQ=SGPLGYDTLA=GNYEFTVDKY=GKIHYAGKNI=EENAPEWTLT


=950===HQNNLKPFDL=TVNKKADNQT=PLKGAKFRLT=GPDTDIELPK=DGKETDTFVF


1000===ENLKPGKYVL=TETFTPEGYQ=GLKEPIELII=REDGSVTIDG=EKVADVLISG


1050===EKNNQITLDV=TNQAKVPLPE=TGGIGRLWFY=LIAISTFVIA=GVYLFIRRPE


1100===GSV


 


EF1092: Nucleotide Sequence


===0===ATGAAAAACG=CACGTTGGTT=AAGTATTTGC=GTCATGCTAC=TCGCTCTTTT
(SEQ ID NO: 10)


==50===CGGGTTTTCA=CAGCAAGCAT=TAGCAGAGGC=ATCGCAAGCA=AGCGTTCAAG


=100===TTACGTTGCA=CAAATTATTG=TTCCCTGATG=GTCAATTACC=AGAACAGCAG


=150===CAAAACACAG=GGGAAGAGGG=AACGCTGCTT=CAAAATTATC=GGGGCTTAAA


=200===TGACGTCACT=TATCAAGTCT=ATGATGTGAC=GGATCCGTTT=TATCAGCTTC


=250===GTTCTGAAGG=AAAAACGGTC=CAAGAGGCAC=AGCGTCAATT=AGCAGAAACC


=300===GGTGCAACAA=ATAGAAAACC=GATCGCAGAA=GATAAAACAC=AGACAATAAA


=350===TGGAGAAGAT=GGAGTGGTTT=CTTTTTCATT=AGCTAGCAAA=GATTCGCAGC


=400===AACGAGATAA=AGCCTATTTA=TTTGTTGAAG=CGGAAGCACC=AGAAGTGGTA


=450===AAGGAAAAAG=CTAGCAACCT=AGTAGTGATT=TTGCCTGTTC=AAGATCCACA


=500===AGGGCAATCG=TTAACGCATA=TTCATTTATA=TCCAAAAAAT=GAAGAAAATG


=550===CCTATGACTT=ACCACCACTT=GAAAAAACGG=TACTCGATAA=GCAACAAGGC


=600===TTTAATCAAG=GAGAGCACAT=TAACTATCAG=TTAACGACTC=AGATTCCAGC


=650===GAATATTTTA=GGATATCAGG=AATTCCGTTT=GTCAGATAAG=GCGGATACAA


=700===CGTTGACACT=TTTACCAGAA=TCAATTGAGG=TAAAAGTGGC=TGGAAAAACA


=750===GTTACTACAG=GTTACACACT=GACGACGCAA=AAGCATGGAT=TTACGCTTGA


=800===TTTTTCAATT=AAAGACTTAC=AAAACTTTGC=AAATCAAACA=ATGACTGTGT


=850===CGTATCAAAT=GCGTTTAGAA=AAGACCGCTG=AACCTGACAC=TGCGATTAAC


=900===AACGAAGGAC=AATTAGTCAC=GGACAAACAT=ACCTTGACTA=AAAGAGCCAC


=950===AGTTCGTACA=GGCGGCAAGT=CTTTTGTCAA=AGTTGATAGT=GAAAATGCGA


1000===AAATCACCTT=GCCAGAGGCT=GTTTTTATCG=TCAAAAATCA=AGCGGGGGAA


1050===TACCTCAATG=AAACAGCAAA=CGGGTATCGT=TGGCAAAAAG=AAAAAGCATT


1100===AGCTAAAAAA=TTCACGTCTA=ATCAAGCCGG=TGAATTTTCA=GTTAAAGGCT


1150===TAAAAGATGG=CCAGTACTTC=TTGGAAGAAA=TCTCTGCACC=AAAAGGTTAT


1200===CTTCTGAATC=AAACAGAAAT=TCCTTTTACG=GTGGGAAAAA=ATTCTTATGC


1250===AACGAACGGA=CAACGAACAG=CACCGTTACA=TGTAATCAAT=AAAAAAGTAA


1300===AAGAGTCAGG=CTTCTTACCA=AAAACAAATG=AAGAACGTTC=TATTTGGTTG


1350===ACGATTGCAG=GCCTGCTAAT=CATTGGGATG=GTAGTCATTT=GGCTATTTTA


1400===TCAAAAACAA=AAAAGAGGAG=AGAGAAAA


 


EF1092 amino acid residues 28-438


===0===MKNARWLSIC VMLLALFGFS QQALAEASQA=SVQVTLHKLL=FPDGQLPEQQ
(SEQ ID NO: 11)


==50===QNTGEEGTLL=QNYRGLNDVT=YQVYDVTDPF=YQLRSEGKTV=QEAQRQLAET


=100===GATNRKPIAE=DKTQTINGED=GVVSFSLASK=DSQQRDKAYL=FVEAEAPEVV


=150===KEKASNLVVI=LPVQDPQGQS=LTHIHLYPKN=EENAYDLPPL=EKTVLDKQQG


=200===FNQGEHINYQ=LTTQIPANIL=GYQEFRLSDK=ADTTLTLLPE=SIEVKVAGKT


=250===VTTGYTLTTQ=KHGFTLDFSI=KDLQNFANQT=MTVSYQMRLE=KTAEPDTAIN


=300===NEGQLVTDKH=TLTKRATVRT=GGKSFVKVDS=ENAKITLPEA=VFIVKNQAGE


=350===YLNETANGYR=WQKEKALAKK=FTSNQAGEFS=VKGLKDGQYF=LEEISAPKGY


=400===LLNQTEIPFT=VGKNSYATNG=QRTAPLHVIN=KKVKESGFLP=KTNEERSIWL


=450===TIAGLLIIGM=VVIWLFYQKQ=KRGERK


 


EF1093 (V583): Nucleotide Sequence


===0===ATGAAGCAAT=TAAAAAAAGT=TTGGTACACC=GTTAGTACCT=TGTTACTAAT
(SEQ ID NO: 12)


==50===TTVGCCACTT=TTCACAAGTG=TATTAGGGAC=AACAACTGCA=TTTGCAGAAG


=100===AAAATGGGGA=GAGCGCACAG=CTCGTGATTC=ACAAAAAGAA=AATGACGGAT


=150===TTACCAGATC=CGCTTATTCA=AAATAGCGGG=AAAGAAATGA=GCGAGTTTGA


=200===TAAATATCAA=GGACTGGCAG=ATGTGACGTT=TAGTATTTAT=AACGTGACGA


=250===ACGAATTTTA=CGAGCAACGA=GCGGCAGGCG=CAAGCGTTGA=TGCAGCTAAA


=300===CAAGCTGTCC=AAAGTTTAAC=TCCTGGGAAA=CCTGTTGCTC=AAGGAACCAC


=350===CGATGCAAAT=GGGAATGTCA=CTGTTCAGTT=ACCTAAAAAA=CAAAATGGTA


=400===AAGATGCAGT=GTATACCATT=AAAGAAGAAC=CAAAAGAGGG=TGTAGTTGCT


=450===GCTACGAATA=TGGTGGTGGC=GTTCCCAGTT=TACGAAATGA=TCAAGCAAAC


=500===AGATGGTTCC=TATAAATATG=GAACAGAAGA=ATTAGCGGTT=GTTCATATTT


=550===ATCCTAAAAA=TGTGGTAGCC=AATGATGGTA=GTTTACATGT=GAAAAAAGTA


=600===GGAACTGCTG=AAAATGAAGG=ATTAAATGGC=GCAGAATTTG=TTATTTCTAA


=650===AAGCGAAGGC=TCACCAGGCA=CAGTAAAATA=TATCCAAGGA=GTCAAAGATG


=700===GATTATATAC=ATGGACAACG=GATAAAGAAC=AAGCAAAACG=CTTTATTACT


=750===GGGAAAAGTT=ATGAAATTGG=CGAAAATGAT=TTCACAGAAG=CAGAGAATGG


=800===AACGGGAGAA=TTAACAGTTA=AAAATCTTGA=GGTTGGTTCG=TATATTTTAG


=850===AAGAAGTAAA=AGCTCCAAAT=AATGCAGAAT=TAATTGAAAA=TCAAACAAAA


=900===ACACCATTTA=CAATTGAAGC=AAACAATCAA=ACACCTGTTG=AAAAAACAGT


=950===CAAAAATGAT=ACCTCTAAAG=TTGATAAAAC=AACACCAAGC=TTAGATGGTA


1000===AAGATGTGGC=AATTGGCGAA=AAAATTAAAT=ATCAAATTTC=TGTAAATATT


1050===CCATTGGGGA=TTGCAGACAA=AGAAGGCGAC=GCTAATAAAT=ACGTCAAATT


1100===CAATTTAGTT=GATAAACATG=ATGCAGCCTT=AACTTTTGAT=AACGTGACTT


1150===CTGGAGAGTA=TGCTTATGCG=TTATATGATG=GGGATACAGT=GATTGCTCCT


1200===GAAAATTATC=AAGTGACTGA=ACAAGCAAAT=GGCTTCACTG=TCGCCGTTAA


1250===TCCAGCGTAT=ATTCCTACGC=TAACACCAGG=CGGCACACTA=AAATTCGTTT


1300===ACTTTATGCA=TTTAAATGAA=AAAGCAGATC=CTACGAAAGG=CTTTAAAAAT


1350===GAGGCGAATG=TTGATAACGG=TCATACCGAC=GACCAAACAC=CACCAACTGT


1400===TGAAGTTGTG=ACAGGTGGGA=AACGTTTCAT=TAAAGTCGAT=GGCGATGTGA


1450===CAGCGACACA=AGCCTTGGCG=GGAGCTTCCT=TTGTCGTCCG=TGATCAAAAC


1500===AGCGACACAG=CAAATTATTT=GAAAATCGAT=GAAACAACGA=AAGCAGCAAC


1550===TTGGGTGAAA=ACAAAAGCTG=AAGCAACTAC=TTTTACAACA=ACGGCTGATG


1600===GATTAGTTGA=TATCACAGGG=CTTAAATACG=GTACCTATTA=TTTAGAAGAA


1650===ACTGTAGCTC=CTGATGATTA=TGTCTTGTTA=ACAAATCGGA=TTGAATTTGT


1700===GGTCAATGAA=CAATCATATG=GCACAACAGA=AAACCTAGTT=TCACCAGAAA


1750===AAGTACCAAA=CAAACACAAA=GGTACCTTAC=CTTCAACAGG=TGGCAAAGGA


1800===ATCTACGTTT=ACTTAGGAAG=TGGCGCAGTC=TTGCTACTTA=TTGCAGGAGT


1850===CTACTTTGCT=AGACGTAGAA=AAGAAAATGC=T


 


EF1093 amino acid residues 33-592


===0===MKQLKKVWYT=VSTLLLILPL=FTSVLGTTTA=FAEENGESAQ=LVIHKKKMTD
(SEQ ID NO: 13)


==50===LPDPLIQNSG=KEMSEFDKYQ=GLADVTFSIY=NVTNEFYEQR=AAGASVDAAK


=100===QAVQSLTPGK=PVAQGTTDAN=GNVTVQLPKK=QNGKDAVYTI=KEEPKEGVVA


=150===ATNMVVAFPV=YEMIKQTDGS=YKYGTEELAV=VHIYPKNVVA=NDGSLHVKKV


=200===GTAENEGLNG=AEFVISKSEG=SPGTVKYIQG=VKDGLYTWTT=DKEQAKRFIT


=250===GKSYEIGEND=FTEAENGTGE=LTVKNLEVGS=YILEEVKAPN=NAELIENQTK


=300===TPFTIEANNQ=TPVEKTVKND=TSKVDKTTPS=LDGKDVAIGE=KIKYQISVNI


=350===PLGIADKEGD=ANKYVKFNLV=DKHDAALTFD=NVTSGEYAYA=LYDGDTVIAP


=400===ENYQVTEQAN=GFTVAVNPAY=IPTLTPGGTL=KFVYFMHLNE=KADPTKGFKN


=450===EANVDNGHTD=DQTPPTVEVV=TGGKRFIKVD=GDVTATQALA=GASFVVRDQN


=500===SDTANYLKID=ETTKAATWVK=TKAEATTFTT=TADGLVDITG=LKYGTYYLEE


=550===TVAPDDYVLL=TNRIEFVVNE=QSYGTTENLV=SPEKVPNKHK=GTLPSTGGKG


=600===IYVYLGSGAV=LLLIAGVYFA=RRRKENA


 


Efae2926: Nucleotide Sequence


===0===ATGACGACCA=CAGGGAAGAA=ACTGAAAGTT=ATTTTCATGC=TGATAATATT
(SEQ ID NO: 14)


==50===GAGTTTATCA=AACTTTGTGC=CATTATCTGC=AATAGCAGAC=ACTACAGATG


=100===ATCCAACAGT=TTTAGAAACA=ATTTCAGCTG=AAGTCATTTC=GGATCAGTCT


=150===GGAAAAAAAG=CACTGAACAT=CAAGCTAAAT=GCGAATAACA=CCAGTGCTGA


=200===AAAGATAGAA=AAAGAAATTG=GTCTAGTCGA=AAATTACTTA=AGTGATGTGG


=250===AAAGAAAAGA=AGGAGATGGC=TATGCTTATC=AGGTAAATAG=CGGGAAAATT


=300===ACGTTGGAAA=TCTCATCAAA=CACTAAACAA=ACTATCGATC=TGAGTTTTCC


=350===AATCGATCCA=GCACTTTACC=ACAGCCAGGC=AAACAAGCTG=ATCGTCGATA


=400===ATAAAGAATA=TGACATTATT=GATGAGACAG=AAAATAAGAA=AGATACAGAT


=450===GTGTCAGTAC=CAAAGCCAGA=CGAAATAGAA=GAAGAATCAT=CAAAAGAAAA


=500===CGAAAATTCT=GTCAGCCCAT=TTACATTGCC=TACATTATCC=TTGCCAGCTG


=550===TGAGTGTGCC=ATCTAATCAA=ACGATTCCTA=CAGAATATAC=AACAGATGAT


=600===CAGGGCACTT=ATCCTAAAGC=CAGTTGGCAA=CCTACAGGAA=ATACAAATGT


=650===TCTTGATCAT=CAAGGCAATA=AAAACGGAAC=AAATCAATGG=GATGGTATAA


=700===ATTCTTGGAA=TGGAGATCCT=AATGATCGGA=CCCATTCGTA=TATCGAATAT


=750===GGAGGAACCG=GTAATCAAGC=AGACTATGCG=ATACGAAAGT=ATGCAAAGGA


=800===AACAAGTACA=CCCGGATTGT=TTGATGTTTA=TTTGAATGCT=CGTGGAAATG


=850===TACAAAAAGA=TATCACGCCT=CTTGATCTCG=TATTGGTCGT=AGACTGGTCA


=900===GGAAGTATGA=ACGACAATAA=TCGGATCGGT=GAAGTAAAGA=TTGGTGTCGA


=950===TCGTTTTGTC=GATACTTTAG=CAGATAGCGG=TATCACAGAC=AAAATCAATA


1000===TGGGATATGT=CGGCTACTCA=AGCGAAGGAT=ATAGCTACAG=TAACGGTGCA


1050===GTACAGATGG=GTTCATTTGA=TTCAGTGAAA=AATCAAGTAA=AATCCATTAC


1100===ACCTTCACGG=ACAAATGGTG=GTACTTTTAC=ACAAAAAGCA=CTAAGAGATG


1150===CAGGAAGCAT=GCTATCCGTT=CCAAATGGAC=ATAAAAAAGT=GATCGTTTTG


1200===CTGACGGATG=GTGTACCAAC=ATTTTCCTAT=AAAGTACAGC=GGGTACACGC


1250===ACAATCAAGC=AGCAATTATT=ACGGAACTCA=GTTTTCTAAT=ACGCAAGATC


1300===GGCCGGGAAA=TACTTCTCTA=ATCTCAAGAA=TCTATGATGC=ACCTGACCAA


1350===AACAATCTAT=CCAGAAGAAT=CGACAGTACG=TTTATCGCAA=CCATCGGAGA


1400===AGCGATGGCA=CTCAAAGAAC=GAGGAATCGA=AATACATGGT=CTTGGCATCC


1450===AACTTCAAAG=CGATCCGGCA=GCTGGTCTCT=CAAAAGCAGA=AGTAGAGTCT


1500===CGTATGCGAC=AAATGGTTTC=ATCAGATGAA=AAAGGCGATC=TTTACTATGA


1550===ATCAGCTGAT=CATGCAACAG=ATATCTCTGA=ATACCTAGCC=AAAAAAGCTG


1600===TACAGATCTC=AGCAACTGTA=AGCAATGGAC=AAATAAATGA=TCCAATCGCA


1650===GAACCATTCA=TTTATCAGCC=TGGTACACTT=TCAGTCAAGA=GTGTGGGGAC


1700===AAGTCCTACA=ACGGTCACTC=CATCTATTTC=CATAGAAGGA=AATACCATCA


1750===AGAGCAATCA=GATCTATTTA=GGAAAAGACC=AAGAAATCCA=AATCCATTAC


1800===CAAGTGAGAA=TCCAAACAGA=AAATGAGGAC=TTCCATCCAA=ATTTCTGGTA


1850===TCAAATGAAC=GGCAGGACAA=CTTTCCAGCC=AAACATTGAT=ACCAATGAAT


1900===TAGCTGAATT=CGGTATACCA=TCTGCTAAAG=CTCCCGGAGT=CAGTCTTCAC


1950===ATCAAAAAGT=TATGGGAAGA=ATTTGACAAC=AATCTAGCTG=ATCGTCCAGA


2000===TCAAGTTACT=TTTGAGATTC=AACGGGAACA=TACGACAAAT=GCTGCAGCTT


2050===GGAAAAACGG=ATATATTCGA=ATCATTAAAC=CAGCTAAAGA=TACAACAAAT


2100===ACGTGGGAAC=GTGCAGACAT=TGACAAATTA=TCTGCAAATA=GCGGAGAAAG


2150===TTATCAAGAG=ATATTATCAC=TACCTCAATA=CAATAATCAA=GGTCAAGCAT


2200===TCAGTTACCA=AACAATCAAA=GAATTACCTG=TACCAGGATA=CGATTCTCAA


2250===CAAATAGATG=CAATGACATG=GAAAAATACT=AAACAATTCA=CACCGTTAAA


2300===CTTGAAAATA=ACGAAAAATT=CCTCTACAGG=TGAAAAGGAT=CTTATTGGCG


2350===CTGTTTTCAA=ATTAACAGGA=GATTCTATTG=ATACTTTACT=AACAGATCAT


2400===GGCGACGGAA=CCTATTCTCT=TCCAGAAAAT=GTCAAATTGC=AAAAAGAAAT


2450===GACCTATACG=CTGACAGAAA=CAAAAGCTCC=AGAAGGGCAT=GGATTAAGCA


2500===AAAAGACTAC=TTGGGAAATC=AAGATCGCTT=CTGATGGTAC=GGTAACCATT


2550===GATGGAAAAA=CAGTCACTAC=TTCCGATGAT=ACGATCCAGT=TGACTATTGA


2600===AAATCCTTTT=GTTGAAGTTC=CTGTAGCAGT=ACGTAAGTAT=GCGATGCAAG


2650===GGACGGACAA=AGAGATAAAT=CTTAAAGGAG=CAGCATTTTC=CCTACAGAAA


2700===AAAGAAGCAA=ATGGTACTTA=TCAGCCAATT=GACAGCCAAA=CAACGAATGA


2750===AAAAGGTCTT=GCCAGTTTTG=ATTCACTCAC=ACCTGGTAAA=TATCGAGTCG


2800===TTGAAACAGC=TGGTCCTGCC=GGATATGATA=CTTCGCCGGG=AAATTATGAA


2850===TTCCAAATCG=ATAAATATGG=AAAAATCATT=TACACGGGAA=AAAATACCGA


2900===GATGACAAAT=AATGTATGGA=CGCTCACTCA=TCAAAATCGA=CTAAAAGCGT


2950===TTGATCTAAC=GGTACACAAA=AAAGAAGACA=ACGGACAGAC=ATTAAAAGGA


3000===GCAAAATTCA=GACTGCAGGG=ACCAGAAATG=GACTTAGAAT=CGCCAAAAGA


3050===TGGACAAGAA=ACAGATACCT=TTCTATTCGA=AAATTTAAAA=CCTGGAACTT


3100===ATACGCTGAC=CGAAACTTTT=ACACCAGAAG=GATACCAAGG=TCTAAAAGAG


3T50===CCAGTTACTA=TAGTTATACA=CGAAGATGGG=TCAATTCAAG=TGGATGGACA


3200===AGATCATGAA=TCTGTTCTGT=CACCAGGAGC=CAAAAACAAC=CAGATTTCTT


3250===TAGACATGAC=GAATCAGGCA=AAAGTACCAT=TACCTGAAAC=GGGAGGAATT


3300===GGCCGTTTAG=GAATCTATCT=AGTAGGGATG=ATTGGTTGTG=CGTTTTCTAT


3350===TTGGTATCTT=TTTTTGAAAA=AAGAAAGAGG=GGGCAGC


 


Efae2926: amino acid residues 53-734


===0===MTTTGKKLKV=IFMLIILSLS=NFVPLSAIAD=TTDDPTVLET=ISAEVISDQS
(SEQ ID NO: 15)


==50===GKKALNIKLN=ANNTSAEKIE=KEIGLVENYL=SDVERKEGDG=YAYQVNSGKI


=100===TLEISSNTKQ=TIDLSFPIDP=ALYHSQANKL=IVDNKEYDII=DETENKKDTD


=150===VSVPKPDEIE=EESSKENENS=VSPFTLPTLS=LPAVSVPSNQ=TIPTEYTTDD


=200===QGTYPKASWQ=PTGNTNVLDH=QGNKNGTNQW=DGINSWNGDP=NDRTHSYIEY


=250===GGTGNQADYA=IRKYAKETST=PGLFDVYLNA=RGNVQKDITP=LDLVLVVDWS


=300===GSMNDNNRIG=EVKIGVDRFV=DTLADSGITD=KINMGYVGYS=SEGYSYSNGA


=350===VQMGSFDSVK=NQVKSITPSR=TNGGTFTQKA=LRDAGSMLSV=PNGHKKVIVL


=400===LTDGVPTFSY=KVQRVHAQSS=SNYYGTQFSN=TQDRPGNTSL=ISRIYDAPDQ


=450===NNLSRRIDST=FIATIGEAMA=LKERGIEIHG=LGIQLQSDPA=AGLSKAEVES


=500===RMRQMVSSDE=KGDLYYESAD=HATDISEYLA=KKAVQISATV=SNGQINDPIA


=550===EPFIYQPGTL=SVKSVGTSPT=TVTPSISIEG=NTIKSNQIYL=GKDQEIQIHY


=600===QVRIQTENED=FHPNFWYQMN=GRTTFQPNID=TNELAEFGIP=SAKAPGVSLH


=650===IKKLWEEFDN=NLADRPDQVT=FEIQREHTTN=AAAWKNGYIR=IIKPAKDTTN


=700===TWERADIDKL=SANSGESYQE=ILSLPQYNNQ=GQAFSYQTIK=ELPVPGYDSQ


=750===QIDAMWIKNT=KQFTPLNLKI=TKNSSTGEKD=LIGAVFKLTG=DSIDTLLTDH


=800===GDGTYSLPEN=VKLQKEMTYT=LTETKAPEGH=GLSKKTTWEI=KIASDGTVTI


=850===DGKTVTTSDD=TIQLTIENPF=VEVPVAVRKY=AMQGTDKEIN=LKGAAFSLQK


=900===KEANGTYQPI=DSQTTNEKGL=ASFDSLTPGK=YRVVETAGPA=GYDTSPGNYE


=950===FQIDKYGKII=YTGKNTEMTN=NVWTLTHQNR=LKAFDLTVHK=KEDNGQTLKG


1000===AKFRLQGPEM=DLESPKDGQE=TDTFLFENLK=PGTYTLTETF=TPEGYQGLKE


1050===PVTIVIHEDG=SIQVDGQDHE=SVLSPGAKNN=QISLDITNQA=KVPLPETGGI


1100===GRLGIYLVGM=IGCAFSIWYL=FLKKERGGS


 


Efae2925: Nucleotide Sequence


===0===ATGAAAAAAC=TTGGTTGGCT=TAGTATGTGT=CTCTTCTTGT=TACTATTTAA
(SEQ ID NO: 16)


==50===ACCAGCTTTT=ACTCAGGTAG=CAACAGAAAC=AGAAACAGAA=ATGGTTCAGA


=100===TTACTTTACA=CAAATTGCTT=TTCCCAAACG=GGCAACTGCC=GAAAAATCAT


=150===CCAAATGACG=GACAAGAAAA=AGCTTTATTA=CAAACGTATC=GAGGATTAAA


=200===TGGTGTCACA=TTCCAAGTTT=ATGATGTCAC=AGATTCTTTT=TACCATCTAC


=250===GGGAAAAGGG=CAAAACGGTA=GAAGAAGCAC=AAGCAGAGAT=CGCAAAAAAC


=300===GGTGCGTCTT=CCGGTATGTT=TACCGCAGAA=GCAACAACTA=CAACTCTTAA


=350===CAACGAAGAT=GGTATCGCTT=CTTTTTCTCT=GGCCGCTAAA=GATCAAGAAA


=400===AAAGAGATAA=AGCGTATCTT=TTCATTGAAT=CCAAAGTACC=AGAAGTCGTC


=450===AAAGAAAAGG=CAGAGAATAT=GGTAGTTGTT=CTTCCTGTAC=ATGGACAAAA


=500===CAATCAAAAA=CTTTCAACTA=TCCATTTGTA=TCCTAAAAAT=GAAGAAAACG


=550===ACTACCCTGA=TCCACCTTTT=GAGAAGGTAT=TAGAAGAGCC=TAGAAATGAT


=600===TTTACGATTG=GTGAAAAAAT=CACTTATTCC=TTGCATACGA=CAATTCCTGT


=650===AAATATCCTT=GACTATCAAA=AGTTCGAATT=GTCAGATAGT=GCGGATGAAG


=700===CATTAACGTT=TTTACCTAAT=AGTTTAACGA=TTTCATCGAA=TGGAGAAAAG


=750===CTGACAGAAG=GCTTTGTCAT=ACACAAGAAA=CCTCACGGAT=TTGATGTTTT


=800===ATTTTCGATC=CCTTCGTTGG=AAAAATATGC=TGGAAAAAAA=CTGACCATTT


=850===CTTATCAGAT=GCAGCTAAGC=AGTACAGCAC=AGGCGAACAA=GGAAATCAAC


=900===AACAACGGAA=CACTGGATTT=TGGTTTTGGT=GTCAGTACAA=AGAAAGTCTC


=950===TGTATATACA=GGGAGTAAGC=AATTTGTCAA=AATCGAGACA=AATAAACCAG


1000===ATAAACGATT=AGCTGGCGCA=GTATTCCTTA=TTAAAAACAA=AGCAGGAAAT


1050===TACCTCCAGC=AAACAGCCAA=CGGATACAAG=TGGACAAAGA=ACGAATCAGA


1100===TGCGCTTCAC=CTGATTTCCG=ATAAAAATGG=CGCTTTTTCA=ATTTCCGGGT


1150===TGAAAACAGG=AAGTTATCGA=TTAAAAGAGA=TCGAAGCACC=TTCTGGTTAT


1200===ATTTTAAGTG=AAACAGAAAT=TCCGTTTACC=ATTTCAACTT=TTCTTTCTGA


1250===GGATAAAGAG=GCGGACAGTA=TATTGAAAGT=AGTCAATAAA=AAAGAAAATA


1300===GCCGTCCATT=TCTTCCAAAA=ACAAACGAAA=CGAAAAATAC=ACTTTTAGGC


1350===GTTGTTGGTA=TGGTATTCGC=AAGCTTTGCA=ATCTGGTTGT=TTATCAAAAA


1400===AAGAACAGGA=GTGAAAAAAT=GA


 


Efae 2925: amino acid residues 30-429


===0===MKKLGWLSMC=LFLLLFKPAF=TQVATETETE=MVQITLHKLL=FPNGQLPKNH
(SEQ ID NO: 17)


==50===PNDGQEKALL=QTYRGLNGVT=FQVYDVTDSF=YHLREKGKTV=EEAQAEIAKN


=100===GASSGMFTAE=ATTTTLNNED=GIASFSLAAK=DQEKRDKAYL=FIESKVPEVV


=150===KEKAENMVVV=LPVHGQNNQK=LSTIHLYPKN=EENDYPDPPF=EKVLEEPRND


=200===FTIGEKITYS=LHTTIPVNIL=DYQKFELSDS=ADEALTFLPN=SLTISSNGEK


=250===LTEGFVIHKK=PHGFDVLFSI=PSLEKYAGKK=LTISYQMQLS=STAQANKEIN


=300===NNGTLDFGFG=VSTKKVSVYT=GSKQFVKIET=NKPDKRLAGA=VFLIKNKAGN


=350===YLQQTANGYK=WTKNESDALH=LISDKNGAFS=ISGLKTGSYR=LKEIEAPSGY


=400===ILSETEIPFT=ISTFLSEDKE=ADSILKVVNK=KENSRPFLPK=TNETKNTLLG


=450===VVGMVFASFA=IWLFIKKRTG=VKK


 


Efae 2924: Nucleotide sequence


===0===ATGAAAAATC=ATAAAAAAAT=AAACGTTATG=TTAGGAGTCC=TTTTCCTTAT
(SEQ ID NO: 18)


==50===TTTACCATTA=CTCACAAACA=GCTTCGGCGC=AAAAAAAGTG=TTTGCAGAGG


=100===AGACAGCAGC=TCAAGTCATC=CTTCATAAAA=AGAAAATGAC=TGATTTACCC


=150===GATCCTTTAA=TCCAAAACAG=CGGGAAAGAA=ATGAGCGAAT=TCGATCAATA


=200===CCAAGGATTA=GCCGATATTT=CATTTTCAGT=TTATAACGTC=ACTCAAGAAT


=250===TTTATGCGCA=ACGAGATAAA=GGAGCGTCCG=TGGATGCAGC=AAAACAAGCA


=300===GTCCAGTCTT=TGACTCCTGG=TACACCAGTT=GCTTCAGGAA=CGACAGATGC


=350===TGATGGAAAT=GTCACTTTAT=CTTTACCTAA=AAAACAAAAT=GGGAAAGATG


=400===CAGTCTACAC=GATCAAAGAA=GAACCAAAAG=ACGGAGTGTC=AGCTGCCGCA


=450===AACATGGTTT=TAGCTTTCCC=TGTATATGAG=ATGATCAAAC=AAGCAGATGG


=500===CTCTTATAAA=TACGGGACAG=AAGAACTAGA=TACTATCCAT=CTCTACCCTA


=550===AAAATACAGT=CGGTAATGAT=GGAACGTTGA=AAGTTACAAA=AATCGGTACT


=600===GCCGAAAACG=AAGCACTAAA=TGGAGCAGAA=TTTATTATTT=CTAAAGAAGA


=650===AGGAACACCA=AGCGTCAAAA=AATACATCCA=AAGTGTCACA=GATGGATTGT


=700===ACACTTGGAC=AACTGATCAA=ACCAAAGCCA=AACATTTCAT=TACTGGTCAT


=750===TCTTATGACA=TCGGCAACAA=TGACTTTGCC=GAGGCATCTA=TTGAAAAAGG


=800===CCAGTTGATC=GTTAATCATT=TAGAAGTTGG=AAAATATAAT=TTAGAAGAAG


=850===TAAAAGCTCC=TGATAATGCG=GAAATGATTG=AAAAGCAAAC=AATCACGCCT


=900===TTTGAGATCC=TGGCAAATAG=CCAAACACCA=GTAGAAAAGA=CCATCAAAAA


=950===TGATACGTCT=AAAGTTGATA=AAACAACACC=TCAATTGAAT=GGAAAAGATG


1000===TCGCAATCGG=TGAAAAAATT=CAATATGAGA=TTTCTGTCAA=TATCCCATTA


1050===GGTATCGCTG=ATAAAGAAGG=AACGCAAAAC=AAGTACACAA=CATTCAAACT


1100===TATCGATACT=CATGACGCTG=CTTTAACATT=TGATAATGAT=TCTTCAGGAA


1150===CGTATGCTTA=TGCCTTATAT=GATGGAAATA=AAGAAATCGA=CCCAGTAAAT


1200===TATTCTGTCA=CTGAGCAAAC=AGACGGATTC=ACGGTTTCAG=TTGATCCGAA


1250===TTATATTCCT=TCATTAACTC=CTGGCGGTAC=ATTGAAATTC=GTTTACTATA


1300===TGCATTTGAA=CGAAAAAGCA=GATCCAACCA=AAGGATTTTC=TAACCAAGCA


1350===AATGTCGATA=ACGGGCATAC=AAATGATCAA=ACACCACCGT=CAGTCGATGT


1400===CGTTACTGGG=GGCAAACGAT=TTGTTAAAGT=AGATGGTGAC=GTTACATCAG


1450===ACCAAACACT=TGCTGGAGCA=GAATTCGTCG=TTCGTGATCA=AGATAGTGAC


1500===ACAGCGAAAT=ATTTATCGAT=CGACCCATCC=ACAAAAGCCG=TCAGCTGGGT


1550===ATCGGCGAAA=GAATCAGCAA=CGGTTTTTAC=AACCACAAGT=AACGGTTTAA


1600===TCGATGTGAC=AGGTCTAAAA=TATGGCACGT=ACTATCTGGA=AGAAACGAAA


1650===GCGCCAGAAA=AATATGTTCC=ATTAACAAAC=CGTGTAGCAT=TTACTATCGA


1700===TGAACAATCT=TATGTAACAG=CAGGACAGTT=GATTTCTCCT=GAAAAAATAC


1750===CAAATAAACA=CAAAGGTACA=CTTCCTTCAA=CAGGCGGTAA=GGGAATCTAT


1800===GTGTATATCG=GTGCAGGAGT=AGTCCTTCTA=CTGATTGCTG=GACTGTACTT


1850===TGCTAGACGC=AAGCACAGTC=AGATTTAG


 


Efae 2924: amino acid residues 55-588


===0===MKNHKKINVM=LGVLFLILPL=LTNSFGAKKV=FAEETAAQVI=LHKKKMTDLP
(SEQ ID NO: 19)


==50===DPLIQNSGKE=MSEFDQYQGL=ADISFSVYNV=TQEFYAQRDK=GASVDAAKQA


=100===VQSLTPGTPV=ASGTTDADGN=VTLSLPKKQN=GKDAVYTIKE=EPKDGVSAAA


=150===NMVLAFPVYE=MIKQADGSYK=YGTEELDTIH=LYPKNTVGND=GTLKVTKIGT


=200===AENEALNGAE=FIISKEEGTP=SVKKYIQSVT=DGLYTWTTDQ=TKAKHFITGH


=250===SYDIGNNDFA=EASIEKGQLI=VNHLEVGKYN=LEEVKAPDNA=EMIEKQTITP


=300===FEILANSQTP=VEKTIKNDTS=KVDKTTPQLN=GKDVAIGEKI=QYEISVNIPL


=350===GIADKEGTQN=KYTTFKLIDT=HDAALTFDND=SSGTYAYALY=DGNKEIDPVN


=400===YSVTEQTDGF=TVSVDPNYIP=SLTPGGTLKF=VYYMHLNEKA=DPTKGFSNQA


=450===NVDNGHTNDQ=TPPSVDVVTG=GKRFVKVDGD=VTSDQTLAGA=EFVVRDQDSD


=500===TAKYLSIDPS=TKAVSWVSAK=ESATVFTTTS=NGLIDVTGLK=YGTYYLEETK


=550===APEKYVPLTN=RVAFTIDEQS=YVTAGQLISP=EKIPNKHKGT=LPSTGGKGIY


=600===VYIGAGVVLL=LIAGLYFARR=KHSQI






Protein Expression and Purification

Using PCR (the oligonucleotides used in the PCR reaction are shown in Table 3), the A domains from EF0089, EF1091, EF1092, EF1093, EF1099, EF1269, EF1824, EF2224, and EF3023 were amplified from E. faecalis V583 or E. faecalis EF1 (EF1099) genomic DNA and subcloned into the E. coli expression vector PQE-30 (Qiagen). One liter culture of E. coli M15(pREP4) cultures harboring appropriate pQE-30 based constructs were grown to OD600=0.6 with an initial 2% inoculation from overnight cultures. After 2-3 h induction with 0.4 mM isopropyl-beta-d-thiogalactoside (IPTG), cells were collected with centrifugation, resuspended in 10 mM Tris-Cl, 100 mM NaCl, pH 7.9 and stored at −80 C.
To lyse the cells and release the expressed protein, cells were passed twice through French Press with a gauge pressure setting at 1200 PSI to give an estimated internal cell pressure of 20,000 PSI. The lysate was centrifuged at RCFmax of 165,000×g and the supernatant was filtered through a 0.45 □m filter. The volume was adjusted to 15 ml with 10 mM Tris-Cl, 100 mM NaCl, pH 7.9 and 0.2 M imidazole in the same buffer was added to increase the imidazole concentration to 6.5 mM in order to minimize non-specific binding. The sample was loaded to a nickel affinity chromatography column (HiTrap chelating, Pharmacia) connected to an FPLC system (Pharmacia) and previously equilibrated with 10 mM Tris-Cl, 100 mM NaCl, pH 7.9. Bound protein was eluted with a linear gradient of 0-100 mM imidazole in 10 mM Tris-Cl, 100 mM NaCl, pH 7.9 over 100-200 ml. Protein-containing fractions were analyzed in SDS-PAGE (FIG. 2) and dialyzed against 25 mM Tris-Cl, 1 mM EDTA, pH 6.5-9 (depending on pI of protein purified) before applying the samples to an ion-exchange column (HiTrap Q, Pharmacia) for further purification. Bound protein was eluted with a linear gradient of 0-0.5 M NaCl in 25 mM Tris-Cl, 1 mM EDTA, pH 6.5-9 over 100 ml. Finally, protein samples were dialyzed extensively against PBS and stored at +4° C.
Alternatively EF1091, EF1092, and EF1093 were expressed in shake flasks or in bioreactors, the cells were harvested by centrifugation and the cell paste frozen at −80° C. Cells were lysed in 1×PBS (10 mL of buffer/1 g of cell paste) using 2 passes through a microfluidizer at 10,000 psi. Lysed cells were spun down at 17,000 rpm for 30 minutes to remove cell debris. Supernatant was passed over a 5-mL HiTrap Chelating (Pharmacia) column charged with 0.1M NiCl2. After loading, the column was washed with 5 column volumes of 10 mM Tris, pH 8.0, 100 mM NaCl (Buffer A). Protein was eluted using a 0-100% gradient of 10 mM Tris, pH 8.0, 100 mM NaCl, 500 mM imidazole (Buffer B). Protein containing fractions were dialyzed in 1×PBS.
Example 3
MSCRAMM® Genes Common to E. faecalis and E. faecium PCR Analysis
Primers for flanking regions of sequences above were used to amplify 1μg genomic DNA from each E. faecalis strain. PCR products from 5 E. faecalis strains in Table 1 were sequenced and compared to the TIGR database sequence. Primers used to amplify the enterococcal MSCRAMM® A-domain gene products are shown below.












Protein
5′=Primer
3′=Primer







ACE40
GAATTGAGCAAAAGTTCAATC
GTCTGTCTTTTCACTTGTTTC



G (SEQ ID NO: 44)
TGTTG(SEQ ID NO: 51)


 


EF1091
CAAGTAAAAAAGCCGGTACAG
AAAGGAACCTTTGCTTGGTTC



C(SEQ ID NO: 45)
(SEQ ID NO: 52)


 


EF1092
TCGCAAGCAAGCGTTCAAG
AAGCCTGACTCTTTTACTTTT



(SEQ ID NO: 46)
TTATTG(sEQ ID NO: 53)


 


EF1093
GAGAGCGCACAGCTCGTG
GGTACCTTTGTGTTTGTTTGG



(SEQ ID NO: 47)
TAC(SEQ ID NO: 54)


 


Efae2924
CGGGATCCCAAAACAGCGGGA
CCCAAGCTTTCATGTACCTTT



AAGAAATGAGCGA
GTGTTTATTTGG



(SEQ ID NO: 48)
(SEQ ID NO: 55)


 


Efae2925
CGGGATCCGAAATGGTTCAGA
TCTGCAGTTCAATTGACTACT



TTACTTTACAC
TTCAATATACTGTC



(SEQ ID NO: 49)
(SEQ ID NO: 56)


 


Efae2926
CGGGATCCAAAGCACTGAACA
CCCAAGCTTTCAGAATGCTTG



TCAAGCTAAATGCG
ACCTTGATTATTGTA



(SEQ ID NO: 50)
(SEQ ID NO: 57)









Homology Among Enterococcal MSCRAMM® Proteins

A blastp search was performed using the AA sequence listed above with the NCBI search engine. The accession number is given for each putative homologue found. Both percent identity and similarity refer to the percentage of AA that match the query sequence exactly while similarity includes conservative AA changes in the matching calculation.







TABLE 4







Comparison of E. faecium homologues of E. faecalis


MSCRAMM ® protein













E. faecalis
E. faecium






Protein
Protein
Accession
%



Similarity
Homologue Name
Number
Identity
%







EF1091
Efae2926
00038011
60
75



EF1092
Efae2925
00038010
48
63



EF1093
Efae2924
00038009
74
83










The “A” domain amino acid sequence from each E. faecalis MSCRAMM® protein was used as a query in a blastp search. Results shown were scored by NCBI computers. Identity is calculated as exact matches between the subject and query sequences while similarity also includes conservative changes in sequence at the same position.
Example 4
Additional Gram Positive Amino Acid Sequences Predicted to Be MSCRAMM® Proteins
List of LPXTG-motif containing cell wall anchored proteins that contain predicted immunoglobulin—like fold. The sequencing center for each genome is indicated in the parenthesis. All the sequence except for those of CNA from S. aureus and Staphylococcus epidermidis can be obtained from TIGR website (www.tir.org), comprehensive microbial resource section. The S. epidermidis RP64A genome is not annotated. However, the nucleotide coordinates of the genes encoding the listed S. epidermidis proteins can be obtained through TIGR website.
Streptococcus pneumoniae TIGR4 (TIGR)


    SP0368
    SP0462
    SP0463
    SP0464

Enterococcus faecalis V583 (TIGR)

    EF2224
    EF1099
    EF1092
    EF3023
    EF1269
    EF0089
    EF1824
    EF1091
    EF1093
    EF1075
    EF1074
    EF1651

Streptococcus mutans UA159 (University of Oklahoma)

    SMU.610
    SMU.987
    SMU.63c

Staphylococcus aureus N315 (Juntendo University, Japan)

    SA2447
    SA2290
    SA2291
    SA2423
    SA0742
    SA0519
    SA0520
    SA0521

Bacillus anthracis Ames (TIGR)

    BA0871
    BA5258










Staphylococcus epidermidis strain RP62A (TIGR)









(SEQ ID NO: 20)









>SERP_GSE_14_6.AA 2402 residues



mknkqgflpnllnkygirklsagtaslligatlvfgingqvkaaetdnivsqngdnktndsessdkelvkseddkts


 


ststdtnlesefdqnnnpssieestnrndedtlnqrtstetekdthvksadtqttnettnknddnattnhtesisdes


 


tyqsddskttqhdnsntnqdtqstlnptskessnkdeatsptpkestsiektnlsndanhqttdevnhsdsdnmt


 


nstpndteneldttqltshdespspqsdnftgftnlmatplnlrndnprinllaatedtkpktykkpnnseysyllndl


 


gydattvkensdlrhagisqsqdntgsviklnltkwlslqsdfvnggkvnlsfaqsdfytqiesitlndvkmdttnng


 


qnwsapingstvrsgligsvtnhdivitlknsqtlsslgysnnkpvylthtwttndgaiaeesiqvasitptldskapnt


 


iqksdftagrmtnkikydssqnsiksvhtfkpnenflqtdyravlyikeqvnkelipyidpnsvklyvsdpdgnpisq


 


dryvngsidndglfdsskineisiknnntsgqlsnartsldrnvffgtlgqsrsytisyklkdgytlesvaskvsaretfd


 


swmevdyldsydsgapnkrllgsyassyidmidrippvapkansittedtsikgtaevdtninltfndgrtlngkvd


 


sngnfsiaipsyyvltgketikitsidkgdnvspaitisvidktppavkaisnktqkvnteiepikieatdnsgqavtnk


 


veglpagmtfdeatntisgtpsevgsyditvtttdengnsetttftidvedttkptvesvadqtqevnteiepikieatd


 


nsgravtnkvdglpdgvtfdeatntisgtpsevgsyditvtttdesgnvtetiftidvedttkptvesiagqtqevntei


 


epikieakdnsgqtvtnkvdglpdgvtfdeatntisgtpsevgsydvtvtttdesgnsetttftievkdttkptvesva


 


dqtqevnteiepikieardnsgqavtnkvdglpdgvtfdeatntisgtpsevgsyditvtttdesgnvtettftievedt


 


tkptvenvadqtqevnteitpitiesednsgqtvtnkvdglpdgvtfdettntisgtpskvgsyditvtttdesgnatet


 


tftievedttkptvenvagqtqeinteiepikieatdnsgqavtnkveglpagvtfdeatntisgtpsevgsytvtvtt


 


mdesgnatettftidvedttkptvesvadqtqevnteitpitiesednsdqavtnkvdglpdgvtfdeatntisgtps


 


evgsytvtvtttdesgnatettftidvedttkptvksvsdqtqevnteitpikieatdnsgqtvtnkvdglpdgitfdeat


 


ntisgtpsevgsyditvtttdesgnatettftinvedttkptvediadqtqevnteiepikieatdnggqavtnkvdglp


 


dgvtfdeatntisgtpsevgsydiivtttdengnsetttftidvedttkptvesvvdqtqevnteitpikieatdnsgqa


 


vankvdglpngvtfdettntisgtpsevgsydiivtttdesgnvtetiftidvedttkptvesiagqtqevnteiepikie


 


atdnsgqavtnkvdglpngvtfdeatntisgtpsevgiytvtvtttdesgnatettftidvedttkptvesvadqtqev


 


nteitpitiesednsgqavtnkveglpagmtfdettntisgtpsevgsytvtvtttdesgnetettftidvedttkptves


 


ianqtqevnteitpikieatdnsgqavtnkvdglpngvtfdettntisgtpsevgsydikvtttdesgnatettftinve


 


dttkptvesvadqtqeinteiepikieardnsgqavtnkvdglpdgvtfdeatntisgtpsevgsyditvtttdesgn


 


atettftidvedttkptveditdqtqeintemtpikieatdnsgqavtnkveglpdgvtfdeatntisgtpsevgkylitit


 


tidkdgntatttltinvidtttpeqptinkvtenstevngrgepgtvvevtfpdgnkvegkvdsdgnyhiqipsettlkg


 


gqpiqviaidkagnkseatttnvidttapeqptinkvtenstevsgrgepgtvvevtfpdgnkvegkvdsdgnyhi


 


qipsderfkvgqqlivkvvdeegnvsepsitmvqkedknseklstvtgtvtknnskslkhkaseqqsyhnkseki


 


knvnkptkivekdmstydysryskdisnknnksatfeqqnvsdinnnqysrnkvnqpvkksrkneinkdlpqtg


 


eenfnkstlfgtlvaslgalllffkrrkkdendeke


 


>SERP_GSE_2_50.AA 892 residues








(SEQ ID NO: 21)









lfglghneakaeentvqdvkdsnmddelsdsndqssneekndvinnsqsintdddnqikkeetnsndaienr



 


skditqsttnvdeneatflqktpqdntqlkeevvkepssvessnssmdtaqqpshttinseasiqtsdneensrv


 


sdfanskiiesntesnkeentieqpnkvredsitsqpssyknidekisnqdellnlpineyenkvrplsttsaqpss


 


krvtvnqlaaeqgsnvnhlikvtdqsitegyddsdgiikahdaenliydvtfevddkvksgdtmtvnidkntvpsdl


 


tdsfaipkikdnsgeiiatgtydntnkqitytftdyvdkyenikahlkltsyidkskvpnnntkldveyktalssvnktitv


 


eyqkpnenrtanlqsmftnidtknhtveqtiyinplrysaketnvnisgngdegstiiddstiikvykvgdnqnlpds


 


nriydyseyedvtnddyaqlgnnndvninfgnidspyiikviskydpnkddyttiqqtvtmqttineytgefrtasyd


 


ntiafstssgqgqgdlppektykigdyvwedvdkdgiqntndnekplsnvlvtltypdgtsksvrtdeegkyqfdgl


 


kngltykitfetpegytptlkhsgtnpaldsegnsvwvtingqddmtidsgfyqtpkyslgnyvwydtnkdgiqgd


 


dekgisgvkvtlkdengniisttttdengkyqfdnlnsgnyivhfdkpsgmtqtttdsgdddeqdadgeevhvtit


 


dhddfsidngyydddsdsdsdsdsdsddsdsdsdsdsdsdsdsdsdsdsdsdsdsdsdsdsdsdsdsd


 


sdsgldnssdkntkdklpdtganedhdskgtllgalfaglgalllgkrrknrknkn


 


>SERP_GSE_9_28.AA 1973 residues








(SEQ ID NO: 22)









mkenkrknnldknntrfsirkyqgygatsvaiigfiiiscfseakadsdkheikshqqsmtnhlttlpsdnqentsn



 


nefnnrnhdishlslnksiqmdelkklikqykainlndkteesiklfqsdlvqaeslinnpqsqqhvdafyhkflnsa


 


gklrkketvsikhersesntyrlgdevrsqtfshirhkrnavsfrnadqsnlstdplkaneinpeiqngnfsqvsggp


 


lptsskrltvvtnvdnwhsystdpnpeypmfytttavnypnfmsngnapygvilgrttdgwnrnvidskvagiyq


 


didvvpgselnvnfistspvfsdgaagaklkisnveqnrvtfdsrlngmgpyptgklsamvnipndinrvrisflpvs


 


stgrvsvqrssrehgfgdnssyyhggsvsdvrinsgsyvvskvtqreyttrpnssndtfaratinlsvenkghnqs


 


kdtyyevilpqnsrlistrggsgnynnatnklsirldnlnpgdrrdisytvdfessspklinlnahllyktnatfrgndgqr


 


tgdnivdlqsiallmnkdvletelneidkfirdlneadftidswsalqekmteggnilneqqnqvalenqasqetinn


 


vtqsleilknnlkyktpsqpiiksnnqipnitispadkadkltityqntdnesasiignklnnqwslnnnipgieidmqt


 


glvtidykavypesvvgandktgnsdasaesritmprkeatplspiveaneervnvviapngeatqiaikyrtpd


 


gqeatlvaskngsswtlnkqidyvnieensgkvtigyqavqpeseviatetkgnsdesaesrvtmprkeatphs


 


piveaneehvnvtiapngeatqiaikyrtpdgqettliaskngsswtlnkqidyvnieensgkvtigyqavqiesev


 


iatetkgnsdasaesritmlrkeatphspiveaneehvnvtiapngeatqiaikyrtpdgqeatlvasknesswtl


 


nkqidhvnidensgkvtigyqavqpeseiiatetkgnsdasaesritmprkeatpipptleasvqeasvtvtpne


 


natkvfikyldindeistiiaskinqqwtlnkdnfgikinpltgkviisyvavqpesdviaiesqgnsdlseesriimptk


 


eeppeppilesdsieakvnifpndeatrivimytslegqeatlvasknesswtlnkqidhvnidensgkvtigyqa


 


vqpeseviatetkgnsdasaesrvtmprkeatphspivetneervnvviapngeatqiaikyrtpdgqettliask


 


ngsswtlnkqidhvnidensgkvtigyqavqpeseiiatetkgnsdasaesritmprkeaiphspiveaneehv


 


nvtiapngettqiavkyrtpdgqeatliasknesswtlnkqidhvnidensgkvtigyqavqpeseviatetkgns


 


dasaesritmpvkektpappisiinesnasveiipqvnvtqlslqyidakgqqqnhiatlnqnqwtlnknvshitvd


 


kntgkvlinyqavypeseviareskgnsdssnvsmvimprktatpkppiikvdemnaslaiipyknntainihyi


 


dkkgiksmvtaiknndqwqldekikyvkidaktgtviinyqivqenseiiataingnsdkseevkvlmpikeftpla


 


plletnykkatvsilpqsnatkldfkyrdkkgdskiiivkrfkniwkaneqisgvtinpefgqvvinyqavypesdila


 


aqyvgnsdasewakvkmpkkelaphspsliydnrnnkiliapnsnatemelsyvdknnqslkvkalkinnrwk


 


fdssvsnisinpntgkivlqpqflltnskiivfakkgnsdasisvslrvpavkkielepmfnvpvlvslnkkriqfddcs


 


gvknclnkqisktqlpdtgysdkasksnilsvlllgfgflsysrkrkekq


 


>|cl|SEPN_5_124.AA 10203 residues








(SEQ ID NO: 23)









MKSKPKLNGRNICSFLLSKCMSYSLSKLSTLKTYNFQITSNNKEKTSRIGVAIALN



 


NRDKLQKFSIRKYAIGTFSTVIAT


 


LVFMGINTNHASADELNQNQKLIKQLNQTDDDDSNTHSQEIENNKQNSSGKTE


 


SLRSSTSQNQANARLSDQFKDTNETSQ


 


QLPTNVSDDSINQSHSEANMNNEPLKVDNSTMQAHSKIVSDSDGNASENKHHK


 


LTENVLAESRASKNDKEKENLQEKDKS


 


QQVHPPLDKNALQAFFDASYHNYRMIDRDRADATEYQKVKSTFDYVNDLLGNN


 


QNIPSEQLVSAYQQLEKALELARTLPQ


 


QSTTEKRGRRSTRSVVENRSSRSDYLDARTEYYVSKDDDDSGFPPGTFFHAS


 


NRRWPYNLPRSRNILRASDVQGNAYITT


 


KRLKDGYQWDILFNSNHKGHEYMYYWFGLPSDQTPTGPVTFTIINRDGSSTST


 


GGVGFGSGAPLPQFWRSAGAINSSVAN


 


DFKHGSATNYAFYDGVNNFSDFARGGELYFDREGATQTNKYYGDENFALLNSE


 


KPDQIRGLDTIYSFKGSGDVSYRISFK


 


TQGAPTARLYYAAGARSGEYKQATNYNQLYVEPYKNYRNRVQSNVQVKNRTL


 


HLKRTIRQFDPTLQRTTDVPILDSDGSG


 


SIDSVYDPLSYVKNVTGTVLGIYPSYLPYNQERWQGANAMNAYQIEELFSQENL


 


QNAARSGRPIQFLVGFDVEDSHHNPE


 


TLLPVNLYVKPELKHTIELYHDNEKQNRKEFSVSKRAGHGVFQIMSGTLHNTVG


 


SGILPYQQEIRIKLTSNEPIKDSEWS


 


ITGYPNTLTLQNAVGRTNNATEKNLALVGHIDPGNYFITVKFGDKVEQFEIRSKP


 


TPPRIITTANELRGNSNHKPEIRVT


 


DIPNDTTAKIKLVMGGTDGDHDPEINPYTVPENYTVVAEAYHDNDPSKNGVLTF


 


RSSDYLKDLPLSGELKAIVYYNQYVQ


 


SNFSNSVPFSSDTTPPTINEPAGLVHKYYRGDHVEITLPVTDNTGGSGLRDVNV


 


NLPQGWTKTFTINPNNNTEGTLKLIG


 


NIPSNEAYNTTYHFNITATDNSGNTTNPAKTFILNVGKLADDLNPVGLSRDQLQL


 


VTDPSSLSNSEREEVKRKISEANAN


 


IRSYLLQNNPILAGVNGDVTFYYRDGSVDVIDAENVITYEPERKSIFSENGNTNK


 


KEAVITIARGQNYTIGPNLRKYFSL


 


SNGSDLPNRDFTSISAIGSLPSSSEISRLNVGNYNYRVNAKNAYHKTQQELNLKL


 


KIVEVNAPTGNNRVYRVSTYNLTND


 


EINKIKQAFKAANSGLNLNDNDITVSNNFDHRNVSSVTVTIRKGDLIKEFSSNLNN


 


MNFLRWVNIRDDYTISWTSSKIQG


 


RNTDGGLEWSPDHKSLIYKYDATLGRQINTNDVLTLLQATAKNSNLRSNINSNE


 


KQLAERGSNGYSKSIIRDDGEKSYLL


 


NSNPIQVLDLVEPDNGYGGRQVSHSNVIYNEKNSSIVNGQVPEANGASAFNIDK


 


VVKANAANNGIMGVIYKAQLYLAPYS


 


PKGYIEKLGQNLSNTNNVINVYFVPSDKVNPSITVGNYDHHTVYSGETFKNTINV


 


NDNYGLNTVASTSDSAITMTRNNNE


 


LVGQAPNVTNSTNKIVKVKATDKSGNESIVSFTVNIKPLNEKYRITTSSSNQTPV


 


RISNIQNNANLSIEDQNRVKSSLSM


 


TKILGTRNYVNESNNDVRSQWSKVNRSGNNATVNVTTTFSDGTTNTITVPVKH


 


VLLEVVPTTRTTVRGQQFPTGKGTSP


 


NDFFSLRTGGPVDARIVWVNNQGPDINSNQIGRDLTLHAEIFFDGETTPIRKDTT


 


YKLSQSIPKQIYETTINGRFNSSGD


 


AYPGNFVQAVNQYWPEHMDFRWAQGSGTPSSRNAGSFTKTVTVVYQNGQTE


 


NVNVLFKVKPNKPVIDSNSVISKGQLNGQ


 


QILVRNVPQNAQVTLYQSNGTVIPNTNTTIDSNGIATVTIQGTLPTGNITAKTSMT


 


NNVTYTKQNSSGIASNTTEDISVF


 


SENSDQVNVTAGMQAKNDGIKIIKGTNYNFNDFNSFISNIPAHSTLTWNEEPNS


 


WKNNIGTTTKTVTVTLPNHQGTRTVD


 


IPITIYPTVTAKNPVRDQKGRNLTNGTDVYNYIIFENNNRLGGTASWKDNRQPDK


 


NIAGVQNLIALVNYPGISTPLEVPV


 


KVWVYNFDFTQPIYKIQVGDTFPKGTWAGYYKHLENGEGLPIDGWKFYWNQQ


 


STGTTSDQWQSLAYTRTPFVKTGTYDVV


 


NPSNWGVWQTSQSAKFIVTNAKPNQPTITQSKTGDVTVTPGAVRNILISGTNDY


 


IQASADKIVINKNGNKLTTFVKNNDG


 


RWTVETGSPDINGIGPTNNGTAISLSRLAVRPGDSIEAIATEGSGETISTSATSEI


 


YIVKAPQPEQVATHTYDNGTFDIL


 


PDNSRNSLNPTERVEINYTEKLNGNETQKSFTITKNNNGKWTINNKPNYVEFNQ


 


DNGKVVFSANTIKPNSQITITPKAGQ


 


GNTENTNPTVIQAPAQHTLTINEIVKEQGQNVTNDDINNAVQVPNKNRVAIKQG


 


NALPTNLAGGSTSHIPVVIYYSDGSS


 


EEATETVRTKVNKTELINARRRLDEEISKENKTPSSIRNFDQAMNRAQSQINTAK


 


SDADQVIGTEFATPQQVNSALSKVQ


 


AAQNKINEAKALLQNKADNSQLVRAKEQLQQSIQPAASTDGMTQDSTRNYKNK


 


RQAAEQAIQHANSVINNGDATSQQIND


 


AKNTVEQAQRDYVEAKSNLRADKSQLQSAYDTLNRDVLTNDKKPASVRRYNEA


 


ISNIRKELDTAKADASSTLRNTNPSVE


 


QVRDALNKINTVQPKVNQAIALLQPKENNSELVQAKKRLQDAVNDIPQTQGMTQ


 


QTINNYNDKQREAERALTSAQRVIDN


 


GDATTQEITSEKSKVEQAMQALTNAKSNLRADKNELQTAYNKLIENVSTNGKKP


 


ASIRQYETAKARIQNQINDAKNEAER


 


ILGNDNPQVSQVTQALNKIKAIQPKLTEAINMLQNKENNTELVNAKNRLENAVND


 


TDPTHGMTQETINNYNAKKREAQNE


 


IQKANMIINNGDATAQDISSEKSKVEQVLQALQNAKNDLRADKRELQTAYNKLIQ


 


NVNTNGKKPSSIQNYKSARRNIENQ


 


YNTAKNEAHNVLENTNPTVNAVEDALRKINAIQPEVTKAINILQDKEDNSELVRA


 


KEKLDQAINSQPSLNGMTQESINNY


 


TTKRREAQNIASSADTIINNGDASIEQITENKIRVEEATNALNEAKQHLTADTTSL


 


KTEVRKLSRRGDTNNKKPSSVSAY


 


NNTIHSLQSEITQTENRANTIINKPIRSVEEVNNALHEVNQLNQRLTDTINLLQPL


 


ANKESLKEARNRLESKINETVQTD


 


GMTQQSVENYKQAKIKAQNESSIAQTLINNGDASDQEVSTEIEKLNQKLSELTN


 


SINHLTVNKEPLETAKNQLQANIDQK


 


PSTDGMTQQSVQSYERKLQEAKDKINSINNVLANNPDVNAIRTNKVETEQINNE


 


LTQAKQGLTVDKQPLINAKTALQQSL


 


DNQPSTTGMTEATIQNYNAKRQKAEQVIQNANKIIENAQPSVQQVSDEKSKVEQ


 


ALSELNNAKSALRADKQELQQAYNQL


 


IQPTDLNNKKPASITAYNQRYQQFSNELNSTKTNTDRILKEQNPSVADVNNALN


 


KVREVQQKLNEARALLQNKEDNSALV


 


RAKEQLQQAVDQVPSTEGMTQQTKDDYNSKQQAAQQEISKAQQVIDNGDATT


 


QQISNAKTNVERALEALNNAKTGLRADK


 


EELQNAYNQLTQNIDTSGKTPASIRKYNEAKSRIQTQIDSAKNEANSILTNDNPQ


 


VSQVTAALNKIKAVQPELDKAIAML


 


KNKENNNALVQAKQQLQQIVNEVDPTQGMTTDTANNYKSKKREAEDEIQKAQQ


 


IINNGDATEQQITNETNRVNQAINAIN


 


KAKNDLRADKSQLENAYNQLIQNVDTNGKKPASIQQYQAARQAIETQYNNAKS


 


EAHQILENSNPSVNEVAQALQKVEAVQ


 


LKVNDAIHILQNKENNSALVTAKNQLQQSVNDQPLTTGMTQDSINNYEAKRNEA


 


QSAIRNAEAVINNGDATAKQISDEKS


 


KVEQALAHLNDAKQQLTADTTELQTAVQQLNRRGDTNNKKPRSINAYNKAIQSL


 


ETQITSAKDNANAVIQKPIRTVQEVN


 


NALQQVNQLNQQLTEAINQLQPLSNNDALKAARLNLENKINQTVQTDGMTQQSI


 


EAYQNAKRVAQNESNTALALINNGDA


 


DEQQITTETDRVNQQTTNLTQAINGLTVNKEPLETAKTALQNNIDQVPSTDGMT


 


QQSVANYNQKLQIAKNEINTINNVLA


 


NNPDVNAIKTNKAEAERISNDLTQAKNNLQVDTQPLEKIKRQLQDEIDQGTNTD


 


GMTQDSVDNYNDSLSAAIIEKGKVNK


 


LLKRNPTVEQVKESVANAQQVIQDLQNARTSLVPDKTQLQEAKNRLENSINQQT


 


DTDGMTQDSLNNYNDKLAKARQNLEK


 


ISKVLGGQPTVAEIRQNTDEANAHKQALDTARSQLTLNREPYINHINNESHLNNA


 


QKDNFKAQVNSAPNHNTLETIKNKA


 


DTLNQSMTALSESIADYENQKQQENYLDASNNKRQDYDNAVNAAKGILNQTQS


 


PTMSADVIDQKAEDVKRTKTALDGNQR


 


LEVAKQQALNHLNTLNDLNDAQRQTLTDTINHSPNINSVNQAKEKANTVNTAMT


 


QLKQTIANYDDELHDGNYINADKDKK


 


DAYNNAVNNAKQLINQSDANQAQLDPAEINKVTQRVNTTKNDLNGNDKLAEAK


 


RDANTTIDGLTYLNEAQRNKAKENVGK


 


ASTKTNITSQLQDYNQLNIAMQALRNSVNDVNNVKANSNYINEDNGPKEAYNQA


 


VTHAQTLINAQSNPEMSRDWNQKTQ


 


AVNTAHQNLHGQQKLEQAQSSANTEIGNLPNLTNTQKAKEKELVNSKQTRTEV


 


QEQLNQAKSLDSSMGTLKSLVAKQPTV


 


QKTSVYINEDQPEQSAYNDSITMGQTIINKTADPVLDKTLVDNAISNISTKENALH


 


GEQKLTTAKTEAINALNTLADLNT


 


PQKEAIKTAINTAHTRTDVTAEQSKANQINSAMHTLRQNISDNESVTNESNYINA


 


EPEKQHAFTEALNNAKEIVNEQQAT


 


LOANSINQKAQAILTTKNALDGEEQLRRAKENADQEINTLNQLTDAQRNSEKGL


 


VNSSQTRTEVASQLAKAKELNKVMEQ


 


LNHLINGKNQMINSSKFINEDANQQQAYSNAIASAEALKNKSQNPELDKVTIEQA


 


INNINSAINNLNGEAKLTKAKEDAV


 


ASINNLSGLTNEQKPKENQAVNGAQTRDQVANKLRDAEALDQSMQTLRDLVNN


 


QNAIHSTSNYFNEDSTQKNTYDNAIDN


 


GSTYITGQHNPELNKSTIDQTISRINTAKNDLHGVEKLQRDKGTANQEIGQLGYL


 


NDPQKSGEESLVNGSNTRSEVEEHL


 


NEAKSLNNAMKQLRDKVAEKTNVKQSSDYINDSTEHQRGYDQALQEAENIINEI


 


GNPTLNKSEIEQKLQQLTDAQNALQG


 


SHLLEEAKNNAITGINKLTALNDAQRQKAIENVQAQQTIPAVNQQLTLDREINTA


 


MQALRDKVGQQNNVHQQSNYFNEDE


 


QPKHNYDNSVQAGQTIIDKLQDPIMNKNEIEQAINQINTTQTALSGENKLHTDQE


 


STNRQIEGLSSLNTAQINAEKDLVN


 


QAKTRTDVAQKLAAAKEINSAMSNLRDGIQNKEDIKRSSAYINADPTKVTAYDQ


 


ALQNAENIINATPNVELNKATIEQAL


 


SRVQQAQQDLDGVQQLANAKQQATQTVNGLNSLNDGQKRELNLLINSANTRT


 


KVQEELNKATELNHAMEALRNSVQNVDQ


 


VKQSSNYVNEDQPEQHNYDNAVNEAQATINNNAQPVLDKLAIERLTQTVNTTK


 


DALHGAQKLTQDQQAAETGIRGLTSLN


 


EPQKNAEVAKVTAATTRDEVRNIRQEATTLDTAMLGLRKSIKDKNDTKNSSKYI


 


NEDHDQQQAYDNAVNNAQQVIDETQA


 


TLSSDTINQLANAVTQAKSNLHGDTKLQHDKDSAKQTIAQLQNLNSAQKHMED


 


SLIDNESTRTQVQHDLTEAQALDGLMG


 


ALKESIKDYTNIVSNGNYINAEPSKKQAYDAAVQNAQNIINGTNQPTINKGNVTT


 


ATQTVKNTKDALDGDHRLEEAKNNA


 


NQTIRNLSNLNNAQKDAEKNLVNSASTLEQVQQNLQTAQQLDNAMGELRQSIA


 


KKDQVKADSKYLNEDPQIKQNYDDAVQ


 


RVETIINETQNPELLKANIDQATQSVQNAEQALHGAEKLNQDKQTSSTELDGLT


 


DLTDAQREKLREQINTSNSRDDIKQK


 


IEQAKALNDAMKKLKEQVAQKDGVHANSDYTNEDSAQKDAYNNALKQAEDIIN


 


NSSNPNLNAQDITNALNNIKQAQDNLH


 


GAQKLQQDKNTTNQAIGNLNHLNQPQKDALIQAINGATSRDQVAEKLKEAEALD


 


EAMKQLEDQVNQDDQISNSSPFINED


 


SDKQKTYNDKIQAAKEIINQTSNPTLDKQKIADTLQNIKDAVNNLHGDQKLAQSK


 


QDANNQLNHLDDLTEEQKNHFKPLI


 


NNADTRDEVNKQLEIAKQLNGDMSTLHKVINDKDQIQHLSNYINADNDKKQNYD


 


NAIKEAEDLIHNHPDTLDHKALQDLL


 


NKIDQAHNELNGESRFKQALDNALNDIDSLNSLNVPQRQTVKDNINHVTTLESL


 


AQELQKAKELNDAMKAMRDSIMNQEQ


 


IRKNSNYTNEDLAQQNAYNHAVDKINNIIGEDNATMDPQIIKQATQDINTAINGLN


 


GDQKLQDAKTDAKQQITNFTGLTE


 


PQKQALENIINQQTSRANVAKQLSHAKFLNGKMEELKVAVAKASLVRQNSNYIN


 


EDVSEKEAYEQAIAKGQEIINSENNP


 


TISSTDINRTIQEINDAEQNLHGDNKLRQAQEIAKNEIQNLDGLNSAQITKLIQDIG


 


RTTTKPAVTQKLEEAKAINQAMQ


 


QLKQSIADKDATLNSSNYLNEDSEKKLAYDNAVSQAEQLINQLNDPTMDISNIQA


 


ITQKVIQAKDSLHGANKLAQNQADS


 


NLIINQSTNLNDKQKQALNDLINHAQTKQQVAEIIAQANKLNNEMGTLKTLVEEQ


 


SNVHQQSKYINEDPQVQNIYNDSIQ


 


KGREILNGTTDDVLNNNKIADAIQNIHLTKNDLHGDQKLQKAQQDATNELNYLTN


 


LNNSQRQSEHDEINSAPSRTEVSND


 


LNHAKALNEAMRQLENEVALENSVKKLSDFINEDEAAQNEYSNALQKAKDIING


 


VPSSTLDKATIEDALLELQNARESLH


 


GEQKLQEAKNQAVAEIDNLQALNPGQVLAEKTLVNQASTKPEVQEALQKAKEL


 


NEAMKALKTEINKKEQIKADSRYVNAD


 


SGLQANYNSALNYGSQIIATTQPPELNKDVINRATQTIKTAENNLNGQSKLAEAK


 


SDGNQSIEHLQGLTQSQKDKQHDLI


 


NQAQTKQQVDDIVNNSKQLDNSMNQLQQIVNNDNTVKQNSDFINEDSSQQDA


 


YNHAIQAAKDLITAHPTIMDKNQIDQAI


 


ENIKQALNDLHGSNKLSEDKKEASEQLQNLNSLTNGQKDTILNHIFSAPTRSQV


 


GEKIASAKQLNNTMKALRDSIADNNE


 


ILQSSKYFNEDSEQQNAYNQAVNKAKNIINDQPTPVMANDEIQSVLNEVKQTKD


 


NLHGDQKLANDKTDAQATLNALNYLN


 


QAQRGNLETKVQNSNSRPEVQKWQLANQLNDAMKKLDDALTGNDAIKQTSN


 


YINEDTSQQVNFDEYTDRGKNIVAEQTN


 


PNMSPTNINTIADKITEAKNDLHGVQKLKQAQQQSINTINQMTGLNQAQKEQLN


 


QEIQQTQTRSEVHQVINKAQALNDSM


 


NTLRQSITDEHEVKQTSNYINETVGNQTAYNNAVDRVKQIINQTSNPTMNPLEV


 


ERATSNVKISKDALHGERELNDNKNS


 


KTFAVNHLDNLNQAQKEALTHEIEQATIVSQVNNIYNKAKALNNDMKKLKDIVAQ


 


QDNVRQSNNYINEDSTPQNMYNDTI


 


NHAQSIIDQVANPTMSHDEIENAINNIKHAINALDGEHKLQQAKENANLLINSLND


 


LNAPQRDAINRLVNEAQTREKVAE


 


QLQSAQALNDAMKHLRNSIQNQSSVRQESKYINASDAKKEQYNHAVREVENIIN


 


EQHPTLDKEIIKQLTDGVNQANNDLN


 


GVELLDADKQNAHQSIPTLMHLNQAQQNALNEKINNAVTRTEVAAIIGQAKLLDH


 


AMENLEESIKDKEQVKQSSNYINED


 


SDVQETYDNAVDHVTEILNQTVNPTLSIEDIEHAINEVNQAKKQLRGKQKLYQTI


 


DLADKELSKLDDLTSQQSSSISNQI


 


YTAKTRTEVAQAIEKAKSLNHAMKALNKVYKNADKVLDSSRFINEDQPEKKAYQ


 


QAINHVDSIIHRQTNPEMDPTVINSI


 


THELETAQNNLHGDQKLAHAQQDAANVINGLIHLNVAQREVMINTNTNATTREK


 


VAKNLDNAQALDKAMETLQQWAHKN


 


NILNDSKYLNEDSKYQQQYDRVIADAEQLLNQTTNPTLEPYKVDIVKDNVLANEK


 


ILFGAEKLSYDKSNANDEIKHMNYL


 


NNAQKQSIKDMISHAALRTEVKQLLQQAKILDEAMKSLEDKTQWITDTTLPNYT


 


EASEDKKEKVDQTVSHAQAIIDKIN


 


GSNVSLDQVRQALEQLTQASENLDGDQRVEEAKVHANQTIDQLTHLNSLQQQT


 


AKESVKNATKLEEIATVSNNAQALNKV


 


MGKLEQFINHADSVENSDNYRQADDDKIIAYDEALEHGQDIQKTNATQNETKQA


 


LQQLIYAETSLNGFERLNHARPRALE


 


YIKSLEKINNAQKSALEDKVTQSHDLLELEHIVNEGTNLNDIMGELANAIVNNYAP


 


TKASINYINADNLRKDNFTQAINN


 


ARDALNKTQGQNLDFNAIDTFKDDIFKTKDALNGIERLTAAKSKAEKLIDSLKFIN


 


KAQFTHANDEIINTNSIAQLSRIV


 


NQAFDLNDAMKSLRDELNNQAFPVQASSNYINSDEDLKQQFDHALSNARKVLA


 


KENGKNLDEKQIQGLKQVIEDTKDALN


 


GIQRLSKAKAKAIQYVQSLSYINDAQRHIAENNIHNSDDLSSLANTLSKASDLDN


 


AMKDLRDTIESNSTSVPNSVNYINA


 


DKNLQIEFDEALQQASATSSKTSENPATIEEVLGLSQAIYDTKNALNGEQRLATE


 


KSKDLKLIKGLKDLNKAQLEDVTNK


 


VNSANTLTELSQLTQSTLELNDKMKLLRDKLKTLVNPVKASLNYRNADYNLKRQ


 


FNKALKEAKGVLNKNSGTNVNINDIQ


 


HLLTQIDNAKDQLNGERRLKEHQQKSEVFIIKELDILNNAQKAAIINQIRASKDIKII


 


NQIVDNAIELNDAMQGLKEHVA


 


QLTATTKDNIEYLNADEDHKLQYDYAINLANNVLDKENGTNKDANIIIGMIQNMD


 


DARALLNGIERLKDAQTKAHNDIKD


 


TLKRQLDEIEHANATSNSKAQAKQMVNEEARKALSNINDATSNDLVNQAKDEG


 


QSAIEHIHADELPKAKLDANQMIDQKV


 


EDINHLISQNPNLSNEEKNKLISQINKLVNGIKNEIQQAINKQQIENATTKLDEVIET


 


TKKLIIAKAEAKQMIKELSQKK


 


ROAINNNTDLTPSQKAHALADIDKTEKDALQHIENSNSIDDINNNKEHAFNTLAHII


 


IWDTDQQPLVFELPELSLQNALV


 


TSEVVVHRDETISLESIIGAMTLTDELKVNIVSLPNTDKVADHLTAKVKVILADGS


 


YVTVNVPVKWEKELQIAKKDAIK


 


TIDVLVKQKIKDIDSNNELTSTQREDAKAEIERLKKQAIDKVNHSKSIKDIETVKRT


 


DFEEIDQFDPKRFTLNKAKKDII


 


TDVNTQIQNGFKEIETIKGLTSNEKTQFDKQLTALQKEFLEKVEHAHNLVELNQL


 


QQEFNNRYKHILNQAHLLGEKHIAE


 


HKLGYVVVNKTQQILNNQSASYFIKQWALDRIKQIQLETMNSIRGAHTVQDVHK


 


ALLQGIEQILKVNVSIINQSFNDSLH


 


NFNYLHSKFDARLREKDVANHIVQTETFKEVLKGTGVEPGKINKETQQPKLHKN


 


DNDSLFKHLVDNFGKTVGVITLTGLL


 


SSFWLVLAKRRKKEEEEKQSIKNHHKDIRLSDTDKIDPIVITKRKIDKEEQIQNDD


 


KHSIPVAKHKKSKEKQLSEEDIHS


 


IPWKRKQNSDNKDTKQKKVTSKKKKTPQSTKKWKTKKRSKK


 


>|cl|SEPN_8_63.AA 1973 residues








(SEQ ID NO: 24)









MKENKRKNNLDKNNTRFSIRKYQGYGATSVAIIGFIIISCFSEAKADSDKHEIKSH



 


QQSMTNHLTTLPSDNQENTSNNEF


 


NNRNHDISHLSLNKSIQMDELKKLIKQYKAINLNDKTEESIKLFQSDLVQAESLIN


 


NPQSQQHVDAFYHKFLNSAGKLRK


 


KETVSIKHERSESNTYRLGDEVRSQTFSHIRHKRNAVSFRNADQSNLSTDPLKA


 


NEINPEIQNGNFSQVSGGPLPTSSKR


 


LTVVTNVDNWHSYSTDPNPEYPMFYTTTAVNYPNFMSNGNAPYGVILGRTTDG


 


WNRNVIDSKVAGIYQDIDWPGSELNV


 


NFISTSPVFSDGAAGAKLKISNVEQNRVLFDSRLNGMGPYPTGKLSAMVNIPNDI


 


NRVRISFLPVSSTGRVSVQRSSREH


 


GFGDNSSYYHGGSVSDVRINSGSYWSKVTQREYTTRPNSSNDTFARATINLS


 


VENKGHNQSKDTYYEVILPQNSRLIST


 


RGGSGNYNNATNKLSIRLDNLNPGDRRDISYTVDFESSSPKLINLNA


 


HLLYKTNATFRGNDGQRTGDNIVDLQSIALLMN


 


KDVLETELNEIDKFIRDLNEADFTIDSWSALQEKMTEGGNILNEQ


 


QNQVALENQASQETINNVTQSLEILKNNLKYKTPS


 


QPIIKSNNQIPNITISPADKADKLTITYQNTDNESASIIGNKLNNQWSLNNNIPGIEI


 


DMQTGLVTIDYKAVYPESWGA


 


NDKTGNSDASAESRITMPRKEATPLSPIVEANEERVNWIAPNGEATQIAIKYRT


 


PDGQEATLVASKNGSSWTLNKQIDY


 


VNIEENSGKVTIGYQAVQPESEVIATETKGNSDESAESRVTMPRKEATPHSPIVE


 


ANEEHVNVTIAPNGEATQIAIKYRT


 


PDGQETTLIASKNGSSWTLNKQIDYVNIEENSGKVTIGYQAVQLESEVIATETKG


 


NSDASAESRITMLRKEATPHSPIVE


 


ANEEHVNVTIAPNGEATQIAIKYRTPDGQEATLVASKNESSWTLNKQIDHVNIDE


 


NSGKVTIGYQAVQPESEIIATETKG


 


NSDASAESRITMPRKEATPIPPTLEASVQEASVTVTPNENATKVFIKYLDINDEIS


 


TIIASKINQQWTLNKDNFGIKINP


 


LTGKVIISYVAVQPESDVIAIESQGNSDLSEESRIIMPTKEEPPEPPILESDSIEAK


 


VNIFPNDEATRIVIMYTSLEGQE


 


ATLVASKNESSWTLNKQIDHVNIDENSGKVTIGYQAVQPESEVIATETKGNSDA


 


SAESRVTMPRKEATPHSPIVETNEER


 


VNWIAPNGEATQIAIKYRTPDGQETTLIASKNGSSWTLNKQIDHVNIDENSGKV


 


TIGYQAVQPESEIIATETKGNSDAS


 


AESRITMPRKEAIPHSPIVEANEEHVNVTIAPNGETTQIAVKYRTPDGQEATLIAS


 


KNESSWTLNKQIDHVNIDENSGKV


 


TIGYQAVQPESEVIATETKGNSDASAESRITMPVKEKTPAPPISIINESNASVEIIP


 


QVNVTQLSLQYIDAKGQQQNLIA


 


TLNQNQWTLNKNVSHITVDKNTGKVLINYQAVYPESEVIARESKGNSDSSNVSM


 


VIMPRKTATPKPPIIKVDEMNASLAI


 


IPYKNNTAINIHYIDKKGIKSMVTAIKNNDQWQLDEKIKYVKIDAKTGTVIINYQIVQ


 


ENSEIIATAINGNSDKSEEVKV


 


LMPIKEFTPLAPLLETNYKKATVSILPQSNATKLDFKYRDKKGDSKIIIVKRFKNIW


 


KANEQISGVTINPEFGQWINYQ


 


AVYPESDILAAQYVGNSDASEWAKVKMPKKELAPHSPSLIYDNRNNKILIAPNSN


 


ATEMELSYVDKNNQSLKVKALKINN


 


RWKFDSSVSNISINPNTGKIVLQPQFLLTNSKIIVFAKKGNSDASISVSLRVPAVK


 


KIELEPMFNVPVLVSLNKKRIQFD


 


DCSGVKNCLNKQISKTQLPDTGYSDKASKSNILSVLLLGFGFLSYSRKRKEKQ






Example 5
Immunization Strategies for Antibody Production Using Three Representative Enterococcal MSCRAMM® Proteins
Purified EF1091, EF1092, and EF1093 proteins were used to generate a panel of murine antibodies. Briefly, a group of Balb/C mice received a series of subcutaneous immunizations of 1-10 mg of protein in solution or mixed with adjuvant as described below in Table 5:











TABLE 5





Conventional






Injection
Day
Amount (μg)
Route
Adjuvant



















Primary
0
5
Subcutaneous
FCA


Boost #1
14
1
Intraperitoneal
RIBI


Boost #2
28
1
Intraperitoneal
RIBI


Boost #3
42
1
Intraperitoneal
RIBI









At the time of sacrifice serum was collected and titered in ELISA assays against MSCRAMM® proteins ACE, EF1091, EF1092 and EF1093 (Table 6).

Serum ELISA

Immulon 2-HB high protein binding 96 well plates were coated with 100 ng/well of the purified A-domains of EF1091, EF1092 or EF1093 and incubated overnight at 2-8° C. Plates were washed four times (350 μl/well) with PBS/0.5% Tween 20 using the Skatron Skanwasher plate washer and then blocked with 1% bovine serum albumin (BSA) solution, 200 μl/well for 1-2 hour at room temperature. Following incubation, the plates were washed as before and 100 μl of 1×PBS, 0.05% Tween 20, 0.1% BSA buffer was added to each well of rows B-H of the 96-well plate. The negative control serum (preimmune Balb/C serum) and hyperimmune samples were then diluted 1:100 in 1×PBS, 0.05% Tween 20, 0.1% BSA buffer. 200 μl of negative control serum was added in duplicate to wells A1 and A2 of the 96-well plate and 200 μl of each diluted hyperimmune test serum were added in duplicate to wells A3 toA12. Two-fold serial dilutions were performed down the plate ending with Row H with the remaining 100 μl being discarded. The plates were incubated for 1 hour at room temperature. The plates were again washed as before followed by the addition of 1:5000 dilution of a secondary antibody solution, Goat anti-mouse IgG (whole molecule)-AP conjugate (Sigma Cat. A-5153), to each well (100 μl/well) and incubated for 1 hour at room temperature. Following incubation, the plates were washed 4 times (350 μl/well) with PBS/0.5% Tween 20. The developing solution, 1 mg/ml 4-nitrophenyl phosphate (pNPP) in 1M Diethanolamine, pH9.8, 0.5mM MgCl2, was added to each well (100 μl/well) and the plates incubated at 37° C. for 30 minutes. After incubation, the absorbance (A405nm) of each well was measured using the Spectra MAX 190 plate reader (Molecular Devices Corp., Sunnyvale, Calif.). The data was analyzed using SOFTmax Pro v.3.1.2. software (Molecular Devices Corp.) The dilution of the hyperimmune sera where the absorbance was 2-fold above the negative control serum absorbance was used as the titre for that hyperimmune serum sample.








TABLE 6







Antibody Titer at Sacrifice










Antigen
Polyclonal Antibody Titre







EF1091
>12,800



EF1092
>12,800



EF1093
>12,800










Example 6
Antibody Reactivity Against E. faecalis MSCRAMM® Proteins
Antisera derived from Balb/c mice (as described in Example 3) was used to identify EF1091, EF1092 or EF1093 natively expressed on the surface of E. faecalis strains.
Flow Cytometry Analysis—Whole Cell Staining
Bacterial samples (Table 7) were collected, washed and incubated with polyclonal antisera or pre-immune sera (control) at a dilution of 1:2000 after blocking with rabbit IgG (50 mg/ml). Following incubation with sera, bacterial cells were incubated with Goat-F(ab′)2-Anti-Mouse-F(ab′)2-FITC which served as the detection antibody. After antibody labeling, bacterial cells were aspirated through the FACScaliber flow cytometer to analyze fluorescence emission (excitation: 488, emission: 570). For each bacterial strain, 10,000 events were collected and measured.







TABLE 7







Whole Cell Staining of E. faecalis and E. faecium











EF1091
EF1092
EF1093
















E. faecalis






ATCC700802
—
—
Not done






(NA)



687097
—
—
ND



V583
—
—
ND



OG110
—
—
ND



OG1RF
+
+
+



TX2708
—
—
ND



TX0020
ND
ND
ND



TX0045
—
—
ND



TX0002
—
—
ND



TX0039
—
—
ND



TX0052
ND
ND
ND



TX0012
—
—
ND



TX0017
ND
ND
ND



TX0008
ND
ND
ND



TX0024
ND
ND
ND



E. faecium



935/01
—
—
ND



TX0016
ND
ND
ND



TX0054
+/−
+/−
ND



TX0074
+
+
ND



TX0078
—
—
ND



TX0080
+/−
+/−
ND



TX0081
+/−
+/−
ND



TX2535
ND
ND
ND



TX2555
+/−
+
+



TX0110
—
—
—



TX0111
ND
ND
ND










Polyclonal antisera raised in mice against EF1091, EF1092 and EF1093 were shown to recognize the native protein expressed on the surface of E. faecalis strains as well as E. faecium strains in flow cytometry studies (Table 7).

Example 7
Immunization Strategies for Monoclonal Antibody Production
With the goal of generating and characterizing monoclonal antibodies (mAbs), strategies were formulated to generate mAbs against EF1091, EF 1092 and EF 1093 that were of high affinity, able to interrupt or restrict the binding of extracellular matrix proteins (ECM) and demonstrate therapeutic efficacy in vivo. E. coli expressed and purified EF1091, EF1092, and EF1093 proteins were used to generate a panel of murine monoclonal antibodies. Briefly, a group of Balb/C or SJL mice received a series of subcutaneous immunizations of 1-10 □g of protein in solution or mixed with adjuvant as described below in Table 8:







TABLE 8







Immunization Schemes












Day
Amount (μg)
Route
Adjuvant















RIMMS Injection






#1
0
5
Subcutaneous
FCA/RIBI


#2
2
1
Subcutaneous
FCA/RIBI


#3
4
1
Subcutaneous
FCA/RIBI


#4
7
1
Subcutaneous
FCA/RIBI


#5
9
1
Subcutaneous
FCA/RIBI


Conventional Injection


Primary
0
5
Subcutaneous
FCA


Boost #1
14
1
Intraperitoneal
RIBI


Boost #2
28
1
Intraperitoneal
RIBI


Boost #3
42
1
Intraperitoneal
RIBI









At the time of sacrifice (RIMMS) or seven days after a boost (conventional) serum was collected and titered in ELISA assays against in immunizing MSCRAMM or on whole cells (E. faecalis and/or E. faecium). Three days after the final boost, the spleens or lymph nodes were removed, teased into a single cell suspension and the lymphocytes harvested. The lymphocytes were then fused to a P3X63Ag8.653 myeloma cell line (ATCC #CRL-1580). Cell fusion, subsequent plating and feeding were performed according to the Production of Monoclonal Antibodies protocol from Current Protocols in Immunology (Chapter 2, Unit 2.).

Example 8
Screening and Selection of Anti-EF1091 Monoclonal Antibodies
Any clones that were generated from the EF1091 fusion were then screened for specific anti-EF1091 antibody production using a standard ELISA assay. Positive clones were expanded and tested further for activity in a whole bacterial cell binding assay by flow cytometry and EF1091 binding by Biacore analysis (Table 9).

ELISA Analysis

Immulon 2-HB high-binding 96-well microtiter plates (Dynex) were coated with 1 pg/well of rEF1091 in 1×PBS, pH 7.4 and incubated for 2 hours at room temperature. All washing steps in ELISAs were performed three times with 1×PBS, 0.05% Tween-20 wash buffer. Plates were washed and blocked with a 1% BSA solution at room temperature for 1 hour before hybridoma supernatant samples were added to wells. Plates were incubated with samples and relevant controls such as media alone for one hour at room temperature, washed, and goat anti-mouse IgG-AP (Sigma) diluted 1:5000 in 1×PBS, 0.05% Tween-20, 0.1% BSA was used as a secondary reagent. Plates were developed by addition of 1 mg/ml solution of 4-nitrophenyl phosphate (pNPP) (Sigma), followed by incubation at 37° C. for 30 minutes. Absorbance was read at 405 nm using a SpectraMax 190 Plate Reader (Molecular Devices Corp.). Antibody supernatants that had an OD405≧3 times above background (media alone,  ̃0.1 OD) were considered positive.

Biacore Analysis

Throughout the analysis, the flow rate remained constant at 10 ml/min. Prior to the EF1091 injection, test antibody was adsorbed to the chip via RAM-Fc binding. At time 0, EF1091 at a concentration of 30 mg/ml was injected over the chip for 3 min followed by 2 minutes of dissociation. This phase of the analysis measured the relative association and disassociation kinetics of the mAb/EF1091 interaction.

Flow Cytometric Analysis

Bacterial samples were collected, washed and incubated with mAb or PBS alone (control) at a concentration of 2 mg/ml after blocking with rabbit IgG (50 mg/ml). Following incubation with antibody, bacterial cells were incubated with Goat-F(ab′)2-Anti-Mouse-F(ab′)2-FITC which served as the detection antibody. After antibody labeling, bacterial cells were aspirated through the FACScaliber flow 10 cytometer to analyze fluorescence emission (excitation: 488, emission: 570). For each bacterial strain, 10,000 events were collected and measured.








TABLE 9







Representative Examples of Hybridoma Supernatants















Flow Cytometric


Fusion-
Immunization
ELISA Data
Biacore
E. faecalis


Clone
Antigen
(EF1091)
Analysis
Staining





85-8
EF 1091
0.70
+
+


85-25
EF 1091
0.75
+
+


85-58
EF 1091
0.76
+
—


85-78
EF 1091
0.83
+
+


85-81
EF 1091
0.84
+
+


85-162
EF 1091
0.78
+
+


85-310
EF 1091
0.30
—
—


85-341
EF 1091
0.31
—
—


85-359
EF 1091
0.48
—
—


85-374
EF 1091
0.39
—
—


85-380
EF 1091
0.32
—
—


85-399
EF 1091
0.98
+
—


85-473
EF 1091
0.55
+
—


85-511
EF 1091
0.85
+
—


85-581
EF 1091
0.88
+
+


85-586
EF 1091
0.88
+
+


85-641
EF 1091
0.45
+
+


85-661
EF 1091
0.32
—
—


85-712
EF 1091
0.30
—
—









Example 9
Binding of Enterococcal MSCRAMM Proteins to Extracellular Matrix (ECM) Proteins
Understanding the potential extracellular matrix proteins that these MSCRAMMs expressed from Enterococcus bind to is of great biological importance with therapeutic implications.
ELISA Based Extracellular Matrix Ligand Screening
To determine the binding activity of the recombinant proteins EF1091, EF1092 and EF1093 (Table 10) with extracellular matrix molecules, duplicate wells of a 96-well Costar micro-titer plate (Corning) were coated overnight at 4° C. with 2 μg of either human collagen type I, III, IV, V or VI (Rockland Immunochemicals), fibrinogen, fibronectin, plasminogen, vitronectin (Sigma) or elastin (CalBiochem) in 100 μL of 1×PBS, pH 7.4 (Gibco). Wells were washed 4 times with 1×PBS, pH 7.4 containing 0.05% Tween 20 (1×PBST). Wells were then blocked with a 1% (w/v) solution of BSA in 1×PBS, pH 7.4 for 1 hour followed by 4 washes with 1×PBST. Next, 5 μg of recombinant protein in 100μL of 1×PBST containing 0.1%BSA (1×PBST-BSA) was added to each well. After incubation with the protein for 1 hour at room temperature, wells were washed 4 times with 1×PBST and 100 □L of mouse polyclonal antisera raised against the respective recombinant protein was added to each well at a dilution of 1:2000 in 1×PBST-BSA. Following the 1 hour incubation at room temperature with antisera, the wells were washed 4 times with 1×PBST. Finally, goat anti-mouse IgG-alkaline phsophatase conjugate (Sigma) was diluted 1:2000 with 1×PBST-BSA and 100 μL was added to each well. This incubation proceeded for 1 hour at room temperature and the wells were then washed 4 times with 1×PBST. The alkaline phosphatase was developed by adding 100 μL of a 1 mg/mL pNP solution (Sigma 104 tablets) to each well and incubating for 30 minutes at room temperature. Development was stopped by addition of 50 μL of 2M NaOH to each well. The absorbance at 405 nm (A405) was measured using a SpectraMax 190 (Molecular Devices). Reactivity was noted as positive if the signal was 2.5× greater than background.

Alternatively, EF0089 and EF2224 binding to components of the ECM (Table 10) was tested by immobilizing 1 □g of each ECM protein (human laminin, fibronectin, fibrinogen, type I, III and IV collagens) in 100 □l PBS, or 3% acetic acid in the case of collagens, on microplate wells (96-well, 4HBX, Thermo Labsystems, Franklin, Mass.) overnight at 4□C. Plates were washed once with PBS and blocked with 1% BSA in PBS for 1 h. Fifty □l of 5 and 10 □M concentrations of purified His-tag proteins in the blocking buffer were added and incubated at ambient temperature for 2 h. Plates were washed three times with 0.05% Tween20 in PBS and incubated 2 h with 1:3000 dilution of His6-tag monoclonal antibody (Amersham Biosciences Corp., Piscataway, N.J.) in blocking buffer. After three washes, 1:3000 dilution of alkaline phosphatase-conjugated anti-mouse antibody in blocking buffer was added to the wells and incubated 2 h. Finally, signal was detected with nitrobluetetrazolium (NBT) and 5-bromo-4-chloro-3-indolyl-phosphate (BCIP) in 0.1 M NaHCO3, 1 mM MgCl2, pH 9.8. Absorbance at 405 nm was measured with an ELISA reader








TABLE 10







MSCRAMM ® Protein Recognition of ECM Proteins












ECM







Proteins
EF0089
EF2224
EF 1091
EF 1092
EF 1093





Fibrinogen
+
+
—
—
+


Fibronectin
—
—
—
—
—


Collagen I
—
—
—
—
—


Collagen III
—
—
—
—
—


Collagen IV
—
—
—
—
—


Collagen V
Not
ND
—
—
—



determined



(ND)


Collagen VI
—
—
—
+
—


Vitronectin
—
—
—
—
—


Elastin
ND
ND—
—
—
—


Plasminogen
ND
ND
+
+
+









Example 10
Serum From Patients Infected With E. faecalis Contain Elevated Levels of Antibodies Against MSCRAMM® Proteins
The presence of antibodies against enterococcal proteins in human sera collected from hospitalized patients with and without a previous E. faecalis infection was tested by an ELISA assay described in (Arduino et al., 1994) (Nallapareddy et al., 2000b) with some modifications (Table 11). Briefly, 20 ng of each purified enterococcal protein in 100 μl PBS was coated on microplates (96 well, 4HBX, Thermo Labsystems, Franklin, Mass.) overnight at 4 □C. The plates were blocked with 1% BSA, 0.01% Tween20 in PBS at ambient temperature for 1 h and 100 μl of the sera in blocking buffer were added. Each serum was tested in triplicate with serial dilutions from 1:100 to 1:6400. Plates were incubated for 2 h at ambient temperature and washed three times with 0.01% Tween20 in PBS. 100 μl of 1:3000 dilution of horseradish peroxidase-conjugated anti human IgG was added and incubated 2 h. After three washes, signal was detected with 3,3′,5,5′-tetramethylbenzidine (TMB) in the presence of H2O2 in 0.1 M citrate-acetate buffer, pH 6.0 at ambient temperature for 15 min. The reaction was stopped with 2 M H2SO4 and absorbance at 450 nm was recorded. Titers were determined after subtracting A450nm values from appropriate controls. To determine a cut-off level for serum titers, four additional control sera from healthy individuals without a prior E. faecalis infection were assayed. The sum of average A450nm values and two times the standard deviations for each dilution of the control sera were set as cut-off levels for positive titers.









TABLE 11









Infection



















≧1:6400
•
•
•
•
•
•

•



•

•

•
•

•



•



•
•

•



•



•
•

•



•






•



•






•



•






•










•


  1:3200

•

•


•


  1:1600


  1:800


  1:400






•


  1:200


•
•
•
•

•





•


•








•


≧1:100
•
•
•
•
•
•
•




•
•
•
•
•
•
•





•
•
•
•

•





•
•
•
•

•





•
•
•


•





•

•


•





•




•




EF1091
EF1824
EF0089
EF3023
EF1092
EF2224
EF1269
EF1093












No infection



















≧1:6400







•


  1:3200


  1:1600


  1:800


  1:400


  1:200

•
•
•
•
•


≧1:100
•
•
•
•
•
•
•
•



•
•
•
•
•
•
•
•



•
•
•
•
•
•
•
•



•
•
•
•
•
•
•
•



•
•
•
•
•
•
•
•



•
•
•
•
•
•
•
•



•
•
•
•
•
•
•
•



•
•
•
•
•
•
•
•



•





•




EF1091
EF1824
EF0089
EF3023
EF1092
EF2224
EF1269
EF1093









The following references referred to in the above description are incorporated as is set forth in their entirety herein:

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## Claims

1. An isolated antibody capable of binding to an amino acid sequence consisting of amino acids 33-592 of SEQ ID NO: 13.

2. The antibody according to claim 1 wherein the antibody is a monoclonal antibody.

3. The antibody according to claim 1 selected from the group consisting of single chain, chimeric, murine, humanized and human monoclonal antibodies.

4. The antibody according to claim 1, wherein said antibody treats an E. faecalis bacterial infection in a human or animal.

5. The antibody according to claim 1, wherein said antibody is suitable for parenteral, oral, intranasal, subcutaneous, aerosolized or intravenous administration in a human or animal.

6. Isolated antisera containing an antibody according to claim 1.

7. A diagnostic kit comprising an antibody according to claim 1 and means for detecting binding by that antibody.

8. A diagnostic kit according to claim 7 wherein said means for detecting binding comprises a detectable label that is linked to said antibody.

9. A pharmaceutical composition comprising an effective amount of the antibody of claim 1 and a pharmaceutically acceptable vehicle, carrier or excipient.

10. The antibody according to claim 1, wherein the antibody is a polyclonal antibody.