CA2283755A1 - Human complement c3-degrading proteinase from streptococcus pneumoniae - Google Patents

Abstract

The present invention relates to the identification and use of a family of human complement C3-degrading proteinases expressed by S. pneumoniae. The proteinase has a molecular weight of about 24 kD to about 34 kD as determined on a 10 % SDS polyacrylamide gel. A preferred proteinase of this invention includes the amino acid sequence of SEQ ID NO:2.

Description

HUMAI'I COMPLEMENT C3-DEGRADING PROTEINASE
s FROM .STREPTOCOCCUS PNEUMONIAE
Field of the Invention 1o This invention relates to Streptococcus pneumnniae and in particular this invention relates to the identification of an S. pneumoniae protein that is capable of degrading human complement protein, C3.
l3ack~round of the Invention This application claims the benefit of a provisional application (Serial ~ 5 No. 60/044.316) filing on April 24, 1997 entitled ''Human complement C 3-degrading proteinase frorr.~ Streptococcus pncumoniae."
Respiratory infection with the bacterium Streptococcu.r pneur?TOrzlaL' (S.
pneumoniae) leads to an estimated X00,000 cases of pneumonia and 47,000 deaths annually. Those persons at highest risk of bacteremic pneumococcal 2o infection are infants under two years of age and the elderly. In these populations, S. pneumonicre is the leading cause of bacterial pneumonia and meningitis. Morf:over. S. pneumoniae is the major bacterial cause of ear infections in children of al.l ages. Both children and the elderly share defects in the synthesis of protective antibodies to pneumococcal capsular polysaccharide ?s after either bacterial colonization, local or systemic infection, or vaccination with purified polysaccharides. S. pneumonicre is the leading cause of invasive bacterial respiratory disease in both adults and children with H1V infection and produces hematogenous infection in these patients (Connor et al. C.'Irrrenl Topics in AIDS 1987;1:185-209 and Janoff et al. Ann. Intern. Med. 1992;117(4):314-30 324).
Individuals who demonstrate the greatest risk for severe infection are not able to make antibodies to. the current capsular polysaccharide vaccines. As a result, there are now four ~~onjugate vaccines in clinical trial. Conjugate vaccines consist of pneumococcal capsular polysaccharides coupled to protein carriers or adjuvants in an attempt to boost the antibody response. However, there are other potential problems with conjugate vaccines currently in clinical trials. For example, pneumococcal serotypes that are most prevalent in the United States are different from the serotypes that are most common in places such as Israel, - 5 Western Europe, or Scandinavia. Therefore, vaccines that may be useful in one geographic locale may not be useful in another. The potential need to modify , currently available capsular polysaccharide vaccines or to develop protein conjugates for capsular vaccines to suit geographic serotype variability entails prohibitive financial and technical complications. Thus, the search for immunogenic, surface-exposed proteins that are conserved worldwide among a variety of virulent serotypes is of prime importance to the prevention of pneumococcal infection and to the formulation of broadly protective pneumococcal vaccines. Moreover, the emergence of penicillin and cephalosporin-resistant pneumococci on a worldwide basis makes the need for ~5 effective vaccines even more exigent (Baquero et al. J. Antimicrob.
Chemnther.
1991;28S;31-8).
Several pneumococcal proteins have been proposed for conjugation to pneumococcal capsular polysaccharide or as single immunogens to stimulate immunity against S. pneumoniae. Surface proteins that are reported to be 2o involved in adhesion of S. pneumoniae to epithelial cells of the respiratory tract include PsaA, PspC/CBP112, and IgAI proteinase (Sampson et al. If~fect.
Immun. 1994;62:319-324, Sheffield et al. Microb. Pathogen. 1992; 13: 261-9, and Wani, et al. Infect. Immun. 1996; 64:3967-3974). Antibodies to these adhesins could inhibit binding of pneumococci to respiratory epithelial cells and 25 thereby reduce colonization. Other cytosolic pneumococcal proteins such as pneumolysin, autolysin, neuraminidase, or hyaluronidase are proposed as vaccine antigens because antibodies could potentially block the toxic effects of these proteins in patients infected with S. pneumoniae. However. these proteins are typically not located on the surface of S. pnea~moniae, rather they are secreted 30 or released from the bacterium as the cells lyse and die (Lee et al.
Vaccine 1994;
12:875-8 and Berry et al. Infect. Immun. 1994; 62:1101-1108). While use of these cytosolic proteins as immunogens might ameliorate late consequences of S. pneumoniae infection. antibodies to these proteins would neither promote pneumococcal death nor prevent initial or subsequent pneumococcal colonization.
A prototypic surface protein that is being tested as a pneumococcal vaccine is the p:neumococcal surface protein A (PspA). PspA is a heterogeneous protein of about: 70-140 lkDa. The PspA structure includes an alpha helix at the amino terminus, followed by a proline-rich sequence, and terminates in a series of 11 choline-binding repeats at the carboxy-terminus. Although much information regarding it s structure is available, PspA is not structurally conserved among a varieay of pneumococcal serotypes, and its function is entirely unknovm (Yothe:r et al. J. Bacterial. 1992;174:601-9 and Yother J.
Bacteriol. 1994;176:2976-2985). Studies have confirmed the immunogenicity of~
PspA in animals (McDaniel et al. Microb. Pathogen. 1994; 17;323-337).
~ 5 Despite the immunogenicity of PspA, the heterogeneity of PspA, its existence in four structural groups (or ciades), and its uncharacterized function complicate its ability to be used as a vaccine antigen.
In patients who cannot make protective antibodies to the type-specific polysaccharide capsule, the third component of complement, C3, and the 20 associated proteins of the alternative complement pathway constitute the first line of host defi~nse against S. pneumoniae infection. Because complement proteins cannot penetrate the rigid cell wall of S. pneumoniae, deposition of opsonic C3b on the pneumococcal surface is the principal mediator of pneumococcal ~~learance:. Interactions of pneumococci with plasma C3 are 25 known to occur during pneumococcal bacteremia, when the covalent binding of C3b, the opsonically active fragment of C3, initiates phagocytic recognition and ingestion (John.ston et all. J. Exp. Med 1969:129:1275-1290, Hasin HE, J.
Immunol. 1972; 109:26-31 and Hostetter et al. .I. Infect. Dis. 1984; 150:653-61 ).
C3b deposits on the pneumococcal capsule, as well as on the cell wall. This 3o method for controlling li. pneumoniae infection is fairly inefficient.
Methods for augmenting S. pneumor~iae opsonization could improve the disease course _3_ induced by this organism. There currently exists a strong need for methods and therapies to limit S. pneumoniae infection.
Summary of the Invention This invention relates to the identification and use of a family of human complement C3-degrading proteinases expressed by S. pneumoniae. The protein has a molecular weight of about 24 kD to about 34 kD as determined on a 10%
SDS polyacrylamide gel. The invention includes a number of proteins isolatable from different C3-degrading strains of S. pnea~moniae.
In one aspect of the invention, the invention relates to an isolated protein comprising at least an 80% sequence identity of SEQ ID N0:2 and capable of degrading human complement protein C3. In a preferred embodiment, the protein is isolated from S. pneumoniae or alternatively the protein is a 15 recombinant protein. Preferably the protein binds human complement protein C3. In a preferred embodiment, the protein has a molecular weight as determined on a 10% polyacrylamide gel of between about 24 kDa to about 34 kDa. A preferred protein of this invention is an isolated protein including SEQ
ID N0:2.
2o The invention also relates to peptides from the C3-degarding proteinase of this invention and preferably peptides of at least 15 sequential amino acids from an isolated protein comprising at least an 80% sequence identity of SEQ
ID
N0:2 and capable of degrading human complement protein C3 and more preferably peptides of at least 15 sequential amino acids from SEQ ID N0:2.
25 The protein of claim 9, wherein the protein is a recombinant protein. In another aspect of this invention, the invention relates to a peptide of at least 1 ~
sequential amino acids from SEQ ID N0:2.
The protein of this invention can comprise SEQ ID N0:2, and preferably has a molecular weight as determined on a 10% polyacrylamide gel of between 3o about 24 kDa to about 34 kDa. Also preferably the protein degrades human complement protein C3. Preferred protein or polypeptides of this invention include a protein, comprising amino acids I-50 of SEQ ID N0:2 and a nucleic acid fragment co~mprisin~; nucleic acids 1246 to 1863 of FIG. 1 A.
In another aspect of the invention the invention relates to a protein that degrades human complennent protein C3 and wherein nucleic acid encoding the S protein hybridizes to SEQ ID NO:1 under hybridization conditions of 6XSSC, ~X Denhardt, O.:p% SDS, and 100 pg/ml fragmented and denatured salmon sperm DNA hybridized overnight at 65°C and washed in 2X SSC, 0.1% SDS
one time at room temperature for about i 0 minutes followed by one time at, 65°C for about 15 minutes followed by at least one wash in 0.2XSSC, 0.1 % SDS
at room temperature for ait least 3-5 minutes.
The invention also relates to an immune-system stimulating composition comprising an ei:fective amount of an immune system-stimulating peptide or polypeptide corr~prising apt least 15 amino acids from a protein comprising at least an 80% sequence identity with SEQ ID N0:2 and capable of degrading ~ 5 human complement protein C3.
Preferabliy the protein is isolatable from S. pnearmoniae. In one embodiment, thf: immune: system stimulating composition further comprises at least one other immune stimulating peptide, polypeptide or protein from S.
pneumoniae.
2o The invention further relates to an antibody capable of specifically binding to a protein comprising at least a 80% sequence identity with SEQ ID
N0:2 and capable of degrading human complement protein C3. In one embodiment, the antibody is a monoclonal antibody an din an other embodiment, the antibody is a polyclonal antibody. In another embodiment the antibody is an 25 antibody fragmf;nt. The antibody or antibody fragments can be obtained from a mouse, a rat, human or a rabbit.
The invention also relates to a nucleic acid fragment capable of hybridizing to S~EQ ID I'l0: l under hybridization conditions of 6XSSC, SX
Denhardt, 0.5% SDS, and 100 ~g/ml fragmented and denatured salmon sperm 30 DNA hybridizes overni~;ht at 65°C and washed in 2X SSC, 0.1% SDS one time at room temperature for about 10 minutes followed by one time at, 65°C
for about 15 minutes followed by at least one wash in 0.2XSSC, 0.1 % SDS at room temperature for at least 3-5 minutes. In one embodiment the nucleic acid fragment is isolated from an S. pneumoniue genome and in another embodiment.
the nucleic acid fragment encodes at least a portion of a protein. In one embodiment, the protein degrades human complement C3 and in another embodiment, the nucleic acid fragment encodes a protein that does not degrade human complement C3.
In another embodiment, the nucleic acid fragment is in a nucleic acid vector and the vector can be an expression vector capable of producing at least a I o portion of a protein. Cells containing the nucleic acid fragment are also contemplated in this invention. In one embodiment. the cell is a bacterium or a eulcarvotic cell.
The invention further relates to an isolated nucleic acid fragment comprising the nucleic acid sequence 15 gctcccagtatgcgtactcgtaaggtagagggaagaaaaaaactagctag.
In another aspect of this invention, the invention relates to a method for producing an immune response to S. pneumoniue in an animal including the steps of: administering a composition comprising a therapeutically effective amount of at least a portion of a protein to an animal, wherein nucleic 2o acid encoding the protein hybridizes to SEQ ID NO:1 under hybridization conditions of 6XSSC, SX Denhardt, 0.5% SDS, and 100 pg/ml fragmented and denatured salmon sperm DNA, hybridized overnight at 65°C and washed in 2x SSC, 0.1% SDS one time at room temperature for about 10 minutes followed by one time at 65°C for about 15 minutes followed by at least one wash in 0.2xSSC, 25 0.1 % SDS at room temperature for at least 3-5 minutes; and obtaining an immune response to the protein. In one embodiment the immune response is a B
cell response and in another embodiment, the immune response is a T cell response. In a preferred embodiment, the composition is a vaccine composition.
Preferably the at least a portion of the protein is at least 15 amino acids in length 3o and also preferably the composition further comprises at least one other protein _6_ from S. pneumoniue. In one embodiment, the protein comprises at least 15 amino acids of SEQ ID I\f0:2.
In a further embodiment, the invention relates to a bacteria comprising an insertional mutaaion, wherein the insertion mutation is in a gene encoding a protein capable of degrading human complement C3. In one embodiment, the bacteria comprises an insertional duplication mutation.
The invention further relates to an isolated protein of about 24 kDa to about 34 kDa from Streptococcus pneumoniae that is capable of binding to and degrading human complement C3 and to a method for inhibiting Streptococcus pneumoniae-me~3iated C=s degradation comprising the step of : contacting a Streptococcus pneumonia bacterium with antibody capable of binding to a protein with at lf~ast 80% amino acid sequence identity to SEQ ID N0:2. The invention further relates t:o an isolated nucleic acid fragment comprising the nucleic acid sequence of SEQ ID NO:1 and to an RNA fragment transcribed by a t 5 double-stranded DNA sequence comprising SEQ ID NO:1.
Etrief Description of the Figures Figure l.A provides a gene sequence and Figure I B provides an amino acid sequence o f a C3 degrading proteinase of this invention.
2o Figure 2 is a diagram of an insertion duplication mutant according to this invention.
Figure 3 is a diagram of the restriction analysis of an insert from an insertion duplic,~tion mutant of this invention.
25 Detailed Description of the Preferred ICmbodiments The present invention relates to the identification and isolation of a C3 degrading proteinase wil.h a molecular weight of about 29 kDa (~ 5 kDa) on a 10% SDS-PAGE gel (wiith a predicted size of about 27.5 kDa based on SEQ ID
3o NO:1 ) and nucleic acid encoding the C3 degrading proteinase. The protein was originally identified by electrophoresis of pneumococcal lysates on SDS-PAGE

gels impregnated with C3. It has been observed that exponentially growing cultures of pneumococci from several serotypes were able to first degrade the (3-chain then degrade the a chain of C3 without producing defined C3 cleavage fragments (Angel, et al. J. Infect. Dis. 170:600-608, 1994). This pattern of degradation without cleavage differs substantially from other microbial products such as the elastase moiety of P.seudomona.s aerugino.sa and the cysteine proteinase of Entamoeba hi.stolytica. The gene sequence (SEQ ID NO:1 ) encoding a C3 degrading protein according to this invention is provided in Figure 1 A and the amino acid sequence (SEQ ID N0:2) of the protein is provided in Figure 1 B.
The term "degrade" is used herein to refer to enzymes that are capable of cleaving proteins into amino acids, peptides and/or polypeptide fragments. The proteins of this invention degrade C3 without producing specific cleavage fragments as observed on a polyacrylamide gel.
A C3-degrading proteinase of about 29 kDa was isolated from a library of insertionally interrupted pneumococcal genes by identifying those clones that had increased C3 degrading activity as compared to wild type S. pnei~moniae.
There is at least some preference of the C3-degrading proteinases of this invention for C3 in that, for example, the C3-degrading proteinase does not 2o degrade other proteins, such as albumin, to a large extent. Exemplary methods for performing insertion duplication mutagenesis and for the identification of clones with elevated C3 degrading activity is provided in Example 1.
A gene encoding a C3-degrading proteinase is contained within a region that includes four open reading frames and interruption of the third open reading frame by homologous recombination severely impaired C3 degradation. ORF3 includes about 726 nucleotides and the sequence of the translated protein shares no substantial homology with proteins registered in either the GenBank or SwissProt databases.
The full length gene encoding a C3-degrading proteinase of this invention was inserted into a gene expression vector for expression in E.
toll.
Recombinant C3-degrading proteinase was isolated as described in the examples.
_g_ Those of ordinary skill in the art recognize that, given a particular gene sequence such as that provided in Figure 1, there are a variety of expression vectors that could be used to express t:he gene. Further, there are a variety of methods known in the art that could be used to produce and isolate the recombinant protein of ' 5 this invention and those of ordinary skill in the art also recognize that the C3 degrading assay of this invention will determine whether or not a particular expression system, in addition to those expression systems provided in the examples, is fun~~tioning, without requiring undue experimentation. A variety of molecular and immunolo;;ical techniques can be found in basic technique texts such as those of Sambrook et al. (~Llolecular Cloning, A Laboratory ~Llanuul.
1989 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY) and Harlow et al. (Antibodie.s: .A Laboratory ~l~lanual. Cold Spring Harbor. NY;
Cold Spring harbor Laboratory Press, 1988).
The gene' encoding the C3 degrading protein of this invention was 15 identified using a plasmicl library made with pneumococcal genomic DNA
fragments from strain CP1200. Although there are a variety of methods known for obtaining a F~lasmid library; in a preferred strategy, a plasmid library was constructed with. Sau 3A digested pneumococcal genomic DNA fragments (0.5 -4.0 kb) from pneumococ:cal strain CP 1200 (obtained from D.A. Morrison, 2o University of Illinois, Champagne-Ilrbana, Illinois and described in Havarstein LF, et al. Proe. ~Vcrtl. Acad. Sci. (U,SA) 1995;92:11140-1 1144) and inserted into the Bam HI site of the integrative shuttle vector pVA 891 (erm', cm'; has origin of replication for E. coli). This library was transformed into an E. cnli DHLa MCR strain by e;lectropo:ration. A total of 14000 E. coli transformants were 25 obtained by elec.troporation. Plasmid extractions of some randomly selected E.
coli transformarns revealed that all of them contained recombinant plasmids.
Plasmid library DNA was extracted from the E. coli transformants and was used to transform the CP 1200 parent pneumococcal strain using insertional mutatgenesis homologocus recombination.
3o The pne;umococc:al strain CP 1200 cells were made competent using a pH shift with HC1 procedure in CTM medium. 'the competent cells were frozen _g_ at -70° C in small aliquots until needed. Eight thousand pneumococcal transformants were produced using these methods.
Individual pneumococcal transformants were screened by ELISA for their altered phenotypic character based on their ability to degrade C3.
Bacterial - 5 cultures were incubated with C3 (0.83 ~g of C3/ml of culture) for about 2 hrs to about 4 hrs and the amount of undegraded C3 left in the samples was detected by enzyme linked immunoadsorbent assays (ELISA) using HRP-conjugated goat polyclonal antibody specific to human complement C3. The assay was standardized so that wells containing undegraded C3 had an O.D. 490 = ~ 1Ø
to Wells containing degraded C3 had a reduced optical density resulting from their reduced ability to bind anti-C3 antibodies. The optical densities of the mutant and parent strains were compared to that of negative controls. The negative controls were culture medium containing different concentrations of C3. The percent of C3 degrading activity was determined as a ratio of optical density of t 5 sample to control. Four mutants (SN3, SN4, SN5 and SN6) were identified with elevated C3 degrading activity (about 2-2.2 fold higher activity) as compared with the activity of the about 29 kDa C3-degrading protein from parent strain CP1200. This finding was confirmed by Western Blot analysis.
Total DNA from mutants SN3, SN4, SNS and SN6 was isolated and used 2o for electroporation into E. coli DHSa MCR. Low excision rates of plasmid DNA
from integrated plasmids within the pneumonocci genome can produce small amounts of free plasmid DNA and this DNA can be recovered when the DNA is transformed into E. coli. This allows further characterization of the plasmid.
Retransformation of the plasmid back into pneumococcus verifies the phenotype 25 of the original mutant.
Protein samples fiom the native C3-degrading protein and from mutants SN3, SN4, SNS, SN6 were incubated with C3 and separated on a 7.5%
SDS-PAGE gel under reducing conditions. C3 degrading activity was assessed using western blot analysis employing HRP-conjugated antibody to C3. Mutant 3o SN4 and mutant SN4-4G were used in further experiments. Mutant SN4-4G was identified after CP 1200 was retransformed with the recombinant plasmid WO 98!48022 PCTlUS98/08281 pLSN4a rescued from SN4. Both mutant SN4 and mutant SN4-4G almost completely degraded C3 after a 4 hr incubation. While the native C3 degrading protein degraded C3, after a 4 hr incubation, C3 degradation was incomplete as compared with a comparable incubation using mutants SN4 and mutant SN4-4G.
The plasmid encoding the protein from mutant SN4 was chosen for further investigation. Plasmid pLSN4a (encoding mutant SN4) was used to retransform the 'wild type CP 1200 strain. This resulted in 48 pneumococcal mutants with elevated C.4 degrading activity. Digestion with restriction endonuclease >-Lind III demonstrated that plasmid pLSN4a was about ~ 7.8 kb to and included an insert that was about ~ 2.3 kb.
Plasmid pLSN4a was used as a hybridization probe in southern hybridization experimenia to verify the presence of the insert in chromosomal DNA samples from the pneumococcal mutants. The results confirmed that the vector with insert (pLSN4a) and also the origin of the inserts in the mutants and SN4 were integrated in the chromosomal DNA. Both mutants SN3 and SN4 consisted of two hybridizing junction fragments of sizes about ~2.2 kb and about 5.8 kb. These fragments were also present in their parent strain CP 1200.
There were two other hybridizing fragments at about ~ 4.2 kb and about ~ 3. 5 kb and these two fragments together gave a total of about ~7.8 kb (pLSN4a is ~ 7.8 kb).
2o These two bands were also present in the vector with insert sample. Both insert and vector included EcoR I sites and represent the recombinant plasmid.
Analysis indicated that a gene duplication had occurred in the SN4 mutant strain:
therefore, the improved C3-degradation activity could be attributed to increased C3-degrading protein in the SN4 mutants.
The sequence of about 1 kb of the 2338 by insert was determined using whole pLSN4a plasmid .as a template. The remaining sequence (about 1338 bp) with just insert (PCR product) as a template, was sequenced by ICBR , University of F'aorida. Both complementary strands were sequenced. The results indicated that there were four open reading frames with the relative locations 3o provided in the schematic below:

WO 98/48022 PCTlUS98/08281 (462bp) (144 bp) (726 bp) ORF4 (358bp) 5' 3"
3' 5"
No significant homology was found between the derived amino acid t o sequence of the above ORFs and protein sequences from the protein databases tested. The ORF3 nucleic acid sequence encoding a C3 degrading proteinase of this invention is provided in Figure 1 A and is designated SEQ ID NO:1. The amino acid sequence of this C3 degrading proteinase is provided in Figure 1 B
and is designated SEQ ID N0:2.
t 5 Out of four opening reading frames (three full and one partial) in the insert, the ORF3 was chosen for ftirther examination because it contained the largest insert. A 620 by internal portion (from nucleic acid 1246 to nucleic acid 1863 of Figure 1 A) of ORF3 (PCR product) region was ligated into the Hind III
site of plasmid pVA 891 and the construct was transformed into CP 1200 2o competent cells to knock out the proteinase activity. The transformants were tested for their ability to degrade C3 after separation on SDS-page gels using western blot analysis. The ORF3 disruption mutant had poor activity in comparison with its parent strain CP 1200.
The entire ORF3 gene (PCR product) was cloned into Nde I and Bam H I
25 sites of pet-28b(+). The vector positions a His-Tag at the N-terminus of the protein. The plasmid construct was transformed into an E. coli (DHLa MCR) strain for stabilization before it was transformed into an E. toll (BL 21 DE3) protease deficient strain for protein expression.
The BL 21 DE3 strain that included the construct (pet 28b(+) with 3o ORF3) was induced for ORF3 protein expression. Total cell protein extracts of the induced and uninduced cultures were tested for C3 degrading activity. The expressed His-tagged ORF3 protein was about ~ 29 kDa (~ 5 kDa) on 10%
SDS-PAGE gels in the induced samples from the insoluble protein fraction.

Solubiliz anon of the ORF 3 protein from induced BL21 DE3 cultures was performed by treating the sample with: a) TES {SOmM, 1 mM, 1 M}; b) 6mM G-HCI + 1 mM DTT; c) 6mM G-HC1 -~ 1 mM DTT + 1 % Tween 20; and d) 6mM G-HC1 + 1mM DTT + 1% Triton X -100. Both treatments "c" and "d"
resulted in soluble protein. Treatment "c" was used to produce solubilized recombinant C3 degrading protein that was used for further protein studies.
Guanidine-HCl and DTT were removed from the expressed His-'fagged ORF3 protein samples b;y dialysis. The protein was subjected to Nickel column purification and the eluted His-Tagged protein was visualized on a 10%
I o SDS-PAGE gel.
The isolated protein encoded by ORF 3 was incubated with human complement C3 for 4 hrs at 37°C in the presence of PBS. Control samples without the protein same>les were used as negative controls for comparative purposes. The samples were run on SDS-PAGE gel under reducing conditions and analyzed for the structure of C3 by Western Blot assay using polyclonal antibodies to human complement C3. The results indicated that the samples contained a protein encoded by the ORF 3 region and that the protein degraded human C3 protf;in. Both a and (3 chains of C3 molecules were susceptible to degradation. In these experiments while the a chain was almost completely ?o degraded, the (3 chain was also degraded, but to a somewhat lesser extent.
The C3 degrading proteins of this invention were designated CppA
proteinases and the genea of this invention are designated cppA. The proteins of this invention have an apparent molecular weight on a 10% 5DS-polyacrylamide gel of about 29 kDa {~5 kDa) and preferably has a molecular weight of about 24 kDa to about 3~l kDa. A,s described above, Example 5 indicates that the proteinase is conserved throughout S. pneumaniae strains. However. those of ordinary skill in the art will recognize that some variability in amino acid sequence is expected and that this variability should not detract from the scope of this invention. For e:Kample, conserved mutations do not detract from this 3o invention nor d.o variations in amino acid sequence identity of less than about 80 amino acid :sequence identity and preferably less than about 90% amino acid sequence identity where the protein is capable of degrading human complement protein C3, and particularly where the protein is isolated or originally obtained from an S. pneumoniae bacterium.
Some nucleic acid sequence variability is expected among the strains as is some amino acid variability. Conserved amino acid substitutions are known in the art and include, for example, amino acid substitutions using other members from the same class to which the amino acid belongs. For example, the nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and tyrosine. The polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine and glutamine. The positively charged (basic) amino acids include arginine, lysine and histidine.
The negatively charged (acidic) amino acids include aspartic acid and glutamic acid. Such alterations are not expected to affect apparent molecular weight as determined by polyacrylamide gel electrophoresis or isoelectric point.
t 5 Particularly preferred conservative substitutions include, but are not limited to, Lys for Arg and vice verse to maintain a positive charge: Glu for Asp and vice versa to maintain a negative charge; Ser for Thr so that a tree -OH is maintained;
and Gln for Asn to maintain a free NH,. A preferred protein of this invention includes a protein with the amino acid sequence of SEQ ID N0:2. Other 2o proteins include those degrading human complement protein C3 and having nucleic acid encoding the protein that hybridizes to SEQ ID NO:1 under hybridization conditions of 6XSSC, SX Denhardt, 0.5% SDS, and 100 pg/ml fragmented and denatured salmon sperm DNA hybridized overnight at 65°C
and washed in 2X SSC, 0.1% SDS one time at room temperature for about 10 25 minutes followed by one time at, 65°C for about 15 minutes followed by at least one wash in 0.2XSSC, 0.1% SDS at room temperature for at least 3-5 minutes are also contemplated in this invention. Polypeptides or peptide fragments of the protein can also be used and a preferred protein of this invention comprises amino acids 1-50 of SEQ ID N0:2.
3o The proteins of this invention can be isolated or prepared as recombinant proteins. That is, nucleic acid encoding the protein, or a pouion of the protein.

can be incorporated into aul expression vector or incorporated into a chromosome of a cell to express the protein in the cell. The protein can be purified from a bacterium or another cell, preferably a eukaryotic cell and more preferably an animal cell. Alternatively, the protein can be isolated from a cell expressing the protein, such as a S. pneu,moniae cell. Peptides of the CppA proteinase are also considered in this invention. The peptides are preferably at least 15 amino acids in length and preferred peptides are peptides with at least 15 sequential amino acids from SEQ ID N0:2. Another preferred protein fragment includes amino acids I-50 of SEQ ID NO:2.
Nucleic acid encoding CppA proteinase is also part of this invention.
SEQ ID NO: I is a preferred nucleic acid fragment encoding a CppA proteinase.
Those of ordinary skill in the art will recognize that some substitution will not alter the CppA proteinase sequence to an extent that the character or nature of the CppA proteinase~ is substantially altered. For example, nucleic acid with an ~ 5 identity of at least 80% to SEQ ID NO: I is contemplated in this invention. A
method for determining whether a particular nucleic acid sequence falls within the scope of this invention is to consider whether or not a particular nucleic acid sequence encoders a C3-degrading proteinase and has a nucleic acid identity of at least 80% as compared with SEQ ID NO: l . Other nucleic acid sequences 2o encoding the CppA proteinase includes nucleic acid encoding CppA where the CppA has the same sequence or at least a 90% sequence identity with SEQ ID
N0:2 but which includes degeneracy with respect to the nucleic acid sequence.
A degenerate codon means that a different three letter codon is used to specify the same amino acid. For example, it is well known in the art that the following 25 RNA codons (and therefore, the corresponding DNA codons, with a T
substituted for a U) can be used interchangeably to code for each specific amino acid:
Phenylalanine (Plhe or F) UUU or UUC
Leucine (Leu or L) UUA, UUG, CUU, CUC, CUA or CUG
3o Isoleucine (Ile or I) AUU, AUC or AUA
Methionine (Met or M) AUG
-IS-WO 98/48022 PCTliJS98/08281 Valine (Val or V) GUU, GUC, GUA, GUG
Serine (Ser or S) UCU, UCC, UCA, UCG, AGU, AGC
Proline (Pro or P) CCU. CCC, CCA, CCG
Threonine (Thr or T) ACU, ACC, ACA, ACG
_ 5 Alanine (Ala or A) GCU, GCG, GCA, GCC
Tyrosine (Tyr or Y) UAU or UAC
Histidine (His or H) CAU or CAC
Glutamine (Gln or Q) CAA or CAG
Asparagine (Asn or N) AAU or AAC
to Lysine (Lys or K) AAA or AAG
Aspartic Acid (Asp or D) GAU or GAC
Glutamic Acid (Glu or E} GAA or GAG
Cysteine (Cys or C) UGU or UGC
Arginine (Arg or R) CGU, CGC, CGA, CGG, AGA, AGC
t 5 Glycine (Gly or G) GGU or GGC or GGA or GGG
Termination codon UAA, UAG or UGA
Further, a particular DNA sequence can be modified to employ the codons preferred for a particular cell type. For example, the preferred codon usage for E. coli is known, as are preferred codons for animals and humans.
2o These changes are known to those of ordinary skill in the art and therefore these gene sequences are considered part of this invention. Other nucleic acid sequences include nucleic acid fragments of at least 30 nucleic acids in length from SEQ ID NO: I or other nucleic acid fragments of at least 30 nucleic acids in length where these fragments hybridize to SEQ ID NO:1 under hybridization 25 conditions of 6XSSC, SX Denhardt, 0.5% SDS, and 100 g.g/ml fragmented and denatured salmon sperm DNA hybridized overnight at 65°C and washed in SSC, 0.1% SDS one time at room temperature for about 10 minutes followed by one time at, 65°C for about 15 minutes followed by at least one wash in 0.2XSSC, 0.1% SDS at room temperature for at least 3-5 minutes.
3o The nucleic acid fragments of this invention can encode all, none (i.e., fragments that cannot be transcribed, fragments that include regulatory portions of the gene, or the like) or a portion of SEQ ID NO:2 and preferably containing a contiguous nucleic acid fragment that encodes at least nine amino acids from SEQ ID N0:2. Because nucleic acid fragments encoding a portion of the CppA
proteinase are contemplated in this invention, it will be understood that not all of the nucleic acid j:ragments will encode a protein, polypeptide or peptide with degrading activity. Further, the nucleic acid of this invention can be mutated to remove or otherwise inactivate the C3 degrading activity of this protein.
Therefore, fragments without C3 degrading activity that meet the hybridization requirements de~~cribed above are also contemplated. Methods for mutating or otherwise altering nucleic acid sequences are well described in the art and the production of an immunogenic, but enzymatically inactive protein can be tested for therapeutic utility. Preferred nucleic acid fragments include get ccc agt atg (Claim 34).
The nucleic acid fragments of this invention can be incorporated into nucleic acid vectors or stably incorporated into host genomes to produce recombinant protein inclu~,ding recombinant chimeric protein. A variety of nucleic acid vectors are known in the art and include a number of commercially available expression plasmids or viral vectors. The use of these vectors is well within the scope of what :is ordinary skill in the art. Exemplary vectors are 2o employed in the examples, but should not be construed as limiting on the scope of this invention.
This invention also relates to antibody capable of binding specifically to a protein of about 29 kDa., and preferably a protein of about 24 kDa to about kDa, from S. pneumoniae and preferably where the protein is capable of degrading huma~a complement C3. Polyclonal antibody can be prepared to a portion of the protein or to all of the protein. Similarly, monoclonal antibodies can be prepared to all or t:o a peptide fragment of the about 29 kDa C3 degrading protein of this invention. Methods for preparing antibodies to protein are well known and well described, for example, by Harlow, et al. (supra). In a preferred 3o example, the antibodies c.an be human derived, rat derived, mouse derived or rabbit derived. 1?rotein-binding antibody fragments and chimeric fragments are also known and are within the scope of this invention.
The invention also relates to the use of immune stimulating compositions. The term "immune stimulating" or "immune system stimulating' refers to protein or peptide compositions according to this invention that activates at least one cell type of the immune system. Preferred activated cells of the immune system include phagocytic cells such as macrophages, as well as T
cells and B cells. Immune stimulating compositions comprising the peptides.
polypeptides or proteins of this invention can be used to produce antibody in an animal such as a rat, mouse, rabbit, a human or an animal model for studying S.
pnea~moniae infection. Preferred immune stimulating compositions include an immune stimulating amount of at least a peptide including at least 15 amino acids from the CppA proteinase. The immune stimulating composition can further include other proteins in a pharmaceutically acceptable buffer, such as PBS or another buffer recognized in the art as suitable and safe for introduction t 5 of proteins into a host to stimulate the immune system. The immune stimulating compositions can also include other immune system stimulating proteins such as adjuvants or immune stimulating proteins or peptide fragments from S.
pneumoniae or other organisms. For example, a cocktail of peptide fragments may be most useful for controlling S. pneumoniae infection. Preferably one or 2o more fragments of the proteins of this invention are used in a vaccine preparation to protect against or limit S. pneumonicre colonization or the pathogenic consequences of S. pneumoniae colonization.
This invention also relates to a method for inhibiting Streptococct.~.s pneumoniae-mediated C3 degradation comprising contacting a Streptococcus 25 pneumonia bacterium with a protein, such as an antibody or another protein that is capable of binding to an isolated protein of about 24 kDa to about 34 kDa from Streptococcus pneumoniae. The protein capable of binding to an isolated protein of about 24 kDa to about 34 kDa can be an antibody or a fragment thereof or the protein can be a chimeric protein that includes the antibody 3o binding domain, such as a variable domain, from antibody that is capable of specifically recognizing an isolated protein of about 24 kDa to about 34 kDa _ lg _ from Streptococcus pneu,moniae having C3 degrading activity.
The isol~~ted S. pnearmoniae protein of this invention can be isolated and purified and the isolated protein or immunogenic fragments thereof can be used to produce antibody. Peptide fragments or polypeptide fragments of the protein without C3 degrading ability can be tested for their ability to limit the effects of S. pneumoniae infection. Similarly, the protein of this invention can be modified, such a.s through mutation to interrupt or inactivate the C3 degrading capacity of the protein. Isolated protein can be used in assays to detect antibody to ,S. pneumoniae or as part of a vaccine or a multi-valent or multiple protein or peptide-containing vaccine for S. pneumoniae therapy.
It is further contemplated that the proteins of this invention can be surface expressed on vertebrate cells and used to degrade C3, for example, where complement deposition (or activation) becomes a problem, such as in xenotransplantation or in complement-mediated glomerulonephritis. For example, the recombinant protein, or a portion thereof, can be incorporated into xenotransplant c.elis and expressed as a surface protein or as a secreted protein to prevent or minimize complement deposition (and/or complement-mediated inflammation).
All references and publications cited herein are expressly incorporated by reference into this disclosure. There are a variety of alternative techniques and procedures available to those of skill in the art which would similarly permit one to successfully perform the intended invention in view of the present disclosure.
It will be appreciated by those skilled in the art that while the invention has been described above in connection with particular embodiments and examples, the invention is not necessarily so limited and that numerous other embodiments, examples, uses, modifications and departures from the embodiments. examples and uses may bf; made without departing from the inventive scope of this application.

Example 1 Generation of Insertional Duplication Mutants and Recovery of Recombinant Plasmids from Selected Mutants In a preferred example, insertion-duplication mutagenesis was used to - isolate a gene encoding the C3 degrading proteinase from Streptococcus pneumoniae of this invention. A plasmid library was created with 0.5 - 4.0 kb chromosomal fragments of pneumococcal strain CP 1200 (derivative of RX1;
Morrison, D. A., et al. J. Bacteriol., 156:281-290,1983) originally obtained from 1 o Dr. Morrsion's lab, University of Illinois at Chicago and inserted into the Bam HI shuttle vector pVA 891 (erm', cm' Marcina, F.L. et. al. Gene 25:115-150, 1983, obtained from Dr. Marcina (Virginia Commonwealth University, Richmond, VA). pVA891 has resistance markers for erythromycin (erm) and chloramphenicol (cm). The vector has an origin of replication for E. coli, but the origin is non-replicative in Streptococci. Recombinant plasmid can survive when it integrates into the pneumococcal chromosomal DNA by homologous recombination .
E. coli DHS oe MCR competent cells were made according to the procedure given in the Bio-Rad Laboratories manual (Richmond, CA) and the library was transformed into the competent cells with Bio-Rad Gene Pulser apparatus (Bio-Rad Laboratories, Richmond, CA) by electroporation.
E. coli cells were maintained as freezer stocks in small aliquots at -80°C, in LB broth in the presence of 10% glycerol. The cells were grown either in LB
or TB broth or on LB agar plates containing appropriate antibiotics (erythromycin 200 ~g/ml or chloramphenicol 15 or 30 pg /ml or kanamycin 30 ~g/ml).
Electroporation was conducted in 0.1 cm cuvette at 1- 2 kV/cm voltages and a capacitance of 200 S2. Transformants were selected on LB medium containing either chloramphenicoi (cm, 30 p,g /ml) or erythromycin (enn, 300 ~g /ml) or combination of erm and cm (200ug/mI + I Sug/ml).

A total of 14000 E. toll transformants were obtained from the library.
Plasmid extractions and :restriction analysis of randomly selected E. toll transformants revealed the presence of recombinant plasmids.
Plasmids or recombinant plasmids were extracted from E. toll strains by polyethylene gl~~col precipitation procedure (Kreig. P. and Melton. D., in Promega Protocols and .Application.s p. 106, 1985-86) or a modified alkaline .
lysis miniprep protocol (Xiang. C., et al., Biotechnigues. 17:30-32, 1994) a modified alkaline extraction procedure (Birnboim H C and J Doly.,1\rucl. Acids Res. 7:1513-15~ 3, 1979), or CsCI-ethidium bromide gradient method or Qiagen 1o kit (Plasmid midi kit., Chartsworth, CA). Solutions containing DNA were cleaned directly from agarose gels by GeneClean II kit (BIO 101, La Jolla. CA) or Qiagen kit (DNA extraction from gels., Chartsorth, CA). DNA was cleaned by Wizard DNA clean up ki.t (Promega Corp., Madison, WI). Amplified gene products were also cleaned by Wizard PCR clean up kit (Promega Corp., ~ 5 Madison, WI).
The plasmids were transformed into Pneucnococcal cells. The pneumococcal strains were always maintained as freezer stocks in small aliquots at -80°C, in THl3 in the presence of 10% glycerol. Pneumococcal cells were grown without shaking in CAT (Morrison, D. A., et al., 1983, szrprcr) or THB
2o medium (broth or agar). For transformation experiments, either complete transformation (CTM) broth (Morrison, D. A., et al.. 1983) or THB+ 0.~% Yeast broth (Mother Janet., et al. J. Bacteriol. 168:1463-1465, 1986) and for ELISA
experiments, SI'rIP, a synthetic medium (see Table 1 ) were used. Erythromycin (0.05 pg /ml) was employed as a selective antibiotic marker for pneumococcal 25 mutants.

Table 1. SMP - a synthetic medium SMP solution # I (final volume 2 liters):
NaCI 10.08; NH4CI 4.Og; KCl 0.88: Na2HP04 0.248; MgS04 0.048e; CaCl2 0.0208;
PeS04.7H20 0.0001 lg; Tribase 9.688 : add d.H2() up to I liter pH to 7.55 and then add the following amino acids:
l.-Arginine 400 mg; L-Asparagine 20 mg (monohydrate 22.8 mg): Glycine 240 mg:
I,-1-listidinc 300 mg;
L-Isoieucine 13.10 mg; L-Leucine 13. (0 mg: L-Lysine 840 mg; 1.-methionine 360 mg: (low-methi.
2.6mg); L-valine ( 1.70 mg; llracil 2 mg. Make it up to a final volume of 2 liters.
SMP solution 2 (vitamins):
Biotin 0.07 mg; Choline 25 mg; Nictinamidc 3.0 mg; ca pantothenatc 12.0 mg;
Pyridoxal HCI 3.0 me:
Ribotlavin l.~ mg; Thiamine 3.0 mg: L-Cysteine I-ICI 0.5 e; L-Glutamine 0.1 g;
Na Pyruvatc 4.Og: add' water and then make up to ~Oml.
Reconstituting SMP:
Start with: ml Solution # 1 100 Add:
Solution #2 I
Solution #3(2~% Glucose) 1.6 Solution # 4f4% BSA) 2 Pneumococcal strain CP 1200 cells were made competent by ''competence induction by pH shift" (procedure obtained from Dr. Morrison~s lab, Univ. of Illinois at Chicago, I11.) in CTM medium and the competent cells were frozen at -70 ° C in small aliquots until required. In this procedure, to 125 ml of CTM added 1.20 ml of 1 M HCl (final concentration 9mM) and 4 ml of 0.2 O.D. (550 nm) of frozen pneumococcal stock cells. This culture was incubated at 37°C and O.D. readings of the culture were taken at 20 minute intervals beginning after 3 hrs of incubation. When the culture reached an O.D. of 0.156 (550 nm), 1.2 ml of 1N NaOH was added at 37"C. After mixing the culture gently, 1 ml of culture was removed as a '0' time point sample, mixed with 100 Ltl of glycerol and kept on a prechilled metal block. Similarly. ten ml samples were drawn at each time point of 13, 17, 21 and 25 min and each sample was added directly to prechilled 1 ml of glycerol. Each time point sample was frozen in small aliquots at - 70°C. Competence was tested for each time point sample by adding 1 yl of DNA ( about 250 ng) to 100 ~tl of cells and incubating at 37°C for 25 min for transformation. The transformation culture was diluted and plated on selective medium (erythromycin 0.05~tg/ml). The time point sample that showed the highest transformation efficiency was used for future transformation experiments. Transformation of the extracted recombinant plasmid library from E. coli transformants into pneumococcal strain CP1200 yielded about 8,000 pneumococcal transformants indicating that the plasmid was inserted into the CP1200 chromosome via homologous recombination.
Extraction of pnc:umococcal chromosomal DNA was performed by a slight modificavtion of the method used in the laboratory of Dr. Donald A.
- 5 Morrison, University of Illinois at Chicago. Pneumococcal cells were grown in THB to an O.D. at 550 run from 0.3-0.4, then rapidly chilled on ice and O.SM.
EDTA was added to a final concentration of 10 mM, the cells were spun at 10,000g for 10 minutes .at 4°C, and the pellets were resuspended in 1:10 volume of cold STE (50mM Tris-HCI (pH 8.0), IOmM EDTA (pH 8.0), and O.1M
Io NaCI). After a second cf:ntrifugation, cells were resuspended in 1/100 volume of cold STE, lysecl with 1°io Triton X-100, and incubated at 37°C
for 5-10 minutes for autolysis. After the addition of 1 % SDS, the cells were swirled in water bath at 50-60°C for '.i min. RNase ( 100 pg/ml) and proteinase K (50 yg/ml) were added sequenti;~lly with incubations of 2 hours and 1 hours. respectively. The ~ 5 cells were extracted twice with one volume of phenol/ehloroform and once with one volume of chloroform and the supernatant was collected for ethanol precipitation. T'he precipitate was washed twice with 70% ethanol, and the pellet was collected and resuspended in TE ( l OmM Tris-HC1 pH 8.0, 1 mM EDTA) or water as required.
2o The plasmid library DNA was extracted by polyethylene glycol precipitation procedure (Kreig. P. and Melton. D. 1985 szrpra), from pooled E.
coli transformants and used to transform CP 1200, the parent pneumococcal strain following the method that was obtained from Dr. Morrison, University of Illinois at Chicago. For pneumococcal transformation, frozen pneumococcal 25 competent cells were thawed on ice and to 100 pl of these competent cells.

ng to 1000 ng of plasmid library was added in a separate eppendorf tube. This tube was incubated at 3'7°C in a water bath for about 25 min to 35 min and the mixture was diluted 1/10 in CAT medium and incubated further for about 1-1.7 hrs. Following the final incubation, the mixture was plated by overlay procedure 30 (method was obtained from Dr. Morrison University of Illinois at Chicago).
The overlay procedure involved pouring four different layers of agar (THB or CAT) in a small petri dish as follows: a) first or base layer: 3 ml of agar; b) second or cells' layer: mixture of 1.5 ml of agar and 1.5 ml of broth containing required concentration of bacterial cells; c) third layer: 3 ml of agar; 4) fourth layer or top layer: 3 ml of agar containing 4X required concentration of antibiotic (erythromycin, at 0.05pg/ml x 4 = 6 pg /ml ). The plates were incubated at 37°C.
Individual transformants were transferred by stab inoculation to individual wells of microtitre plates containing 100y1 of THB and erythromycin (O.OSyg/ml). The recovered transformants in microtitre plates were diluted 1:10 in SMP medium and grown until early log phase, and screened for their ability to degrade C3 by ~ o ELISA.
Spontaneous excision of recombinant plasmids occur in these kind of pneumococcal mutants with low frequency and therefore, chromosomal DNA
preparations of these mutants often include low levels of plasmid DNA (Pearce B J., et al., Mol. Microb. 9(5):1037-1050, 1993). Electroporation of E. coli is a t5 highly efficient way of isolating the plasmid constructs in E. coli for further study. Chromosomal DNA ( 100 ng-200 ng in a final volume of 2 ~ls) fcom the individual pneumococcal mutants of interest was electroporated into E. coli DHS
a MCR competent cells to obtain E. coli transformants with recombinant plasmids. One of the recovered recombinant plasmids (pLSN4a) (see Table 2}
2o was introduced back into wild type CP 1200 pneumococcal strain by transformation. The transformant SN4-4G was again evaluated for its C3 degrading activity by ELISA.
DNA fragments were analyzed by horizontal electrophoresis in agarose gels (0.5 % to I .0%) with Tris-borate EDTA (TBE) buffer or Tris-acetic acid 25 EDTA (TAE) buffer (Sambrook, J. E. Fritsch and T.Maniatis.1989). One kb ladder from Gibco BRL or Hindi III or Hind III lEcoRl digested lamda DNA
from Boehringer Mannheim, was employed as a molecular weight standard.
Restriction endonucleases, calf intestinal phosphatase, T4 DNA ligase, from Gibco BRL Life Technology, Grand Island, NY., Boehringer Mannheim , 3o Indianapolis, IN., Promega Corp., Madison, WI., Bethesda Research Laboratories, G;zithersburg, MD., or New England Biolabs., Inc., Beverly, MA., were used as described by the manufacturers' instructions.
DNA fragments were analyzed by Southern hybridization. DNA was transferred from. gels to PvISI Magnagraph nylon membranes (Micron Separations, Inc., Westboro, MA) for hybridization and detection using Genius nonradioactive DNA labeling and detection kit (Boehringer Mannheim Biochemicals, hadianapolis, IN) following the instructions provided with the kit.
Chromosomal or plasmid DNA either from the pneumococcal or E. coli culture was isolated as described in earlier sections. About 100 ng - 400 ng of each sample was digested with required restriction enzymes and run on 0.7% agarose gel, transblotted onto Magnagraph-nylon membrane overnight. The rest of the procedure was performed as instructed by the manufacturer.
Bacterial strains <~nd plasmids used in this example and the examples that follow are summarized in Table 2 below.

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x Example 2 Identification of Mutants with altered C3-degrading activity Individu;~l pneumococcal transformants were screened by ELISA for their altered C3 degradin;7 activity. The pneumococcal transformants were grown individually in THB in the presence of erythromycin (0.05 yg/ml) in microtitre plates up to log ~~hase and diluted 1/0 in SNIP medium (O.OS~g of erythromycin/ml). The S1VIP bacterial cultures were grown up to log phase and incubated with C:3 (0.83 ~_~g of C3/ml of culture) for 2-4 hrs. After incubation 1 o with C3, 100 p.I s of each individual transformant was transferred to an ELISA
binding plate and incubated overnight at 4°C. The plates were washed with PBS
(10 pM phospha.te buffer saline + 0.05% Tween-20) three times. 100 yl of HRP-conjugated goat polyclonal antibody specific to human complement Cs (1:10000 dilution of 48m~;/ml) was added to each well and the plates were incubated for I -~5 2 hrs at 37°C. Each microtitre plate was washed with PBS as described above.
100 pl of 30% t~PD (12 mg of O-Phenylenediamine (Zymed, South San Francisco, CA) i.n 30m1 of Citrate buffer (200mM Na,HPOa and I OOmM citric acid-pH 5.0), and 12 pl of 30% H,O,) was added to each well and the plates were incubated for 30 min in dark. The reaction was stopped by the addition of 50 GIs 20 of 2.SM H,SOa t.o each well. The amount of undegraded C3 left in the samples was detected by HRP-conjugated goat polyclonal antibody specific to human complement C3. The assay was standardized so that wells containing undegraded C3 had an O.D. 490 = ~ 1Ø Wells with degraded C3 had reduced optical density readings resulting from decreased binding of anti-C3 antibodies.
25 The optical den:~ities of t)!le mutant and parent strains were compared to that of negative controls (medium with different concentrations of C3) to calculate the percent of C3 degrading activities. There were four mutants, SN3. SN4, SNS
and SN6, with elevated C.'3 degrading activity (2.2 fold- Table 3) compared to the activity of their parent strain CP1200. This finding was confirmed later by 3o Western immunoblotting, for the pneumococcal mutant SN4. SN4-S 10 (disrupted cppA gene) were also mutants of CP1200 with reduced C3 degrading activity.

Table 3. )JLISA results for C3 degradation by parent and hyper active mutants of pneumococcal strains -strains ELISA reading at 490nm *Percentage of C3 degraded in each sample or controls **negative control 0.608 0%
CP 1200 (parent) 0.30 5 f SN3 (mutant) 0.20 67.2%
SN4 (mutant) 0.162 73.4%
SN5 (mutant) 0.23 60.0%
SNS (mutant) 0.23 60.0%
*, averaee of minimum of 4 individual expts. conducted at different times **, negative sample is medium only (THB or SMP) with C3 and without bacterial cells Immunoblotting was performed using ECL Western blotting protocols (Amersham Life Sciences, Arlington Heights, IL). The pneumococcal mutants or E. coli cultures with or without plasmids were grown from freezer stock cultures.
in THB or LB up to log phase and incubated with C3 (0.83 pg of C3 / ml) for 2-4 hrs, the cultures were spun down (2,500 rpm for 1 min RT or 4°C) and the supernatants were collected. The optical densities of the cultures were carefully monitored and samples were equalized before being subjected to incubation with C3. Equal amounts of all collected supernatants containing undegraded C3 were applied to 7.5% or 10% SDS-PAGE gels under reducing conditions. The gel was transblotted to nitrocellulose membrane (75 volts; 4°C) for 1 hr.
Proteins were transferred in this example and in subsequent examples from gels to nitrocellulose membranes using a Hoeffer transfer apparatus in Towbin buffer (3.03g Tris, 14.4g glycine and 200m1 Methanol in 1 litre volume pH.8.3; Towbin et al. (1979) PNAS:4350-4354) for lhr at 70 volts or gels were stained with 0.125% Coomassie Brilliant Blue R-250 (Pierce, Rockford, IL) made in 50%
Methanol and 10% Acetic acid.
The blot was incubated in 10% skim milk (skim milk powder) for 1 hr (room temperature) or overnight (4°C) with gentle shaking. The blot was washed in TTBS (0.1% Tween, 20 mM Tris, 137mM Saline Buffer) several times and incubated with a 1:1000 dilution of HRP- conjugated goat antihuman C3, polyclonal antibody, IgG fraction (ICN Pharmaceuticals/Cappel, Costa Mesa, CA) made in 3X TTBS+3% BSA for 1 hr with gentle shaking. The incubated blot was washed again several times in TTBS and incubated for one minute in chemiluminescent reagents ( 1:1 ratio of 2X luminol/Enhancer and 2X stable peroxide solutions, Pierce, Rockford, IL). This blot was exposed to films for ~
sec to several seconds in the dark and the films were developed. The SDS-- 5 PAGE gels alw;~ys contained pre-stained high molecular weight markers (Bethesda Rese;~rch laboratories, life Sciences, Grand Island, NY) ranging from 200 kd to 19 kd. The washes and incubations were performed at room temperature with a gentle shaking unless stated otherwise.
Electroporation of chromosomal DNA from the hyper-active to pneumococcal mutants, SN3, SN4, SNS and SN6 into E. coli DHS a. MCR
competent cells gave risf° to E. coli transformants with rescued recombinant plasmids. E. coli DHS cx MCR transformants. LSNp, LSN4. LSNS, LSN6, LSN4G contained plasmids (Table 2 from pneumococcal mutants, SN3, SN4 SNS, SN6 and SN4-4G mutants respectively). Details of E. coli strains ~ 5 containing different constructs are listed in Table 2 (supra). Restriction analysis (Hind III) revealed that the inserts were indeed recombinant plasmids.
Different sizes of recombinant plasmids were obtained from each hyperactive pneumococcal mutant. Recombinant plasmids, pLSN3 and pLSN4 recovered from mutants SN3 and S'~N4 were the same size (~7.8kb) and their insert size was 20 ~2.4kb. The size of the insert of an ~1 lkb recombinant plasmid, pLSNS, obtained from the pneumcoccal mutant SNS was about 5.6 kb. The fourth pneumococcal mutant, SN6, gave two different, ~6.Skb and ~10.5kb recombinant plasmids, pLSNci;, and pLSN6~, which had inserts of 1.1 kb and S.1 kb respectively. These pneumococcal mutants were also examined by 25 southern hybridization. 'rhe hyperactive pneumococcal mutant SN4 was chosen for further studies of C3 degradation and therefore, the recombinant plasmid pLSN4 which was rescued from the mutant SN4 was subjected to a full investigation.
Plasmid pLSN4 was used as a probe against EcoRl digested 30 chromosomal L>NA samples of the pneumococcal mutants and this confirmed the integration of the vector + insert (pLSN4) in the mutants SN3 and SN4. Both SN3 and SN4 hyperactive mutants included two hybridizing fragments of sizes 2.2 kb and ~ 5.8 kb which were also present in parent strain CP1200. There were two other hybridizing vector/insert junction fragments at ~ 4.2 and ~ 3.5 and these two together gave a total of ~ 7.8 kb (pLSN4 is ~ 7.8 kb). These two bands were also present in the EcoRl digested pLSN4 DNA sample. Both insert and vector had EcoRl sites and represented recombinant plasmid. The pattern of the other hyperactive mutants, SNS and SN6, suggested that these mutants may have had different inserts in their integrated recombinant plasmids.
The same plasmid pLSN4 was used to retransform the parent pneumococcal strain CP1200 to confirm its involvement in hyperactivity. As expected, the obtained mutant SN4-4G (Table 2) reproduced the phenotype of enhanced C3 degradation.
example 3 Isolation and identification of C3-degrading gene Double stranded DNA sequence analysis was performed on the insert part of the recombinant plasmid pLSN4. Since this insert was associated with degrading hyper-activity, we expected t:~ see insertion either in regulatory region of the corresponding gene or duplication of the gene; however, there was no 2o indication of insertion in a regulatory region on the basis of the protein data base search. This suggested the possibility of gene duplication. There were three full open reading frames (ORFs) and one partial open reading frame with no significant homology between the derived amino acid sequences of the above ORFs and the proteins as provided in searches of GenBank, Blast and SwissProt databases. Preliminary data (Cathryn A S., et al., J. Inf. Dis. 170:600-608, 1994) suggested that the C3 degrading proteinase might be cell wall associated (exported protein) and therefore, we looked for the presence of a signal sequence, a proline rich domain or a LPXTG motif. None of the four ORFs had these sequence patterns and we chose ORF3, the largest ORF for further 3o analysis.

Double-stranded DNA of plasmid pLSN4a was prepared using CsCI
gradient /ethidium bromide isolation and used as a template. Oligonucleotide primers were synthesized using an applied Biosysterns 391 automated synthesizer, by ~3ibco BRL, or by Oligo I DOOM DNA synthesizer (Beckman Instruments Inc. La Brea, CA) Using the dideoxy chain terminator method (Sanger F., et al., Proc. 1'Jcrtl. Acad. Sci. (USA) 82:1074-1078, 1977) and employing Sequenase 2.0 (U.S. Biochem) and [a-;'S] dATP (Amersham life Sciences, Arlington Heights, IL) sequencing was done with an apparatus: 20110 Macrophor Electrophoresis unit (LKB Bromma) as indicated by Sequenase version 2.0 (Amersham life sciences).
The insert (see Fig 3) in the recombinant plasmid pLSN4, recovered from the hyper active pneumococcal homologous-recombinant mutant SN4 seemed to have restriction sites for Hinc II, Nru I, EcoR I. Cla I, EcoR V and Hpa I out of about 20 enzymes tested and this data correlated with the sequence data.
After reviewing the sequencing data, an internal fragment, 620bp, of the cppA gene (ORh3 of the insert) was generated by gene amplification (see Table 4 for primers) with overhangs containing Hind III restriction sites. This fragment was subcloned into Hind. III sites in the vector pVA891, electroporated into E.
coli and tested for the pr~°sence of the insert. Finally, this subclone was 2o transformed into wt CP1200 pneumococcal competent cells to inactivate the original cppA gene in thc: wild type CP 1200.
DNA amplifications were carried out using a Hybaid Omnigene machine with primers (sc:e Table 4 for primers' sequences and amplification cycle conditions) complimentary to the 5' and 3' ends of the required DNA fragments.
All the primers were constructed to include a restriction site on both ends.
The amplification reaction (final volume 0.1 ml volume) utilized 10 pl of l OX
vent buffer (final concentration, 1X contains: IOmM KC1, lOmM (NH~)SO~. 20mM
Tris-HCI (pH 8.8 at 25°(:), 2mM MgS04, 0.1 % triton X-100), 4p.ls of 100mM
MgS04(final cancentrati.on 4 mM), 3 yl of l OmM dNTP s {final concentration 300pM), SOng 'template. 1 ~M primers and 1 ~1 of 2000units/ml of vent polymerase (final concentration 2 units; enzyme was supplied in l OmM KCI, 0.1M EDTA, lOqM Tris-HCl (pH 7.4), 1mM DTT. 0.1% Triton X-100) in a final volume of 100 ~l with water. Vent buffer, Vent polymerase enzyme and MgSO~ were purchased from New England Biolabs, MA, and dNTPs were bought from Gibco BKL.
' 5 Additional sequence was generated via fluorescent sequencing usW g Applied Biosystems Model 373a DNA sequencer (DNA Sequencing Core Facility, Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, FL). A Robotlo Workstation (ABI Catalyst 800) and a Perkin Elmer-Cetus PEC 9600 thermocycler were used in cycle sequencing reactions. The template, an amplified gene product that represented the whole insert from plasmid pLSN4a, was cleaned directly from 0.7% agarose gel by Qiagen kit before it was used for automated sequencing. The sequencing analysis was conducted with programs (fasta, blast and other programs) available in the GCG software package.

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C3-degrading Protein Isolation and Studies Log phase cultures of hyperactive mutants and their parent strains were incubated with C3 for 2-4 hrs and the culture supernatants were run on 7. S%
SDS-Page gels under reducing conditions and were checked for their increased C3 degrading activity by immunoblotting with HRP-conjugated polyclonal antibody to C3. This experiment demonstrated that mutants SN4 and SN4-4G
(obtained by retransformation of CP 1200 with the recombinant piasmid pLSN4 i o rescued from SN4) were more active than their parent strain CP 1200 in C3 degradation. Both oc and (3 chains C3 were almost completely degraded by th~~
mutants after 4 hours incubation whereas the degradation was incomplete for the parent strain. The CppA protein appeared to preferentially degrade the C3 a chain.
1S A 620 by internal portion of the cppA gene was Iigated into Hind III site of pVA 891 and the construct was transformed into CP 1200 competent cells.
The obtained transformant was tested for its ability to degrade C3. The ORF3 mutant was found to have a poor activity. The oc chain of the C3 molecule was degraded and the [3-chain was less degraded, by SDS-PAGE and western blotting 2o analysis in comparison with its parent strain CP 1200. The reduced activity rather than a complete absence of activity in the mutant indicated that the potential for the presence of another fully functional gene encoding another degrading proteinase in the mutant.
The entire cppA gene was amplified and cloned into Nde I and Bam H I
2S sites of pet-28b(+) (Novagen, INC. Madison, WI) and the gene was incorporated with a His-Tag in its N-terminus region. The entire gene was positioned in the vector in frame as confirmed by sequence analysis. The plasmid construct was transformed into E. coli DHS ~ MCR strain for stabilization and the presence of the insert was verified before the vector and insert were transformed into E.
coli 3o BL 21 D3 (Novagen) protease deficient strain for expression. The colonies containing the plasmid constructs were selected on LB medium containing kanamycin (30qg/ml).

Protein was isolated according to the Pet System manual (Madison, WI) for small scale o~r large scale preparations. The BL 21 DE3 strain containing the construct (pet 28b(+)::OItF3 (cppA gene) was induced by IPTG and the expressed protein, CppA., was solubilized. For solubilization, the induced bacterial cultures were centrifuged and the pellet was resuspended in TES (50 mM Tris; 1 mM EDTA; 100 mM NaCI). The resuspension was sonicated (6x. i 5 sec pulses at a high output setting: about 50 watts) on ice and spun down to collect the peller.. The pel',let was washed in TES (50 mM Tris; 1 mM EDTA;

mM NaCI) twice and finally the pellet was treated with 6mM G-HC1 + 1mM
DTT + I % Twe~en-20 for 3 hrs at 4°C.
The solubilized protein was diluted 1:10 in TTS (1% Tween, 50 mM
Tris, 0.7M NaCI) and dialyzed against TTS (1% Tween. 50 mM Tris Ø7M
NaCI) to remove Guanidine-HC1, DTT and EDTA. The dialysed CppA protein was purified by Nickel column chromatography using the Pet system manual instructions (Novagen, INC. Madison, WI). Nickel column (2.5 ml) was poured and after removal of Guanidine-HCI, DTT and EDTA, the expressed His-Tagged CppA protein was applied to the Nickel column for purification. The eluted fractions were tested for His-Tagged-CppA protein by I O% SDS-PAGE gel and Coomassie Brilliant Blue: R- 250 staining. The protein was kept on ice at 4°C or 2o frozen in small ~~liquots at -80°C until required.
The CpfrA protein (about 600 ng per ml of the reaction mixture] was incubated with l.mman complement C3 (0.83 pg of C3 per ml of the reaction mixture) for 4 hrs at 37°C in the presence of PBS and a negative control without protein was simultaneously set up. The samples were analyzed by 7.5% or 10%
SDS-PAGE gel under reducing conditions and western-blotting (ECL Western blotting protocols -Amersham Life Sciences, Arlington Heights, IL).
As descn.°ibed above, the PCR product of the whole ORF3 gene was subcloned into het vector pET28b(+) (Novagen, Madison, WI) with a His-tag in the amino terminus position and the construct was introduced into protease 3o deficient strain E. toll BL 21 DE3 (Table 2) after it was stabilized in E.
cola DHSa MCR. The E. toll BL 2I DE3 with the construct was subjected to ~-35-induction by IPTG. Total cell protein extracts of the induced and uninduced cultures were tested. The expressed His-tagged ORF3 protein ( ~ 29 kd) was identified in the insoluble fraction of the induced protein sample on 10% SDS-Page gel.
The following reagents were used for solubilization for 3 hrs at 4°C or I
hr at room temperature: TES (50mM Tris, 1 mM EDTA, 1 M NaCI; (b) 6mM G-HC1 + 1 mM DTT ; (c) 6mM G-HC1 + I mM DTT + 1 % Tween 20; (d) 6mM G-HCl + 1 mM DTT + 1 % Triton X -100. Both "c" and "d" treatments made the expressed protein soluble as it was observed on 10 % SDS-PAGE gel. The treatment with "c" reagent was chosen for subsequent large scale preparations.
The solubilized protein was dialysed followed by purification through the nickel column and examined for its function against C3.
For SDS-PAGE gels used in this example and above, total cell proteins or soluble or insoluble protein fractions were extracted according to Pet-system manual (Madison, WI). The proteins were separ-ated by SDS-PAGE gels (7.5%
or 10% or I S% resolving gel and 4.5% stacking gel) in the discontinuous system of Laemmli (Laemmli, U. K., Nature 227:680-685,1970). Briefly, samples were combined with loading buffer (final concentration in samples was 7.57 mg/ml of Tris, 2% SDS, 10% Glycerol and 1.25mg/ml of Bromphenol blue, ~ 5% (3-2o mercaptoethanol) and either boiled 5 min or loaded directly on the resolving gels. Pre-stained high molecular weight standards (Protein markers (kd) lysozyme, 14,300; (3-lactoglobulin, 18,400; carbonic anhydrase, 29,000;
ovalbumin, 43,000; bovine serum albumin, 68,000; phophorylase B, 97,400 myosin, 200,00 (Bethesda research laboratories, life sciences, Grand Land, NY) were included on the gels. The large SDS-PAGE gels were electrophoresed at I SmA for 14 hrs or l OmA for 20I1r. Mini gels were electrophoresed around 2-3 hrs at a constant voltage (100 -150 volts).
The expressed protein was incubated with C3 and the amount of C3 present was assessed by Western immunoblotting.
3o Immunoblotting analysis suggested that the samples that contained the expressed protein degraded C3 molecules. The undegraded C3 was detected by polyclonal antibodies specific to human complement C3 and this was clearly seen on the developed film in the case of the negative sample. Both oc and (3 chains of C3 molecules vrere seemed to be susceptible to the activity of the ORF3 protein in comparison with the negative control which did not contain any - 5 ORF3 protein; however, 'the oc chain was almost completely degraded while the (3 chain was partially degraded in the ORF3 samples.
Example 5 Conservation of the C3-degrading gene in Clinical Isolates to To examine the conservation of the gene cppA, an internal fragment of cppA was used a.s a probe: to determine the presence of gene cppA in EcoRl digested genomic DNA of different clinical (serotypes) of pneumococcal isolates by southern hybridization. In the same experiment, the pneumococcal 15 parent CP 1200 and the hyperactive mutants SN4 and SN4-4G (both mutants containing the same plasmids-see Table 2) were also included to confirm the duplication of th.e cppA gene in the mutants. Southern hybridization was performed using non-radiioactive DIG labeled internal fragment of the gene as a probe. The clinical isolates, typel, type3, type 14F and virulent type 23F
2o showed a hybridized band of about 2.3kb which was also present in the control pneumococcal strain CP1200 and in the SN4 mutants. This common band indicates that they cppA gf.ne was present in all isolates tested. The SN4 mutants also contained a second band with a size of about 3.Skb indicating the presence of a gene duplication. The 3.5 kb size is consistent with the observation that 25 plasmid pLSN4 has two restriction endonuclease recognition sites for EcoRl.
one in the insert region and a second in the vector. Hence the restriction digestion with EcoRl produces two fragments of about 4.175 kb ( 3.531 kb of vector +
0.649 kb of insert) and 3.539kb (-~-1.67kb form insert + about 1.869 kb from vector) from the recombinant plasmid. The cppA gene was located on the 1.67kb 30 portion of the insert and hence the 3.539 kb restricted fragment of the recombinant pla.smid contained the cppA gene and only this band would hybridize to the probe wl.iich was an internal fragment of the cppA gene;

therefore, in the case of the mutants with duplicated cppA gene, the second hybridized band at ~ 3.Skb represented the duplicated cppA gene.

Claims (46)

What is claimed is:

1. An isolated protein comprising at least an 80% sequence identity of SEQ
ID NO:2 and capable of degrading human complement protein C3.

2. The protein of claim 1 wherein the protein is isolated from S.
pneumoniae.

3. The protein of claim 1 wherein the protein binds human complement protein C3.

4. The protein of claim 1, wherein the protein is a recombinant protein.

5. The protein of claim 1 wherein the protein is an isolated protein.

6. The protean of claim 1 having a molecular weight as determined on a 10% polyacrylamide gel of between about 24 kDa to about 34 kDa.

7. A peptide comprising at least 15 sequential amino acids from the protein of claim 1.

8. An isolated protein comprising SEQ ID NO:2.

9. A peptide comprising at least 15 sequential amino acids from SEQ ID
NO:2.

10. A protein comprising SEQ ID NO:2, wherein the protein has a molecular weight as determined on a 10% polyacrylamide gel of between about 24 kDa to about 34 kDa.

11. The protein of claim 10 wherein the protein is isolatable from S.
pneumoniae.

12. The protein of claim 10 wherein the protein is a recombinant protein.

13. The protein of claim 10 wherein the protein degrades human complement protein C3.

14. A protein comprising amino acids 1-50 of SEQ ID NO:2.

15. A nucleic acid fragment comprising nucleic acids 1246 to 1863 of Figure 1A.

16. A protein that degrades human complement protein C3 and wherein nucleic acid encoding the protein hybridizes to SEQ ID NO:1 under hybridization conditions of 6XSSC, 5X Denhardt, 0.5% SDS, and 100 µg/ml fragmented and denatured salmon sperm DNA hybridized overnight at 65°C
and washed in 2X SSC, 0.1% SDS one time at room temperature for about 10 minutes followed by one time at, 65°C for about 15 minutes followed by at least one wash in 0.2XSSC, 0.1% SDS at room temperature for at least 3-5 minutes.

17. An immune-system stimulating composition comprising an effective amount of an immune system-stimulating peptide or polypeptide comprising at least 15 amino acids from a protein comprising at least an 80% sequence identity with SEQ ID NO:2 and capable of degrading human complement protein C3.

18. The composition of claim 17 wherein the protein is isolatable from S.
pneumoniae.

19. The immune system stimulating composition of claim 15 further comprising at least one other immune stimulating peptide, polypeptide or protein from S. pneumoniae.

20. An antibody capable of specifically binding to a protein comprising at least a 90% sequence identity with SEQ ID NO:2 and capable of degrading human complement protein C3.

21. The antibody claim 20 wherein the antibody is a monoclonal antibody.

22. The antibody of claim 20 wherein the antibody is an antibody fragment.

23. The antibody of claim 20, wherein the antibody is a polyclonal antibody.

24. The antibody of claim 20, wherein the antibody is obtained from a mouse, a rat, human, or a rabbit.

25. A nucleic acid fragment capable of hybridizing to SEQ ID NO:1 under hybridization conditions of 6XSSC, 5X Denhardt, 0.5% SDS, and 100 µg/ml fragmented and denatured salmon sperm DNA hybridized overnight at 65°C
and washed in 2X SSC, 0.1% SDS one time at room temperature for about 10 minutes followed by one time at, 65°C for about 15 minutes followed by at least one wash in 0.2XSSC, 0.1% SDS at room temperature for at least 3-5 minutes.

26. The nucleic acid of claim 25 isolated from an S. pneumoniae genome.

27. The nucleic acid of claim 25 wherein the nucleic acid fragment encodes at least a portion of a protein.

28. The nucleic acid of claim 27 wherein the protein degrades human complement C3.

29. The nucleic acid fragment of claim 27 wherein the nucleic acid fragment encodes a protein that does not degrade human complement C3.

30. The nucleic acid of claim 25 in a nucleic acid vector.

31. The nucleic acid of claim 30 wherein the vector is an expression vector capable of producing at least a portion of a protein.

32. A cell comprising the nucleic acid of claim 25.

33. The cell of claim 32 wherein the cell is a bacterium or a eukaryotic cell.

34. An isolated nucleic acid fragment comprising the nucleic acid sequence gctcccagtatgcgtactcgtaaggtagagggaagaaaaaaactagctag.

35. A method for producing an immune response to S. pneumoniae in an animal comprising the steps of:
administering a composition comprising a therapeutically effective amount of at least a portion of a protein to a mammal, wherein nucleic acid encoding the protein hybridizes to SEQ ID NO:1 under hybridization conditions of 6XSSC, 5X Denhardt, 0.5% SDS, and 100 µg/ml fragmented and denatured salmon sperm DNA, hybridized overnight at 65°C and washed in 2x SSC, 0.1% SDS one time at room temperature for about 10 minutes followed by one time at 65°C for about 15 minutes followed by at least one wash in 0.2xSSC.
0.1% SDS at room temperature for at least 3-5 minutes; and obtaining an immune response to the protein.

36. The method of claim 35 wherein the immune response is a B cell response.

37. The method of claim 35 wherein the immune response is a T cell response.

38. The method of claim 35 wherein the at least a portion of a protein is at least 15 amino acids in length.

39. The method of claim 35 wherein the composition further comprises at least one other protein from S. pneumoniae.

40. The method of claim 35 wherein the protein comprises at least 15 amino acids of SEQ ID NO:2.

41. A bacteria comprising an insertional mutation, wherein the insertion mutation is in a gene encoding a protein capable of degrading human complement C3.

42. The bacteria of claim 41 wherein the bacteria comprises an insertional duplication mutation.

43. An isolated protein of about 24 kDa to about 34 kDa from Streptococcus pneumoniae that is capable of binding to and degrading human complement C3.

44. A method for inhibiting Streptococcus pneumoniae-mediated C3 degradation comprising the step of:
contacting a Streptococcus pneumonia bacterium with antibody capable of binding to a protein with the amino acid sequence of SEQ ID NO:2.

45. An isolated nucleic acid fragment comprising the nucleic acid sequence of SEQ ID NO:1

46. An RNA fragment transcribed by a double-stranded DNA sequence comprising SEQ ID NO:1.