AU704745B2 - Gene serum opacity factor - Google Patents

Description

WO 95/06721 PCT/US94/09926 1 GENE SERUM OPACITY FACTOR FIELD OF THE INVENTION This invention relates to composition and processes for use as diagnostics for qualitative and quantitative testing for high density lipoprotein

(HDL)

in body fluids. It relates also to DNA sequences for the production of polypeptides useful for such purposes because of the apolipoproteinase activity (ALA) of such polypeptides.

Apolipoproteins are particles in the blood that are intimately involved in coronary heart disease.

They are amalgams of proteins, cholesterol and lipids that appear to be the principal factors participating in the transportation and deposition of cholesterol in human blood. The most abandant of the apolipoproteins are low density lipoprotein (LDL) and HDL LDL appears to be principally responsible for the deposition of cholesterol in arterial palque. In contrast,

HDL

appears to be principally responsible for transportation of cholesterol to the liver for metabolism and elimination. These contrasting mechanisms account for the association of increased risk of coronary disease with high LDL levels and low HDL levels.

It has been observed that lipoprotein levels can be modified by diet and exercise so as to increase the relative proportion of HDL in human blood. It is, therefore, important to provide the diagnostic capability of determining the level of HDL in human blood both qualitatively and quantitatively.

WO 95/06721 PCT/US94/09926 2 Opacity factor (OF) is a product of Streptococcus pyogenes which is associated with the generation of opalescence of serum. This promotion of opacity in mammalian sera is associated with the ALA of a surface protein of S.pyogenes strains by which a substantial fraction of apoprotein Al is cleaved from HDL leading to coagulation of the remaining fraction with resulting opalescence. This observation makes it apparent that OF would be a useful tool for qualitatively determining the concentration of HDL in mammalian sera.

Unfortunately however, the protein responsible for ALA has not been available in sufficient quantitities and purity to permit the development and use of such a test.

The present invention utilizes recombinant

DNA

techniques to produce DNA sequences which can be introduced into a cloning vehicle such as a phage or a plasmid (which is subsequently employed to transform a host cell such as E.coli) to enable the expression of OF, or segments of OF, having ALA activity. The polypeptides thus produced are then isolated, purified and, if desired modified, for example, by labeling, for use in detecting HDL qualitatively and/or quantitatively in mammalian sera.

Recombinant DNA technology involves the technique of DNA cloning whereby a specific DNA fragment is inserted into a genetic element called a vector which is capable of replication and transcription in the host cell. The vector can be either a plasmid or a virus.

I I II II I WO 95/06721 PCTIUS94/09926 -3- Plasmids are small, circular molecules of doublestranded DNA that occur naturally in both bacteria and yeast, where they replicate as independent units as the host cell proliferates. These plasmids generally account for only a small fraction of the total host cell DNA, and often carry genes that confer resistance to antibiotics. These genes, and the relatively small size of the plasmid DNA, are exploited in recombinant DNA technology.

The inserted DNA fragment of a recombinant

DNA

molecule may be derived from an organism which does not exchange information in nature with the host organism, and may be wholly or partially synthetically made.

Construction of recombinant DNA molecules using restriction enzymes and ligation methods to produce recombinant plasmids has been described in U.S. Pat.

No. 4,237,224, issued to Cohen and Boyer. The recombinant plasmids thus produced are introduced and replicated in unicellular organisms by means of transformation. Because of the general applicability of the techniques described therein, U.S. Pat. No.

4,237,224 is hereby incorporated by reference into the present specification.

A different method for introducing recombinant

DNA

molecules into unicellular organisms is described by Collins and Hohn in U.S. Pat. No. 4,304,863 which is also incorporated herein by reference. This method utilizes a packaging/transduction system with bacteriophage vectors.

WO 95/06721 PCT/US94/09926 4 Because it is supercoiled, plasmid DNA can easily be separated from the DNA of the host cell and purified. For use as cloning vectors, such purified plasmid DNA molecules are cut with a restriction nuclease and then annealed to the DNA fragment that is to be cloned. The hybrid plasmid DNA molecules produced are then reintroduced into bacteria that have been made transiently permeable to macromolecules (competent). Only some of the treated cells will take up a plasmid and these cells can be selected for the antibiotic resistance conferred on them by the plasmid since they alone will grow in the presence of antibiotic. As these bacteria divide, the plasmid also replicates to produce a large number of copies of the original DNA fragment. At the end of the period of proliferation, the hybrid plasmid DNA molecules are purified and the copies of the original DNA fragments are excised by a second treatment with the same endonuclease.

Regardless of the method used for construction, the recombinant DNA molecule must be compatible with the host cell, capable of autonomous replication in the host cell. The recombinant DNA molecule should also have a marker function which allows the selection of host cells transformed by the recombinant

DNA

molecule. In addition, if all of the proper replication, transcription and translation signals are correctly arranged on the plasmid, the foreign gene will be properly expressed in the transformed cells and their progeny.

WO 95/06721 PCTIUS94/09926 5 BRIEF SUMMARY OF THE INVENTION Methods and compositions are provided for the cloning and expression of DNA sequences comprising the gene for the OF and segments thereof having ALA in single cell organisms. Also described are methods of culturing these novel single cell organisms to produce OF and polypeptides having ALA as well as methods of identifying such gene products. Still further, the invention comprises the use of the products expressed by such genes to detect HDL qualitatively and/or quantitively. The methods and compositions of the invention are also useful for detecting streptococcal infection by streptococcal strains that produce opalescence, for the regulation of HDL, and fibronectin binding activity.

BRIEF DESCRIPTION OF THE FIGURES The present invention may be more fully understood by reference to the following detailed description of the invention and the figures in which: Fig. 1 is a sketch showing the general structure of the polypeptide comprising the OF expressed by a DNA sequence of this invention.

Fig. 2 SOR (overlay) assay of SOF22 protein from strain 22 streptococcus D734 and recombinant phage lysates. D734 released from of SOF22 PROTEIN FROM STREPTOCOCCAL STRAIN d734. RECOMBINANT PHAGE LYSATES: WO 95/06721 PCT/US94/09926 6 lsof22.3 sAU3a CLONE, 2456BP INSERT; lsof22.4 EcoRI clone, 9kb fragment containing the whole sof22 open reading frame; EMBL4 vector lysate. Recombinant phage crude lysate was directly loaded on the gel.

Molecular weight standards (in kD) are indicated.

Fig. 3 Restriction map of sof22 locus and surrounding region on the chromosome of D734.A. Bar denotes the sof22 open reading frame (ORF). 3'termini of sof22 ORF.B-BamHI; E-EcoRI; H-HindIII; P- PstI; S-SacI; X-XhoI. B. Determination of N-terminal consensus required for SOF activity. Bars represent sof22 ORF fragments in the two deletion clones, aligned with the restriction map in A. 2643, 2383 the length of 3'-terminal deletion clones of sof22 ORF in correspondent clones.

Fig. 4 Nucleotide sequence of sof22 gene from strain D734 and flanking regions. Underlined putative promotor boxes -10) and ribosome binding site Also underlined are the restriction sites: XhoI, SacI, PstI, Sau3A 2 543 (the end of Sau3A clone), proline-rich regions, and LPASGD sequence. The arrows above DNA sequence (3193 3208) putative transcription termination signal; asterisk stop codon, vertical arrow putative signal sequence cleavage site; R1, R2, R3, R4 repeats.

Fig. 5 Block diagram of SOF22 protein. Symbols: S.S.-signal sequence; P proline-rich region; I, II, III, IV repeats; LPASGD SPXTGX motif. Boxes: black I

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WO 95/06721 PCT/US94/09926 7 hydrophobic sequences hatched boxes repeated sequences; white boxes unique sequences. b. Secondary structure prediction. T turn, C- coil H- helix, E extended. Four levels of line in the plot correspond to the highest of four likelihoods for each residue to be in the indicated secondary structure. c.Relative hydropathy of SOF22. Hydrophobic domains are located above the central line, and hydrophilic domains are below. The x axis represents the amino acid number of the SOF22 sequence.

Fig. 6 SOF22 repeats. Repeats of SOF22 are aligned and residues that are the same in the two or more repeats in bold. Dashes gaps introduced for the alignment purpose. B. Alignment of SOF22 repeat unit with repeats from gram-positive fibronectin-binding repeats. Numbers of subscript: the position of repeats in the respective amino acid sequences; percentile numbers percent identity with the SOF22 repeat.

Fig. 7 Comparison of the C-terminal end of the deduced amino acid sequence of the SOF22 protein with the C terminal region of the surface proteins from gram-positive bacteria. M6 M6 protein from Streptococcus pyogenes, Prot. H protein H, M49 M49 protein from Streptococcus pyogenes, m2.2 -m2.2 protein from Streptococcus pyogenes, SCP Carboxypeptidase from Streptococcus pyogenes and Prot. G protein

G

from group G streptococci. Also shown are: WapA wall-associated protein A from Streptococcus mutans and Prot A Protein A and FnBP fibronectin-binding I WO 95/06721 PCT/US94/09926 8 protein from Staphilococcus aureus. The LPXTGX motif is separated from the rest of the sequence with a space. bold residues conserved in SOF22 and at least one of the proteins aligned. Conservative replacement of T with S in the LPXTGX motif of sof22 is underlined.

Fig. 8 Alignment of promoter regions of scpA and sof22. The 5' noncoding sequences of scpA and sof22 were compared manually, introducing gaps to increase the overlapping of common motifs. Dashes represent gaps. Putative -35 and -10 boxes and VirR elements are underlined.

Fig. 9 A. Autoradiogram of Sau3A hybridization patterns of representative streptococcal strains.

Washes were done under conditions that allow mismatch. Probe mpSOF69.2 was cloned from M22 strain D734. This probe is homologous to the sof22 intragenic Sau3A fragment spanning from nucleotide 890 to 2543 of the sequence shown in Figure 3. The exposure of autoradiogram was 10 hrs, with the exception of D734 line which was exposed for 30 min in order to decrease the intensity of the signal. B. The probe and the sau3A map of sof22 locus from strain D734. S Sau3A restriction site; 3' margins of sof 22 DETAILED DESCRIPTION OF THE INVENTION Fig. 1 which is not to scale is a sketch showing the general structure of OF proteins first isolated and made available in useful highly purified form in WO 95/06721 PCT/US94/09926 9 accordance with this invention. The skilled artisan will recognize the similarity in structure between this surface protein and the antiphagocytic M protein of Streptococcus pyogenes.

As shown, and more fully explained below, it is a protein of 1025 residues expressed by a gene having 3107 base pairs with a molecular weight of about 112,000. The protien has a leader sequence at the amino end which is released as the protein becomes bound to the streptococcal surface. The amino end as shown below is the enzyme active segment of the molecule. While there is serological variation among SOF from different strains, sufficient homology amongst enzyme active segments from different strains exists so that it is possible to utilize the gene, or gene segment, which expresses the enzyme active segment of one strain as a probe to locate the gene which expresses the enzyme active segment of another strain.

Each OF therefore has at least one apolipoproteinase segment located at amino end of the molecule.

The OF also includes the hexameric LPXTGX motif characteristic of gram positive bacteria as well as 4 repeats flanked by proline rich stretches within its C-terminal domain. Deletion analysis, as shown below, has been used to establish that the C-terminal domain is not involved in the apolipoproteinase activity of the protein. The repeats are the site of the fibronectin binding activity.

I

WO 95/06721 PCT/US94/09926 10 The protein shown in Fig. 1 is representative of the class of OF proteins each having apolipoproteinase activity and isolatable from various streptococcal species. Although there is significant homology amongst the proteins from the various strains, there is also appreciable variation.

There follows a description of the production and isolation of the DNA sequence which expresses the OF of the streptococcal strain D734. The OF protein expressed in this representative example is identified as SOF22. The gene used to express the protein is sof22. This is in accordance with the standard nomenclature system used in this art. Related testing, cloning, subcloning, expression and probing procedures are also described.

MATERIALS AND METHODS Bacterial strains, plasmids and bacteriophages.

Group A streptococcal strain D734 (M type 22), was the original parent strain of the gene, sof22, described in this study. This strain and all other group

A

streptococcal strains used in this study were from the Rockefeller University collection and are described in Table 1. E.coli strain P2392 served as the host for lambda phage EMBL1. XL1-BLUE (Stratagene Cloning Systems, La Jolla, Ca.) was the host strain for M13 mpl8/19, and plasmid pUC9.2 and pBluescript SK+. These two E. coli strains did not create an opacity reaction -I

I

WO95/06721 PCT/US94/09926 11 when incubated with heat-inactivated horse serum. The strains and the lambda phage are known and readily available.

WO 95/0672 1 PCT/US94/09926 12 Table 1. DNA hybridization with InpSOF89.2 probe.

STRAIN M HYBRID BANDS

SOR

TYPE CLASS D7 34 B234 B401 F312 B344 12 D691 D4 74 D7 42 B737 D976 D3 98 A9 56 D4 59 D7 94 1.60 3.50, 3.50, 3.50, 1.70 1.60, 1.20, 1.60 2.50, 0.40 0.80, 0.18 0.22 0.22 0.23 0.60 0.60 0.60 0.35 0.23, 0.90 0.20 0.60, 0.23 D7 B7 88 D4 71 S43 A3 74 D469 1RP2 8 4 D6 17 D4 66 D421 0.80, 0.60, 0.23 1.90 1.90, 0.23 WO 95/06721 WO 95/672 1PCTJUS94/09926 13 D463 D4 32 D4 42 D7 35 D7 39 NT a NT a WO 95/06721 PCT/US94/09926 14 Chemicals and enzymes. Restriction and T4 DNA ligase were purchased from New England BioLabs, Inc.

(Beverly, Alkaline phosphatase (from calf intestine), human fibronectin and Random primed

DNA

labeling kits were obtained from Boehringer Mannheim Corp. (Indianapolis, DNA sequences were determined by using Sequenase version 2.0 kits (United States Biochemical Corp. Cleveland, Oh.).

Unidirectional deletions of M13mpl8/19 clones were generated using the Cyclone 1 Biosystem (International Biotechnologies, Inc, New Haven, Na 125 I and radionucleotides -32PdATP and -35S]dATP were obtained from New England Nuclear (Boston,

DNA

oligomers were purchased from Operon Technologies (Alameda, or United States Biochemical Corp.

Polymerase chain reactions (PCR) were achieved using the GeneAmp PCR reagent kit (The Perkin-Elmer Corp., Norwalk, Heat-inactivated horse serum was purchased from Life Technologies, Inc. (Gaithersburg, Md). All other chemicals were purchased from Sigma Chemical Co. (St. Louis, unless otherwise indicated.

Serum Opacity Reaction Assays. OF expressed by colonies of strain D734 was detected by growing bacteria on serum opacity reaction (SOR) assay medium, containing 50% heat-inactivated horse serum and Todd Hewitt broth (Difco Laboratories, Detroit, Mi) in 0.9% Oxoid Ion agar No.2 (Colab Laboratories, Chicago Heights, Recombinant phage plaques expressing

I

WO 95/06721 PCT/US94/09926 15 OF activity were screened on plates containing Luria broth instead of Todd Hewitt broth. After transferring phage lawns to nitrocellulose filters, the OF-positive plaques were detected by replica plating the filters on SOR assay medium for 10-12 h at 37 C. Serum opacity activity in solutions, including supernatants of phage or bacterial cultures, was measured as previously described Briefly, the liquid solution to be tested was mixed 1:5 in heatinactivited horse serum, containing 0.02% merthiolate, and incubated for 2 h at 370C. Opacity was quantitated by spectrophotometric measurement at 475 nm.

To visualize OF protein bands after denaturing SDS-PAGE electrophoresis, the gel was incubated on solid SOR assay medium containing 0.02% merthiolate. OF protein was detected as opaque bands in the SOR assay medium and photographed under indirect light.

Extraction of OF From Streptococci. Late log phase cultures of strain D734 were washed with 200 mM sodium phosphate buffer, pH 7.5, at 4 0 C and resuspended in 1/100 of the original culture volume of the same buffer. Extraction of OF proceeded by incubating the bacterial suspension of 2 hours at 37 C, followed by centrifugation and filtration of the resulting supernatant through a 0.45 um nitrocellulose filter (Schleicher and Schuell, Inc., Keene, OF was precipitated from the supernatant in WO 95/06721 PCT/US94/09926 16 saturated ammonium sulfate and collected by centrifugation (31,500 g x 10 min.). The precipitate was resuspended in 100mM Tris-HC1, pH 7.5, and dialyzed in 4 liters of the same buffer for 48 hours at 4 C.

Cloning Procedures. Streptococcus chromosomal DNA for all work was prepared by the known phage lysin extraction procedure.

Chromosomal DNA from strain D734, used in creating recombinant libraries, was either partially digested with Sau3AI, or completely digested with EcoRI. Sau3AI digest was dephosphorylated with calf intestinal phosphatase, and ligated to lambda phage EMBL4 arms digested with BamHI and Sail. The EcoRI digest was ligated to dephosphorylated EMBL4 arms prepared by BamHI and EcoRI cleavage. Ligation mixtures were packaged in vitro using Gigapack II gold packaging extracts (Stratagene).

Unamplified libraries were plated on strain P2392 and screened for recombinant phage plaques expressing an OF phenotype. Four positive phage (LSOF22.1- LSOF22.3 and LSOF22.4 from the Sau3A and EcoRI libraries, respectively) were isolated and plaque purified.

Subcloning Procedures. For OF expression studies and DNA sequencing of the 5' portion of sof22, a 2,560 bp EcoRI-SalI fragment, containing the entire 2,543 bp I I WO 95/06721 PCT/US94/09926 17 insert of phage LSOF22.3, was electrophoretically purified and than ligated to both M13 mpl8 and mpl9 digested with both EcoRI and SalI, creating mpSOF22.2 and mpSOF22.1, respectively. Ligation mixtures used to transform XL1-Blue yielded numerous recombinant plaques, as detected by plating on SOR assay agar.

Sets of nested deletion clones for DNA sequencing were then prepared from both M13 clones using the Cyclone I kit (IBI). To sequence the 3' portion of sof22, an 3,100 bp SacI-EcoRI (Fig. 3) fragment was subcloned from LSOF22.4 into both M13 mpl8 and mpl9, creating mpSOF22.4 and mpSOF22.3, respectively. The 2543bp insert of phage LSOF22.3 was also cloned into pBluescript KS (pSOF22.1).

DNA Sequence and Sequence Analysis. Single stranded templates of M13 and mpl8/19 clones were prepared for chain termination sequencing by known methods. DNA sequences of mpSOF22.1 and mpSOF22.2 derived deletion clones were determined using the M13 20 forward universal primer, Sequenase 2.0, and P]dATp. The 3' portion of sof22, cloned in mpSOF22.3 and mpSOF22.4, was sequenced by primer walking.

DNA sequence data was aligned using the STADEN program package (Roger Staden, MRC Laboratory of Molecular Biology, Cambridge, This software package was also used to predict structural features WO 95/06721 PCTIUS94/09926 18 of the deduced OF protein. The Genbank database was accessed to establish regions of homology between SOF22 and other known proteins.

Subcloning of the Fibronectin Binding Domain (FNBD22). The RF form of mpSOF22.3 served as the template for amplification of the FNBD of sof22. The primer, CCCAAGCTTCAGGAAAATAAAGAT, designed to place the FNBD coding sequence in frame with the upstream lacZ gene fragment, corresponded to bases 2641 to 2658 (Fig. 4) and a HindIII site (underlined), while the 3' primer, CGGGATCCGCTCGTTATCAAAGTGG, consisted of nucleotides 3002 to 2986 (Fig. 4) and a BamHI site.

The PCR reaction consisted of 20 cyles of a three step reaction (1 min at 94 C, 3 min at 55 C, and 3 min at 72 employing the GeneAmp PCR reagent kit, native TaqDNA polymerase, and a DNA Thermal Cycler (The Perkin-Elmer Corp.). The products, of expected size, from 3 independent PCRs, were pooled, purified by phenol/chloroform extraction, digested with HindIII and BamHI, and isolated from a low melting temperature agarose gel. Purified DNA was then ligated to the HindIII and BamHI sites of pUC9.2, creating the FNBD expressing clone, pFNBD22.1.

Fibronecting Binding Studies. The recombinant fibronectin binding domain was prepared from the whole cell lysates of clone pFNBD22.1, separated by denaturing SDS-PAGE and eletroblotted to nitrocellulose. The blots were then blocked by incubation in 10 mM HEPES buffer, containing 150mM WO 95/06721 PCT/US94/09926 19 NaCI, 10 10 mM MgC1 2 2mM CaC12, 50 mM KC1, 0.04% NaN 3 and 0.5% BSA, pH 7.4, for 2-3 h at room temperature. Subsequently, blots were then probed for 3-4 h at room temperature in the same buffer containing 125I fibronectin adjusted to 3 x 105 cpm/ml. Blots were then washed three times with blocking buffer, dried and exposed to Kodak Blue Brand film in the presence of an intensifying screen, for 24 -36 h, at -70 0

C.

Radioiodination of fibronectin was achieved using lodobeads (Pierce Chemical CI., Rockford, The labeled protein was separated from free iodine by filtration through Sephadex G-25 (PD-10; Pharmacia

LKB

Biotechnology Inc.) and collected in 100 mM phosphate buffer saline, pH 6.5. The specific activity of the iodinated fibronectin was xl06 cpm/ug.

ApoAI Cleavage Assay. Crude lysates of clones LSOF22.3 or EMBL4 were mixed with purified human HDL in microtiter plate wells and incubated for 16 h at 37 C in the presence of 0.02% NaN 3 -HDL was adjusted to a final apoprotein concentration of 30 ug/100 llysate. When included in the reaction, aspartic protease inhibitor pepstain A(5 ug/ml) was incubated with lambda lysates for 30 min prior to the addition of HDL. Opacity reactions were assessed by observation in indirect light. Cleavage of ApoAI was analyzed by denaturing SDS-PAGE observation in indirect light. Cleavage of ApoAI was analyzed by denaturing SDS-PAGE (15) of 10 ul of each reaction.

WO 95/06721 PCTfUS9409926 20 Electroblotted filters were probed with alkaline phosphatase-conjugated sheep anti-ApoAI antibody (Biodesign International, Kennebunkport, ME) and developed.

DNA Hybridization. Chromosomal DNA prepared from streptococci was digested to completion with restriction enzymes and electrophoresed in 0.6% or 1.05% agarose gels prior to transfer to Hybond membranes (New England Nuclear). DNA probes, consisting of either restriction fragments or PCR products, were isolated from preparative low melting temperature agarose gels and then radiolabeled with 32P]dATP, using random primed DNA labelling kits (Boehringer Mannheim Corp.).

Blots were incubated in a prehybridization solution (6X SSC, 0.5% SDS, 100 ug/ml denatured salmon sperm DNA, 5X Denhardt's solution and 50% formamide), at 30 C overnight, and then hybridized with radiolabeled probes in a hydrization solution (6X SSC, SDS, 100 ug/ml denatured salmon sperm DNA and formamide), at 42 C overnight in accordance with known procedures. Blots that physically mapped the sof22 and emm2 loci were washed at high stringency conditions that allowed for less than 5% bp mismatch (twice in 0.1% SSC and 0.1% SDS for 30 min at Probes used for restriction mapping of sof22 were inserts from M13 deletion clones mpSOF22.81 and mpSOF22.792, corresponding to nucleotides 1 to 781 and 1,160 to 2,543, respectively (Fig. Blots WO 95/06721 PCTIUS94/09926 21 detecting sof22 homologs in other group A streptococcal strains were sequentially washed at both high and low stringency conditions. Whereas high stringency washes allowed for less than 5% mismatched, relaxed wash conditions (twice in 0.2% SSC and SDS for 30 min at 370C) allowed up to 20% mismatch.

The probe in these experiments was the insert from the M13 clone mpSOF22.692, corresponding to an internal Sau3A fragment (bp 976 to 2,543) encoding the serum opacity domain (SOD).

RESULTS

Extraction of Serum Opacity Activity From Streptococcus pyogenes. The serum opacity factor of group A streptococci can be detected in both extracellular and membrane bound fractions isolated from bacterial cell cultures. To both ascribe the basis of the serum opacity reaction to a specific molecule(s) and judge the feasibility of molecularly cloning the serum opacity factor, a maximum yield method to extracting the released form of the factor was established as described above. The protein extract of SOF-producing strain D734 was analyzed by SDS-PAGE under denaturing conditions and used in a serum opacity reaction assay. As can be seen in Figure 2, these methods isolated and detected at least two closely migrating species, with molecular weights of 10kD that are capable of independently producing a serum opacity reaction. Thus, a simple and I I WO 95/06721 PCT/US94/09926 22 dependable assay capable of detecting molecules responsible for a serum opacity reaction was established.

Cloning of sof22. Two streptococcus genomic libraries, containing either Sau3AI or EcoRI restriction fragments of strain D734 chromosomal

DNA,

were constructed in EMBL4 vector and screened for recombinant phage clones exhibiting a serum opacity phenotype. For the detection of SOF protein expression in phage plaques, the method described above was employed. By assaying for positive plazues in this manner, four phages, SOF22.1 to SOF22.3 from the Sau3AI library and SOF22.4 from the EcoRI library, were identified, isolated,and confirmed as serum opacity producing phages. Crude phage lysates of clones SOF22.1 to SOF22.3 were all found to contain a protein with serum opacity activity that corresponds in size, 100 kDa, with the streptococcal serum opacity factor (Fig. In contrast, phage SOF22.4 expressed at least four different molecular species, ranging from 100 kDa to 175 kDa in size, with serum opacity activity (Fig. 2).

The differences in both the number and mobility of the major reactive species of SOF expressed by recombinant clones SOF22.1 to SOF22.3 and SOF22.4 were found to parallel the insert sizes of these clones.

All three clones from the Sau3AI library had identical inserts flanked by EMBL4 linkers and Sail stuffer fragments. Phage SOF22.4 harbored an EcoRI

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WO 95/06721 PCT/US94/09926 23 fragment, which contained the Sau3AI cloned in LSOF22.1 LSOF22.3 (Fig. Thus, with codon requirements for the expression of a 100 kD protein in mind (typically 3 kb), it was concluded that phages SOF22.1 to SOF22.3 encode a truncated sof22 gene, and that, minimally, phage SOF22.4 encodes the entire sof22 locus. In that one species of SOF released from streptococci comigrated with the solitary SOF species expressed by SOF22.3, we concluded that at least one form of SOF released from streptococci is smaller than the native cell bound form. These were verified by sequencing subclones of these phages (described below).

Subcloning and Sequencing of sof22. To prepare DNA templates for DNA sequencing, the SOF22.3 phage insert was sublconed in Ml3mpl8 and mpl9, creating mpSOF22.2 and mpSOF22.1, respectively. The insert was, therefore, in both orientations relative to the lacZ promoter. SOF was expressed from both recombinant phages. Increased levels of IPTG did not increase the level of periplasmic SOF activity. Thus, it was indicated that sof22 was expressed from its streptococcal promoter in these recombinant phages.

Sequence analysis of the 2,543 bp fragment from a set of nested deletion clones derived from mpSOF22.2 and mpSOF22.1 detected an ORF, 2,470 nucleotides long, starting at nucleotide 83 and lacking the stop codon.

All other ORFs detected were smaller than 1,500 pb.

The 2,470 bp long ORF, (sof22), was the only one corresponding to the size of SOF22 produced by

I

LSOF22.3. The 3' portion of sof22 of ORF was located on a 3,100 bp SacI-EcoRI fragment by hybridization, using a probe homologous to the sequences downstream from a unique SacI941site (Fig. 3, This 3,100 bp SacI-EcoRI restriction fragment, contained in the EcoRI insert of phage SOF22.4, was subcloned in both M13mp18 and mp 19, and sequenced by primer walking. The 3' end of sof22 ORF was located at nucleotide 3,178,644 bp downstream of the end of 2,543 Sau3A fragment.

Analysis of the sof22 Gene Sequence. The nucleotide sequence of sof22 with its deduced amino acid sequence is shown in Fig. 4. The nucleotide sequence (SEQ ID NO: 2) begins at the Sau3A site (position 1) and ends at position 3,240. Restriction 0*@g S* sites XhoI, SacI, PstI and one Sau3A (the 3' end of Sau3A LSOF 22.3 insert) are Sindicated in the figure. Sof22 ORF starts at the position 83 and ends at the position 3,187. The longest protein that could be coded for by this ORF starts with the alternate start codon UUG at position 113 and codes for a protein of 1,025 aminoacids with a size 112, 735.1, about 10% larger than the largest major SOF band released from D734.

Although there were a few standard (AUG) start codons downstream of proposed UUG codon, none of the deduced protein sequences contained hydrophobic signal sequence that would allow export of SOF from the *5

S

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WO 95/06721 PCT/US94/09926 25 cytoplasm (Fig. 5C). Position of the signal sequence cleavage site, predicted by the method of Von Heijne, was between G29 and Analysis of the amino acid composition of OF22 protein revealed that the most abundant amino acids were lysine serine threonine and glutamine Secondary structure analysis predicts a proteinconsisting of 39.3% helix, 28.2% random coils, 18.15% beta sheet and 14.3% turns (Fig. 5B). Consistant with the low helix potential for the molecule, analysis of the sequence employing the "Matcher" algorythm showed no significant seven residue periodicity, excluding the possibility of coiled coil structure. Hydrophaticity analysis by the Kyte and Doolittle algorythm shows strong hydrophobic regions both at the first N-terminal 30 amino acids, in the position of the signal sequence, and at the C terminus, in the position of a possible membrane anchor segment (Fig. 5C). C-terminal to the hydrophobic segment (at the C-terminal end of the protein) are eight charged and two polar amino acids.

Three residues N-terminal from the hydrophobic domain is a hexameric LPXTGX motif found in the surface proteins from gram positive bacteria, with conservative replacement T to S.

WO 95/06721 PCTIUS94/09926 26 Analysis of internal homology by Diagon proportional algorithm showed 4 repeats (Fig. 7).

Repeats are flanked by proline rich stretches (Fig.

6A). All these motifs are present in the majority of streptococcal surface proteins.

The 214 C-terminal amino acids, including repeats and downstream proline rich region, are dispensable for serum opacity activity, as concluded from the SOF activity of the truncated SOF22. Further shortening of 2,543 bp Sau3A fragment in clone mpSOF22.1 by the deletion of 60 C-terminal amino acids (180 3' base pairs) abolishes SOF activity (Fig. Therefore, the sequence necessary SOF activity is between amino acid 752 and 811.

Sequence Homology With The Membrane Anchor Region of Streptococcal Surface Proteins. Comparisons of deduced amino acid sequence of the SOF22 protein with a protein sequence database revealed homologies of about 30 to 35% confined primarily to the C terminal region, including the LPXTGX motif, hydrophobic domain and charged tail of streptococcal proteins deduced from DNA sequence. These include ennX and emm49 genes from M type 49, emm6 from M type 6, emml2 from M type 12, emm5 from M type 5, protein G protein H and protein Arp4. Comparison of the anchor regon of several surface proteins from the Gram positive bacteria is shown in Figure 7.

I I WO 95/06721 PCT/US94/09926 27 Features of sof22 Upstream Sequences. Putative promoter region shows significant homology to the scpA promoter. Comparison of the two sequences shown on Figure 9 yields highest degree of homology in the regions around -10 box and upstream of -35 box including 2 putative VirR binding consensus elements upstream of -35 box.

Homology of sof22 With Other Streptococcal sof Genes. Probe mpSOF69.2 homologous to 1.5kb long internal Sau3A fragment (nucleotide 890 to 2465) was used for the Southern blot analysis of chromosomal DNA Sau3A digests of 15 OF and 15 OF- strains that belong to different M types (Figure 9, Table This probe detects the sequence encoding for the functional domain of OF. Under high stringency washing conditions only DNA of strain D734, from which the sof22 gene is cloned, hybridized with the probe.

Under relaxed stringency washing (allows 20% mismatch) hybridization patterns obtained with DNAs from non-M22 SOF producing strains were different from that of D734. Unexpectedly, the signals obtained from the strains of the same M types differed among themselves.

Both the intensity of the signal and the restriction fragment pattern (length and number) were different for the two strains of M type 13. Two different patterns were obtained within the M type 22 strains.

4 M22 strains analyzed fall into the two groups: B243, B401 and F312 in one, and D734 in the other.

Out of 15 OF strains analyzed one of the 2 M6 strains and a M12 strain gave positive signals. The only

I

28 class I strain that gave a positive SOF reaction was D421 (M41). It gave a positive signal upon southern hybridization (relaxed conditions). The other M41 strain tested was OF and showed no signal in the southern blot analysis.

Physical Map Around sof22 Gene and Relation to M Protein. Two probes homologous to the sequences upstream (mpSOF2279.2) and downstream (mpSOF228.1) of the XhoI and SacI sites, were used in Southern blots to construct a physical map around sof22 gene (Fig. Nonoverlapping restriction map was constructed from the autoradiographs obtained after hybridization of an emm22 probe. Calculated from the size of the largest restriction fragments on which sof22 is positioned, its distance from the emm22 gene is at least 30 kbs in the upstream and 15 kbs in the downstream direction.

In Fig. 4, the OF segment amino acid residue 1 to 1025.

The enzymatic active segment is amino acid 1 to 811. The S segment 1 to 29 is the leader sequence, LSOF 22.4 and PSOF22.1 identified above have been deposited on 1st September 1993 at the American Type Culture Collection (ATCC) under the numbers 75541 and 75542 respectively.

What has been described is a cloning and subcloning procedure in which a DNA sequence comprising OF from D734 has been isolated and subcloned to identify the enzyme active S segment. The OF of D734 and the enzyme active segment are useful to WO 95/06721 PCT/US94/09926 29 qualitatively and quantitatively identify HDL by contact with a mammalian fluid suspected of containing it and determining if there has been a reaction. One procedure is to observe the development of opacity qualitatively. The determination can be made quantitative by labeling the protein, for example with a radioactive or enzymatic label and comparing the results with known or preestablished standard curves.

The degree of opacity could also be used for quantitation, using a standard curve of known HDL.

The insertion of the selected DNA sequence into a phage or a plasmid to permit the expression of a selected OF or enzyme active segment has also been described.

Claims (14)

1. 9.. .9 f-: THE CLAIMS DEFINING THE INVENTION ARE AS FOLLOWS: 1. A process for producing an isolated polypeptide having apolipoproteinase activity, wherein the process comprises culturing a prokaryotic unicellular organism containing a recombinant plasmid comprising a DNA sequence coding for said polypeptide having apolipoproteinase activity and capable of being replicated, transcribed and translated in the unicellular organism, and isolating said polypeptide having apolipoproteinase activity from the culture, said polypeptide being encoded by a sequence selected from the group consisting of: 0 the DNA sequence of Fig 4 (SEQ ID NO: 2); (ii) DNA sequences that hybridize to the DNA sequence of under high stringency hybridization conditions; and (iii) DNA sequences that encode an amino acid sequence encoded by a DNA sequence of or or enzymatically active segments thereof. S2. A process of claim 1 wherein the DNA sequence is sof22 and codes for SOF22. 3. A process of claim 1 wherein the DNA sequence is sof22.1 and codes for the fragment of SOF 22 which enzymatically hydrolyzes APO-1 from high density 3: lipoprotein. 4. A process for preparing a prokaryotic unicellular organism having a DNA sequence coding for a polypeptide having apolipoproteinase activity, wherein the process comprises introducing a recombinant plasmid comprising a DNA sequence coding for said polypeptide having apolipoproteinase activity and capable of being replicated, transcribed and translated in the unicellular organism, said sequence being selected from the group consisting of: the DNA sequence of Fig 4 (SEQ ID NO: 2); (ii) DNA sequences that hybridize to the DNA sequence of under high stringency hybridization conditions; and (iii) DNA sequences that encode an amino acid sequence encoded by a RA. DNA sequence of or or enzymatically active segments thereof. if I A process of claim 4 wherein the DNA sequence is sof22 and codes for SOF22. 6. A process of claim 4 wherein the DNA sequence is sof22.1 and codes for the fragment of SOF22 which enzymatically hydrolyzes APO-1 from high density lipoprotein. 7. A purified DNA sequence coding for a polypeptide having apolipoproteinase activity, said DNA sequence being selected from the group consisting of: the DNA sequence of Fig 4 (SEQ ID NO: 2); (ii) DNA sequences that hybridize to the DNA sequence of under high o 0 stringency hybridization conditions; and 0 (iii) DNA sequences that encode an amino acid sequence encoded by a SoDNA sequence of or or enzymatically active segments thereof. *0 015 0. go 8. A purified DNA sequence of claim 7 which codes for SOF22. 9. A purified DNA sequence of claim 7 which codes for the fragment of SOF22 S: which enzymatically hydrolyzes APO-1 from high density lipoprotein.
2. 10. A cloning vector comprising the DNA sequence of claim 7.
3. 11. A cloning vector of claim 10 which is LSOF22.4 and codes for the production of SOF22.
4. 12. A cloning vector of claim 10 which is pSOF22.1 and codes for the production of the fragment of SOF22 which enzymatically hydrolyzes APO-1 from high density lipoprotein.
5. 13. A unicellular organism containing the vector of claim S /i4. A unicellular organism containing the lambda phage of claim 11. Ii 32 A unicellular organism containing the plasmid of claim 12.
6. 16. An Escherichia coli bacterium containing the recombinant plasmid of claim 12.
7. 17. A purified DNA probe which binds specifically, under high stringency conditions, to a DNA sequence coding for a polypeptide having apolipoproteinase activity, or any portion of said DNA sequence having such activity, wherein said DNA probe comprises at least 15 nucleotides, said DNA sequence being selected from the group consisting of: the DNA sequence of Fig 4 (SEQ ID NO: and DNA sequences that hybridize to the DNA sequence of under high stringency hybridization conditions. gS 0• 20 S 0
8. 18. A diagnostic test for high density lipoprotein in a body fluid which comprises: contacting the body fluid with a polypeptide having apolipoproteinase activity, said polypeptide being encoded by one of the following sequences: the DNA sequence of Fig 4 (SEQ ID NO: 2); DNA sequences that hybridize to the DNA sequence of under high stringency hybridization conditions; and DNA sequences that encode an amino acid sequence encoded by a DNA sequence of or or enzymatically active segments thereof; (ii) detecting cleavage of apoprotein Al; and (iii) correlating said cleavage with the presence of high density lipoprotein.
9. 19. The test of claim 18 wherein the polypeptide is the enzymatic fragment of SOF22 which enzymatically hydrolyzes apoprotein Al from high density lipoprotein. I A process for producing an isolated polypeptide, according to any one of claims 1 to 3, substantially as described herein and with reference to any one of the accompanying drawings.
10. 21. A process for preparing a prokaryotic unicellular organism having a DNA sequence coding for a polypeptide having apolipoproteinase activity, according to any one of claims 4 to 6, substantially as described herein and with reference to any one of the accompanying drawings.
11. 22. A purified DNA sequence coding for a polypeptide having apolipoproteinase activity, according to any one of claims 7 to 9, substantially as described herein and with reference to any one of accompanying Figures 3, 4, 8 and 9. o
12. 23. A cloning vector according to any one of claims 10 to 12, substantially as described herein.
13. 24. A unicellular organism according to any one of claims 13 to 16, substantially as described herein. S 20 25. A purified DNA probe according to claim 17, substantially as described herein S. and with reference to any one of accompanying Figures 3, 4, 8 and 9.
14. 26. A diagnostic test for high density lipoprotein in a body fluid, according to claim 18 or claim 19, substantially as described herein and with reference to accompanying Figure 9. Dated this 8th day of February 1999. THE ROCKEFELLER UNIVERSITY By its Patent Attorneys MADDERNS v-O cC