Methods and reagents for detecting fungal pathogens in a biological sample
The present invention provides novel methods and materials for detecting the presence of a fungus in a biological sample. The inventive methods and materials exploit the fact that the amino acid sequence of the &agr;-aminoapidate reductase molecule is highly conserved in fungi. Inventive hybridization probes, nucleic acids, PCR primers, antibodies, epitopes, reagents and methods are provided.
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[0001] This application is a continuation-in-part of U.S. patent application Ser. No. 08/650,809 filed May 20, 1996.
BACKGROUND OF THE INVENTION[0002] 1. Field of the Invention
[0003] The present invention relates to novel methods for identifying fungal pathogens in a biological sample. In particular, this invention relates to methods for screening biological samples for the presence of fungal pathogens using hybridization methods and probes capable of sensitively and specifically detecting and distinguishing nucleic acid sequences unique to fungi. Also provided are antibodies capable of binding selectively to fungal proteins.
[0004] 2. Background of the Invention
[0005] Candida albicans (hereinafter referred to as “C. albicans”), once considered a relatively minor fungal pathogen, has recently become a particularly serious health concern as the causative agent of candidosis (also called candidiasis). The incidence of C. albicans infections is rising rapidly with the increase in immune deficiency diseases and immunosuppressive therapy (Bodey and Fainstein, In Systemic Candidiasis, pp. 135 (Eds., Raven Press, New York 1985). Candidosis is a common nosocomial infection afflicting both immunosuppressed and postoperative patients. (Holmes, A. R., et al. Yeast-specific DNA probes and their application for the detection of Candida albicans, J. Med. Microbiol., 37:346-351 (1992)). Although candidosis is a particular concern among immunocompromised individuals, Candida infections are not limited to this group. C. albicans is the major opportunistic fungal pathogen in humans (odds, F. C., In Candida and candidosis, (Ed.) Leicester University Press, Leicester, United Kingdom (1989)) and is capable of establishing infection whenever the host immune system or normal flora are perturbed.
[0006] Although the C. albicans species is a particular health concern, other species of the Candida genus are also pathogenic. The genus Candida is comprised of approximately 200 diverse yeast species classified together due to their lack of a sexual cycle (Meyer et al., In Genus 4, Candida, pp. 1-12, (Ed.) N. J. W. Kregervan Riij, Elsevier, Amsterdam (1984)). A minority of Candida species are pathogenic and 80% of the clinical isolates are either C. albicans or C. tropicalis (Hopfer, R. L. In Mycology of Candida Infections, G. P. Bodey. an V. Fainstein (eds.), Raven Press, New York (1985)).
[0007] In immunocompromised hosts, candidosis is a life threatening condition. The prognosis for a patient infected with C. albicans can be improved markedly, however, with prompt antifungal treatment. Treatment may be delayed until a positive diagnosis of Candidosis is obtained since antifungal drugs are toxic. (See Holmes, et al., 1992.)
[0008] Diagnostic tests for the identification of C. albicans or other fungal pathogens in vivo often require complete cultural identification protocols (Musial et al., Fungal Infections of the Immunocompromised Host: Clinical and Laboratory Aspects, Clin. Microbiol. Rev. 1:349-364 (1988)). Methods currently used for the diagnosis of fungal pathogens include: cultural identification, biopsy, serodiagnosis, identification of metabolites, isoenzyme determination, pulsed field gel electrophoresis and analysis of restriction fragment length polymorphisms. Most of these methods are time consuming, laborious and provide inconclusive results.
[0009] Potential methods for diagnosing fungal infections through DNA screening have focused on detecting specific nucleotide sequences such as ribosomal DNA (Hopfer, R. L. et al., Detection and differentiation of fungi in clinical specimens using polymerase chain reaction (PECR) amplification and restriction enzyme analysis J. Med. Vet. Pharm. 31:65-75 (1993)) and the p450 genes (Buchman, T. G. et al., Detection of surgical pathogens by in vitro DNA amplification. Part I. Rapid identification of Candida albicans by in vitro amplification of a fungal specific gene. Surgery, 108:338347 (1990)). However, no commercial diagnostic techniques embodying methods related to the identification of these genes in biological samples are known.
[0010] The sequences of approximately 1800 C. albicans genes are available in computerized databases. The relatively small amount of fungal specific or unique genetic information available for C. albicans places limitations upon the number of DNA sequences that can be used as targets for screening probes and concomitantly reduces the likelihood of identifying a sequence unique to fungi and amenable to identification through DNA screening techniques. For example, very few of available sequences are from genes involved in fungal amino acid biosynthesis pathways. One impediment to developing nucleic acid based screening techniques for Candidosis is that basic information about uniquely fungal metabolic pathways and cognate genes of C. albicans is lacking (Kurtz et al., Molecular Genetics of Candida Albicans, pp. 21-73, Kirsch, Kelly and Kurtz (eds.) CRC Press Inc. Boca Raton, Fla. (1990)).
[0011] Similar impediments exist to developing immunological methods of identifying a fungus present in a biological sample. Relatively few antigenic determinants unique to fungi are known, and none are believed to have been successfully utilized as targets for antibody binding in commercially available form.
[0012] Among the proteins that have been studied in C. albicans and other pathogenic fungi are the enzymes that make up the &agr;-aminoadipate pathway for the biosynthesis of lysine. This unique pathway has only been identified in Phycomycetes, Euglenids, yeasts and other higher fungi (Bhattachajee, The &agr;-aminoadipate Pathway for the Biosynthesis of Lysine in Lower Eukaryotes, CRC Critical Rev. in Microbiol. 12:131-151 (1985); Lejohn, Enzyme Regulation, Lysine Pathways and Cell Wall Structures as Indicators of Evolution in Fungi, Nature 231:164-168 (1971); and Vogel, Two Modes of Lysine Synthesis Among Lower Fungi: Evolutionary Significance, Biochim. Biophys. Acta 41:172-174 (1960); (Garrad, R. Masters Thesis, Miami University (1989) and, Garrad and Bhattachaijee, Lysine biosynthesis in selected pathogenic fungi: Characterization of lysine auxotrophs and the cloned LYS1 gene of Candida albicans, J. Bacteriol. 174:7379-7384 (1992)). Lysine biosynthesis is an example of a biochemical divergence between higher fungi, which use the &agr;-aminoadipic acid pathway (distinct from the diaminopimelic acid pathway used by bacteria and plants), and human host cells, which cannot synthesize lysine. The aminoadipate pathway for lysine biosynthesis, therefore, offers a unique opportunity to develop molecular probes for detection of fungal pathogens and as a potential drug target.
[0013] The &agr;-aminoadipate pathway consists of eight enzyme catalyzed steps; there appear to be seven free intermediates in S. cerevisiae (Bhattachaxjee, The &agr;-aminoadipate pathway for the biosynthesis of lysine in lower eukaryotes, CRC Critical Review in Microbiol. 12:131-151 (1985)). An understanding of the genetics, biochemical aspects, and regulation of the &agr;-aminoadipic acid pathway has been obtained by studies in the model orgamsms Saccharomyces cerevisiae, Schizosaccizaromyces pombe, and in the yeast Candida maltosa (Bhattacharjee 1992; Feller et al. 1994; Hinnebusch 1992; Schmidt et al. 1985). The final reversible step of the &agr;-aminoadipate pathway is catalyzed by saccharopine dehydrogenase, which is encoded by the LYS1 gene of S. cerevisiae and C. albicans, and the LYS5 gene of Y. Lipolytica (Fujioka, Chemical mechanism of saccharopine dehydrogenase (NAD, L-lysine forming) as deduced from initial rate pH studies, Arch. Biochem. Biophys. 230:553-559 (1984); Garrad and Bhattachaijee, Lysine biosynthesis in selected pathogenic fungi: Characterization of lysine auxotrophs and the cloned LYS1 gene of Candida albicans, J. Bacteriol. 174:7379-7384 (1992); and Xuan et al., Overlapping reading frames at the LYS5 locus in the yeast Yarrowia lipolytica Mol. Cell. Biol. 10:47954806 (1990)).
[0014] The conversion of aminoadipic acid to &agr;-aminoadipic semialdehyde is an obligatory step for the biosynthesis of lysine in yeast and is catalyzed by the enzyme, the &agr;-aminoadipate semialdehyde dehydrogenase, commonly known as &agr;-aminoadipate reductase (AAR) (Bhattacharjee 1985; Broquist 1971). AAR is a heterodimeric enzyme encoded by two unlinked genes LYS2 and LYS5 in S. cerevisiae, the equivalent genes in S. pombe being lys1+ and lys7+ (Rajnarayan et al. 1992; Sinha and Bhattachajee 1970; Ye and Bhattacharjee 1988).
[0015] The necessity of methods that provide rapid, sensitive and selective detection of fungal pathogens in biological samples and particularly for detection of C. albicans in biological samples increases each year is understood by those skilled in the art. The increasing use of immunosuppressive drugs in connection with organ transplants, autoimmune diseases, cancer, and the increasing number of patients suffering from acquired immunodeficiency syndrome, have resulted in a dramatic increase in the incidence of candidosis and other fungal infections. Because fungal infections are life threatening, physicians may prescribe antifungal drugs even in the absence of a definitive diagnosis. Due to the sometimes toxic effects of such drugs, however, their administration without such a definitive diagnosis is undesirable. Provided herein is a methodology for identification of a fungal pathogen in a biological sample by detection of nucleic acid sequences unique to fungi. The present invention fills a need in the art such that rapid identification of a fungal pathogen may be accomplished. As such, treatment of affected patients may be begun more rapidly that the art currently allows. Using the methods of the present invention, a more favorable prognosis may be associated with fungal diseases.
SUMMARY OF THE INVENTION[0016] An object of this invention is to provide method of identifying the presence of a pathological fungus in a biological sample. It is an additional object of the invention to provide nucleic acid constructs for use in screening biological samples for the presence of fungal pathogens.
[0017] It is also an object of the invention to provide such nucleic acid constructs comprising nucleotide sequences that are specific to fungal organisms, preferably those causing pathological consequences in a host. Yet another object of the present invention is to provide improved materials and reagents for use in screening biological samples for the presence of C. albicans. It is a further object of the present invention to provide nucleic acid constructs for use in screening biological samples for the presence of C. albicans.
[0018] Another object of the invention is to provide antibodies for use in screening biological samples for the presence of fungal pathogens. It is another object of the invention is to provide antibodies that are sensitive and specific for fungal proteins, preferably proteins of fungi having pathological effects in a host. It is a further object of the present invention to provide antibodies for use in screening biological samples for the presence of C. albicans.
[0019] In one embodiment, the present invention provides novel nucleic acids, reagents and PCR primers capable of selectively amplifying a nucleotide sequence found in fungal genomic DNA but not in higher eukaryote genomic mateial. In a preferred embodiment, the nucleic acids and PCR primers are derived from genomic DNA of C. albicans. In a more preferred embodiment, the present invention provides PCR primers and methodologies for sensitively and selectively amplifying LYS2 (US 8133; SEQ ID NO.: 1) nucleotide sequence from a biological sample containing C. albicans DNA.
[0020] In one preferred embodiment, nucleic acid hybridization probes are provided which comprising a nucleotide sequence illustrated in SEQ ID NO.:7 and homologues or labeled variants thereof.
[0021] In another preferred embodiment, the nucleic acid sequence comprises the sequence:
VB21 5′-TTAACAAAGAGATTGTTT-3′ (SEQ ID NO.:2)
VB22 5′-CTGAAACCTCTAATCTT-3′ (SEQ ID NO.: 3)
[0022] and homologues or labeled variants thereof.
[0023] In yet another embodiment, peptide sequences are provided from which antibodies may be generated to detect fungus-specific polypeptides in a biological sample. In a preferred embodiment, the peptide sequences are derived from &agr;-aminoadipate reductase. In a more preferred embodiment, the peptide sequence comprises LTKRDCLKIRGFT (SEQ ID NO.: 4).
[0024] In another embodiment, the invention provides methods of using antibodies reactive to a fungus-specific peptide in a biological sample. In a preferred embodiment, a method of detecting fungal &agr;-aminoadipate reductase encoded by LYS2 is provided. The invention additionally provides novel antibodies that may be labeled for use in a detection assay such as the enzyme-linked immunosorbent assay (ELISA). In an alternative embodiment, these epitopes may be labeled and used to detect the presence of a fungus in a biological sample, for example, by competitively inhibiting antibody binding in a radioimmunoassay. Reagents and kits comprising the inventive antibodies and epitopes are also provided.
BRIEF DESCRIPTION OF THE DRAWINGS[0025] FIG. 1 illustrates a pathway for synthesis of lysine is the alpha aminoadipate pathway (“the &agr;-AA pathway”).
[0026] FIG. 2 is a map of the plasmid pCaLYS2. The plasmid contains the 4.8 kb BamHI-Hindifi insert carrying the LYS2 gene of C. albicans in the vector pEMBLYe23. The arrow indicates the direction of transcription.
[0027] FIG. 3. Nucleotide sequence of the C. albicans LYS2 gene and its flanking region. The TATA box, CAAT boxes and poly(dA-dT) regions are underlined. The GCN4 box is shown in italics and underlined. The 3′ transcription termination signal is also underlined. The deduced amino acid sequence is shown below the nucleotide sequence. The serine residues encoded by CUG codon are shown with an asterisk. The AMP binding site signature and the alcohol dehydrogenase family signature are shown as bold and underlined.
[0028] FIG. 4. Comparison of protein sequences within the amino acid activation domain of peptide antibiotic synthetases from Penicillium chrysogenum (ACVT, ACVS), Aspergillus nidulans (ACVS) Cephalosporium acremonium (ACVS), Nocardia lactamdurans (ACVS), Bacillus brevis with deduced Lys2p sequence from Candida albicans and Saccharomyces cerevisiae. The identical residues are boxed and shaded. Dots indicate gaps introduced to maximize alignment. The core sequences (1-6) of the six domains of peptide synthetases are shown below the compared sequences. Residues common to ACV synthetases and LYS2p sequence is shown with an asterisk.
[0029] FIG. 5. Northern Blot analysis of C. albicans LYS2 RNA. (MM=minimal medium, MM+LYS=minimal medium supplemented with lysine, YEPD=yeast extract-peptone-dextrose medium). As a control, the same blot was hybridized with 18s rDNA probe.
[0030] FIG. 6. Sequence of Amplified LYS2 Product.
[0031] FIG. 7. Amplified product from Candida albicans.
DETAILED DESCRIPTION OF THE INVENTION[0032] Although approximately 1800 genes of the C. albicans genome have been sequenced, very few of the genes involved in amino acid biosynthesis had been sequenced prior to the current invention. One pathway for synthesis of lysine is the alpha aminoadipate pathway (“the &agr;-AA pathway”), which is illustrated in FIG. 1.
[0033] The degeneracy of the genetic code allows for the probes and primers of the present invention be described in terms of the polypeptides for which they code. Evolution results in related organisms using different codons to code for identical amino acids. Thus, the probes and primers of the present invention are those described in terms of the amino acid sequences for which they code, although exemplary sequences are identified herein. For the purposes of the present invention, when a probe or a primer is identified by its sequence, such probe or primer shall be taken to include the complementary sequence.
[0034] Certain hybridization probes expected to be useful in detecting fungi in biological samples include the nucleotide sequences of the LYS 2 gene of C. albicans that code for amino acid sequences conserved among fungi. The amino acid sequences which are conserved between C. albicans and S. cerevisiae, and the corresponding nucleotide sequence from C. albicans coding for those conserved sequences are set forth in Table I. 1 TABLE 1 C. albicans LYS 2 NUCLEOTIDE CONSERVED AMINO SEQUENCE CODING FOR AMINO ACID ACID SEQUENCE SEQUENCE Penicillium chrysogenum pcbAB (GenBank Accession No. M57425) ACVT, ACVS acvA (GenBank Accession No. X54296) Aspergillus nidulans AcvA (GenBank Accession No. X54853) ACVS Nocardia lactamdurans AcvA (GenBank Accession No. X53710) ACVS Cephasporium acremonium AcvA ACVS
[0035] AAR is a key enzyme of the unique aminoadipate pathway of fungi. AAR catalyzes the conversion of &agr;-aminoadipate to &agr;-aminoadipate semialdehyde in three steps. The first step is activation of &agr;-aminoadipate to adenyl-&agr;-aminoadipate (Sagisaka and Shimura 1962; Sinha and Bhattachajee 1970; Sinha and Bhattacharjee 1971). LYS2 encodes the large subunit of AAR and the sequence of this gene as isolated from C. albicans is shown in SEQ ID NO.: 1 (GenBank Accession No. U58133).
[0036] The present invention may be used to identify whether a subject is infected with a fungal pathogen as distinguished from a viral, bacterial or other biological pathogen. AAR is not known to be expressed by bacteria or any other non-fungal organisms provides a unique starting point for the methods claimed herein. The invention may also be used to select appropriate anti-fungal drugs for use in therapeutic intervention relatively early in the disease state. It believed that the invention is appropriate for detecting in biological samples fungal pathogens including but not limited to the following: C. albicans, Yarrowia lipolytica and Cryptococcus neoformans. It is possible that the invention may also be appropriate for detecting Aspergillus fumigatus and Histoplasma capsulatum in a biological sample.
[0037] Biological samples screenable via the present invention include samples obtained from healthy subjects or those with frank or occult disease. Samples appropriate for use in the current invention should be obtained from a site on or in the body where fungi do not constitute the normal flora. The at-risk patients from which the samples are obtained include, but are not limited to mammals suffering from acquired immune deficiency syndrome, those under treatment with immunosuppressive drugs, postoperative patients and other immunocompromised patients. The samples may comprise tissues, including but not limited to swabbings from mucocutaneous membranes such as swabs from the oral cavity or the vagina, or fluids including but not limited to urine, blood, semen, cerebrospinal fluid or other bodily fluids. In a preferred embodiment, the sample is a throat swab.
[0038] The nucleic acids derived from the biological samples of the present invention may be DNA, such as genomic or cDNA, and RNA, such as mRNA. RNA derived from such samples may be enriched for fungal RNAs as the fungal cells divide rapidly during infection. Thus, RNA derived from a biological sample is an important starting material for the methods of the present invention. RNA may be isolated from mixtures of DNA and RNA by using selective exonucleases, such as DNase, and other means well known in the art. Alternatively, RNA obtained from the sample can be converted to cDNA prior to employing the inventive methods.
[0039] In the present invention, nucleic acids may be isolated from the biological samples or may remain embedded in such samples. As used herein, “nucleic acids derived from a biological sample” encompasses DNAs and RNAs either isolated from or contained in a biological sample. As used herein, the phrases “polypeptide fragments derived from &agr;-aminoadipate reductase expressed by wild type Candida albicans” or “amino acid sequences derived from &agr;-aminoadipate reductase expressed by wild type Candida albicans” shall be taken to mean polypeptides having an amino acid sequence identical to any fragment of the &agr;-aminoadipate reductase protein derived from wild type C. albicans.
[0040] In methods where nucleic acids are first isolated from the biological sample prior to screening, the nucleic acid should be obtained in a manner so as to maintain it in an essentially undegraded state. It will be understood by those with skill in the art that by “essentially undegraded” is meant that the nucleic acid samples will be of sufficient integrity that the genes or messenger RNAs coding for &agr;-aminoadipate reductase in the sample will be detectable by the methods of this invention. Essentially undegraded nucleic acid is isolated by means well known to those with skill in the art. See, Sambrook et al., 1990, Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Press: New York), hereby incorporated by reference. Nucleic acid samples used according to the invention may be transferred directly onto a membrane, such as a nitrocellulose or a nylon membrane, or another solid support. Conversely, isolated nucleic acids may be put into solution. Britten and David (cite] describes such methods generally and is hereby incorporated by reference.
[0041] In one particularly important aspect of the invention, the nucleic acids are not isolated from the biological sample. In such methods, hybridization probes are applied directly to a biological sample in a manner known as in situ hybridization. Biological samples appropriate for use in in situ hybridization include tissues that may optionally be sliced or embedded in a support such as wax. The tissues may also be applied to a slide. Alternatively, in situ hybridization may be conducted in vivo and hybridization determined though detection methods such as computer aided tomography. Such methods are particularly desirable as they allow for rapid processing of samples to be tested and are particularly suited to laboratory conditions or kits for clinical use.
[0042] The present invention provides for detection of a fungal pathogen in a biological sample using hybridization probes directed to nucleic acid sequences (and corresponding homologues) encoding polypeptide fragments of AAR as expressed by wild type C. albicans. The hybridization probes of the present invention are not homologous to and do not cross react with nucleotide sequences of the human genome. These probes may be labeled, such as with radioactive isotopes, antigens or fluorescent compounds, to allow detection and quantification of probe hybridization.
[0043] Techniques for nucleic acid hybridization are described in Nucleic Acid Hybridization, eds. Hames, B D and Higgens, S. I., IRL Press, Oxford (1985) which is hereby incorporated by reference. In the inventive method, nucleic acids derived from a sample (whether in single stranded or double stranded form) may be transferred to a support, such as a nitrocellulose filter or nylon membrane, or may be put into solution. If transferred to a support, the nucleic acid may be applied as a single sample or as a series of samples. Samples of double stranded DNA may then be denatured using a salt solution. The DNA may be processed prior to transfer onto the support, for example, by digesting the DNA with restriction enzymes and separating the resulting fragments on a gel.
[0044] The pattern of distribution of nucleic acid on the filter is selected based on considerations such as whether the nucleic acid bound to the filter will be hybridized with a single probe species or multiple probe species.
[0045] In one embodiment, a series of nucleic acid samples are applied to a support. These samples are bound to the support as described above. To each support, a labeled hybridization probe contained in a reagent, preferably a hybridization buffer, is applied. Such probes should be made single stranded prior to application, such as by heating briefly. The supports so treated are then incubated for approximately 6-48 hours, and washed with a moderate to high stringency wash to remove non-specifically-hybridized probes.
[0046] The present inventive methods employ inventive reagents for the detection of a fungus in a sample. The reagents comprise inventive hybridization probes and appropriate hybridization buffers, which are known to those of skill in the art.
[0047] Probes preferred for use in the present invention have a maximum length of about 400 base pairs and a minimum of about 15 base pairs. In a preferred embodiment, the probes are from about 15 to about 100 base pairs long. In an especially preferred embodiment, the probes are approximately 15-40 base pairs long. Such sequences will hybridize selectively to fungal sequences under moderately stringent conditions as provided by the methods of the invention.
[0048] The inventive probes may be made by methods well known in the art, such as chemical synthesis. They may be synthesized manually or by machine. They may also be synthesized by recombinant methods using products available from Promega (Madison, Wis.). The probes may be single stranded or double stranded and may comprise DNA, cDNA or RNA.
[0049] The present inventive reagents may contain hybridization probes having only a single sequence, or may contain a combination of probes homologous to a variety of nucleotide sequences. The probes may be labeled, such as with radioisotopes, fluorescent compounds or antigens, to allow their detection following hybridization. In one embodiment of the present invention, an inventive reagent contains samples of a number of different hybridization probes each sample containing a label detectable by a different method. Use of such a reagent may, for example, be used as a control wherein a positive result would require binding of more than one type of probe to the sample.
[0050] In addition to hybridization probes, the inventive reagents may contain components including but not limited to formamide, phosphate buffers, dextran sulphate, yeast tRNA, SDS and salt. The reagents may also comprise acetyl triammonium boride, which renders the hybridization mixture to be dependent on probe length. The present invention contemplates the use of mixed pools of hybridization probes. Such pools would incorporate a variety of probes, such as degenerate probes or probes directed to more than one nucleotide sequence.
[0051] Hybridization is detected in a manner appropriate to the label, such as by autoradiography or fluoroscopy. Methods for detecting and quantifying hybridization are well known to those of ordinary skill in the art. In a preferred embodiment, appropriate negative (i.e. nucleic acids derived from uninfected tissue) and positive (i.e. fungal derived nucleic acids) controls are conducted to identify false negative and false positive hybridization.
[0052] Low stringency conditions are preferably employed during the annealing process to maximize hybridization of probes to homologous nucleic acid sequences. Following annealing, the filters are preferably washed under conditions of higher stringency to eliminate probes bound non-specifically.
[0053] In one embodiment, the nucleic acid sample is screened in solution. In such a method, the isolated nucleic acid may be optionally digested such as with a restriction enzyme. Hybridization probes are added to the solution and allowed to anneal. Stringency conditions should be selected to maximize hybridization (i.e. low stringency) and then should be raised to disrupt hybridization of probes bound to non-homologous nucleic acids. Detection and quantification of hybridization may be achieved as described above.
[0054] The results of the foregoing hybridization procedures are then used to identify the presence of a fungal pathogen in the biological sample from which the nucleic acid was obtained. This information can then be used to select appropriate therapeutic agents for treatment.
[0055] In situ hybridization methods are also encompassed by the present invention. In such methods, biological samples may be applied directly to a solid support and then treated with a labeled hybridization probe. Non-annealed probes are then removed, for example, by washing. Detection of hybridization may be achieved by autoradiography, fluoroscopy or visually, such as by detecting a color change.
[0056] A particularly advantageous embodiment of the present invention would be provided by a kit comprising one or more of the following elements: a solid support, a device for obtaining a biological sample from a mucocutaneous membrane (i.e. a swab), a solution containing nucleic acid hybridization probes labeled with a visually detectable label and a washing solution. Such kits may be employed, for example, by first applying the biological sample to the support, treating the sample with a solution containing the visually detectable probe, washing away the unannealed probes and visually detecting hybridization probes bound to the biological sample.
[0057] In an additional embodiment of the present invention, hybridization probes are used to detect restriction fragment length polymorphisms in nucleic acids isolated from a biological sample. In such method, nucleic acids are isolated from the sample and digested with a restriction endonuclease. The digested biological sample from which the nucleic acid was obtained. This information can then be used to select appropriate therapeutic agents for treatment.
[0058] In one embodiment, the present invention provides PCR primers based on LYS2, the gene encoding the large subunit of aminoapidate reductase for amplification of a 526 base pair sequence from C. albicans.
[0059] The primers of the present invention should be long enough to allow specific binding to fungal derived nucleic acid sequences and should have a sequence that is sufficiently homologous to a portion of the LYS2 gene to allow hybridized probes to remain bound under conditions of relatively high stringency. Each member of a primer pair to be used in connection with the present invention is selected from the group consisting of nucleic acids having nucleotide sequences coding for polypeptides that are (a) derived from AAR that is expressed by wild type C. albicans, and (b) conserved among fungi, wherein the nucleic acids neither are homologous to nor cross-react with nucleic acids derived from mammals. Preferably, each member of the primer pairs consist of nucleic acids having at least a portion of the nucleotide sequences set forth in Table I above. More preferably, the members of the primer pairs have the following nucleotide sequences:
VB21 5′-TTAACAAAGAGATTGTTT-3′ (SEQ ID NO.:2)
VB22 5′-CTGAAACCTCTAATCTT-3′ (SEQ ID NO.: 3)
[0060] The primers may comprise a first and a second oligonucleotide. The first oligonucleotide (VB21) has the sequence 5′-TTAACAAAGAGATTGTTT-3′. VB21 is identical to a sequence contained in the sense strand of the C. albicans LYS 2 gene encoding the large subunit of AAR. The sequence to which VB21 is complementary shall be identified herein as VB21C.
[0061] The second primer has the sequence:
5′-CTGAAACCTCTAATCTT-3′ (SEQ ID NO.: 3)
[0062] and shall be identified herein as VB22. VB22 is identical to a sequence contained in the antisense strand of the C. albicans gene for the large subunit of aminoadipate reductase. The sequence to which VB22 is complementary shall be identified herein as VB22C.
[0063] Primers representing shortened or lengthened versions of VB21 and VB22 are also considered to be included in the present invention to the extent that they remain specific to the large subunit of the C. albicans gene for aminoadipate reductase. Furthermore, the primers amplify a 526 base pair sequence of the LYS2 gene.
[0064] In one aspect, the present invention allows for the screening of a biological sample for the presence of a 526 base pair sequence of the Candida LYS2 gene that is unique to C. albicans. Provided the 526 base pair sequence is present in the screened biological sample at a detectable copy number (generally, 10-100 copies/ml), the 526 base pair sequence will be amplified and detected. Detection of the amplified oligonucleotide following PCR confirms the presence of C. albicans in the original biological sample.
[0065] Using the method in another embodiment, the presence of a fungal pathogen may be detected using nucleic acid hybridization probes, each probe having a nucleotide sequence selected from the group consisting of nucleotide sequences that code for a polypeptide that is (a) derived from the AAR molecule expressed by wild type C. albicans, and (b) conserved among fungi, wherein such probes are not homologous to and do not cross react with nucleic acid sequences found in the human genome. Because humans do not express AAR and the human genome is not known to contain a gene for this molecule, this molecule provides a unique starting point for generating hybridization probes that can be used to selectively detect fungal pathogens in a biological sample.
[0066] Homologues of such hybridization probes are also contemplated by the present invention. The presence of such fungal pathogens may also be detected using antibodies to such fungal specific C. albicans polypeptides. The inventive methods and reagents allow for the rapid and accurate identification of the infecting organism and therefore facilitate early therapeutic intervention.
[0067] In an additional embodiment of the present invention, hybridization probes are used to detect restriction fragment length polymorphisms in nucleic acids isolated from a biological sample. In such method, nucleic acids are isolated from the sample and digested with a restriction endonuclease. The digested nucleic acids are electrophoresed and blotted, as previously described. A sample known not to contain fungal nucleic acids is used as a negative control. Labeled probes having a nucleotide sequence that codes for a polypeptide that is (a) derived from AAR expressed by C. albicans, and (b) conserved among fungi, wherein such nucleotide sequences are not homologous to and does not cross react with nucleotide sequences found in the human genome, are then used to detect the presence of characteristic fragments of fungal nucleic acids in the biological sample.
[0068] As used herein, the term “oligonucleotide” is defined as a molecule composed of two or more deoxyribonucleotides or ribonucleotides, but which does not comprise all of the codons necessary for the expression of a full protein. For the purposes of the present invention, an oligonucleotide is considered to include (but not be limited to) the 526 base pair amplification product of the present invention.
[0069] A nucleic acid that is “complementary” to a reference nucleic acid shall be defined as a nucleic acid that is the antisense of the reference nucleic acid. As indicated below, primers VB21 and VB22 have been found to be most useful in the present invention. Minor modifications to such primers may nevertheless allow amplification of the desired 526 base pair oligonucleotide, and therefore such closely related primers are also considered to be within the scope of the present invention.
[0070] A reagent, for the purposes of this disclosure, shall be defined as a composition of matter used in performing diagnostic or research procedures (particularly PCR) that incorporates at least one of the invention primers. Such reagents also may comprise water and/or a buffer (especially Tris).
[0071] As used herein, a nucleic acid amplification kit shall be taken to mean a kit containing one or more components designed to be used in conducting PCR. In addition to at least one of the inventive PCR primers identified herein (which may be lyophilized or may optionally be provided dissolved in a solvent containing such components as water, Tris, or other components known to those of ordinary skill in the art) such kits may optionally include the following: a buffer (full strength or concentrated), which may contain Tris, DMSO and/or other additives; Taq enzyme (or similar thermostable DNA polymerase used by those of skill in the art in conducting PCR), preferably in solution, such solution containing glycerol and/or water; magnesium chloride; and dATP, dCTP, dGTP, and dTTP. The contents of such PCR kits and the foregoing compositions may be modified by those of ordinary skill in the art to achieve specific results and such kits and compositions are intended to be part of the present invention.
[0072] Reaction volumes for performing PCR are preferably from 20 &mgr;l to 100 &mgr;l depending upon the preference of the user.
[0073] The inventive primers and nucleic acids may be made by methods well known in the art, such as chemical synthesis. They may be synthesized manually or by machine. They may also be synthesized by recombinant methods using products available from Promega (Madison, Wis.).
[0074] The primers of the present invention may be labeled, such as with radioactive isotopes, antigens, colorimetric compounds, fluorescent compounds, or other labelling agents known to those of ordinary skill in the art, to allow detection and quantification of DNA amplification. Furthermore, the nucleoside triphosphates used in the course of the amplification may also be labeled for detection using labels and detection procedures well known to those of ordinary skill in the art.
[0075] The present inventive methods employ inventive reagents for the detection of C. albicans in a sample. The inventive reagents comprise the inventive primers and optionally comprise buffers, water, Tris-C1, EDTA and/or additional components. Primers may also be supplied in lyophilized forms which may be reconstituted using solvents and methods known to those of ordinary skill in the art.
[0076] The present invention may be used to identify whether a subject is infected with C. albicans. Because AAR is not known to be expressed by bacteria or any other non-fungal organisms, it provides a unique starting point for the materials and methods claimed herein. It is believed that the invention is appropriate for detecting C. albicans in biological samples and may detect other fungal pathogens in such samples.
[0077] Biological samples screenable via the present invention include samples obtained from healthy subjects or those with frank or occult disease. Samples appropriate for use in the current invention should be obtained from a site on or in the body where fungi do not constitute the normal flora. Blood is the preferred biological sample to be screened using the inventive materials and methods, as blood is presumed to be sterile and has no normal flora. The at-risk patients from which the samples are obtained include, but are not limited to mammals suffering from acquired immune deficiency syndrome, those under treatment with immunosuppressive drugs, postoperative patients and other immunocompromised patients. The samples may comprise tissues, including but not limited to solid tissues and swabbings from mucocutaneous membranes such as swabs from the oral cavity or the vagina, or fluids including but not limited to urine, blood, semen, cerebrospinal fluid or other bodily fluids. In a preferred embodiment, the sample is blood.
[0078] Nucleic acids screenable via the present invention include DNA (genomic DNA and cDNA). It is also possible that RNA may be screenable via the present invention in the event that the technique known in the art as RT-PCR (reverse transcriptase PCR) is used. Other variations on the PCR technique known to those of ordinary skill in the art are also expected to be useful when conducted using the inventive primers. Therefore, use of such techniques are considered to be part of the present invention.
[0079] In the present invention, nucleic acids may be isolated from the biological samples or may remain embedded in such samples. In a preferred embodiment, the DNA is isolated from the biological samples. As used herein, “nucleic acids originating in a biological sample” encompasses DNAs either isolated from or contained in a biological sample.
[0080] In methods where nucleic acids are first isolated from the biological sample prior to screening, the nucleic acid should be obtained in a manner so as to maintain it in an essentially undegraded state. It will be understood by those with skill in the art that by “essentially undegraded” is meant that the nucleic acid samples will be of sufficient integrity that the genes in the sample will be detectable by the methods of this invention. Essentially undegraded nucleic acid is isolated by means well known to those with skill in the art. See, Sambrook et al., 1990, Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Press: New York), hereby incorporated by reference.
[0081] Certain factors should be considered when implementing the present invention on a large scale, such as in a clinical laboratory. In general, technicians should take all reasonable steps to avoid contamination of samples to be screened by environmental materials. Such precautions are particularly important in connection with the present invention, because, as described below, a positive result in the PCR amplification may result from screening a sample containing a very small number of fungal cells. Thus, even small levels of fungal contamination have the potential for causing false positive results, and for this reason technicians should be particularly careful to keep contamination to a minimum. Those of ordinary skill in the art are aware of the steps generally applied in maintaining aseptic technique; procedures consistent with such aseptic technique should be used in obtaining and maintaining the biological samples to be screened via the present invention.
[0082] In order to avoid possible contamination of clinical specimens with Candida genomic or plasmid DNA, it is desirable to store clinical specimens and materials used in connection with the present invention in a location physically separate from any general use, clinical or molecular biology laboratory. If possible, it is desirable to set aside a separate laboratory solely for the storage, handling and processing of clinical tissue samples to be screened via the present invention. The work surfaces of such laboratories should be easy to clean and disinfect. Preferably, specific equipment dedicated for use in connection with PCR should include refrigerators and freezers in which to store reagents and tissue samples as well as a microcentrifuge capable of handling up to 24 tubes simultaneously, a dry bath incubator (temperature adjustable), and pipette devices capable of handling volumes of 0.5-10 &mgr;L, 10-50 &mgr;L, 40-200 &mgr;L and 100-1000 &mgr;L. Although autoclaved distilled water may be brought in from another laboratory, the room used for sample preparation and extraction should have its own stocks of reagent chemicals allowing extraction and storage buffers to be prepared in situ. The room should contain lab coats and gloves for the use o the workers; such materials should not leave the PCR laboratory. Disposable materials such as gloves, tubes and pipette tips should be ordered specifically for this lab and should not be stored in a general area or transferred from another laboratory. Unless a balance and pH meter may be accessed in a laboratory which is guaranteed to be free from contamination with fungi, it may be necessary to have this equipment in the PCR/extraction lab for the preparation of reagents.
[0083] Materials that should preferably be ordered specially for the PCR lab include plastic eppendorf style pipette tips (0.5-10, 10-200 and 100-1000 sizes) polypropylene microcentrifuge tubes, 0.5 and 1.5 ml sizes; polypropylene tube racks for above; disposable gloves; laboratory coats; ice buckets.
[0084] After samples have been isolated from a patient, clinical samples should be packaged in a manner to prevent contamination of the sample by fungi not originating in the sample. These samples should be delivered directly to the PCR/extraction lab where packaging may be removed. Upon receipt by the PCR/extraction lab, samples should be catalogued and divided into aliquots. Samples should be preserved at −20° C. if the need arises for an individual test to be repeated. A containment hood is not necessary in which to carry out the extractions, but may be desirable for maintaining sterile conditions. At a minimum, a specific bench should be designated for the work which should be regularly disinfected.
[0085] Inside a freezer in the PCT/extraction lab, samples of tissue should be stores which are used as the positive and negative controls for the extraction. The negative control may be any blood sample from a healthy individual. Such blood samples may be possibly obtained from blood transfusion services, especially if the testing is being carried out by a hospital having blood transfusion services. Ideally, the positive control should be a blood or tissue sample from a patient known to be infected systemically with C. albicans. However, in practice it may not be practical to obtain such blood samples in large enough quantities to allow use as a positive control in repeated tests. In practice the use of a blood sample which has had C. albicans cells added to a given concentration as a positive control may be more feasible.
[0086] PCRs may be set up in the PCR/extraction lab on a designated bench. It is often convenient to designate a buffer bench, which is a DNA-free area where lysis buffers, extraction buffers and PCR ingredients are mixed. Such materials are then transferred to other benches where the extractions will be carried out and samples or template DNAs are added to the PCRS. In order to standardize the PCR, it is common practice to make “master-mix” reactions rather than to set up reactions individually, i.e., if 20 PCRs are to be set up, a sample containing sufficient reaction buffer, primers, nucleotides and enzyme to complete all PCR reactions should be made up in one tube and then divided among 20 tubes whereupon the given DNA templates/sample aliquots should be added individually to each tube. (All chemical reagents identified herein were obtained from Fisher Scientific, Pittsburgh, Pa., unless otherwise noted).
[0087] Having prepared the PCR reaction mixtures, for example, as described in this specification, the reactions may be run in a thermocycler, the location of which in the laboratory is not critical, however, the completed reactions should on no account be brought back into the PCR/extraction lab. After completion of the amplifications, the reactions may be analyzed by agarose gel electrophoresis. Electrophoresis may be carried out at any convenient location, however, the electrophoresis lab should be physically separate from the PCR/extraction lab and no materials should be transferred from the electrophoresis area into the PCR/extraction laboratory.
[0088] Amplification may be detected in a manner appropriate to the label (if any), such as by autoradiography or fluoroscopy. Unlabelled amplification products may be detected through ethidium bromide staining. Methods for detecting and quantifying the amplified DNA are well know to those of ordinary skill in the art. Although this specification refers to a specific extraction method for extraction of DNA from biological samples, any extraction method that results in isolated, essentially undegraded DNA of adequate yield may be used as long as the users adhere to the general conditions for the prevention of contamination.
[0089] One of ordinary skill in the art will be familiar with the techniques used to adjust the stringency of the reaction conditions and therefore minimize false positive and false negative amplifications. For example, use of a PCR optimization kit (for example, the PCR optimization kit available from Promega (Madison, Wis.)) may be desirable depending on the primer selected.
[0090] The present inventive reagents may contain a single inventive primer or multiple inventive primers. In addition, the inventive reagents may contain a variety of primers, each capable of causing amplification of fungal-specific oligonucleotides.
[0091] The PCR technique is described in PCR Technology Principles and Application for DNA Amplification (Erlich ed. 1989) and U.S. Pat. No. 4,683,202, the teachings of which are hereby incorporated by reference. It is also possible that the PCR method known as “Touchdown” PCR would be useful in the amplifying DNA from fungi when the primers to be used are degenerate. This technique is described in R. H. Don, et al., ‘Touchdown’ PCR to circumvent spurious priming during gene amplification. Nucleic Acids Research, 19:4008 (1991) which is hereby incorporated by reference. Likewise, the technique of “hot start” PCR (Chou, Q. et al., Nucleic Acids Research, 20:1717 (1992)) may also be useful in the present invention.
[0092] The present invention also provides for the detection of fungal pathogens in biological samples following amplification of a portion of a AAR gene, such as the LYS2 gene. In such a method, for example, biological samples are first obtained and nucleic acids isolated as described above. Portions of genes or mRNAs coding for AAR contained in the nucleic acid sample are then amplified by PCR (polymerase chain reaction), a technique well known to those of ordinary skill in the art. The PCR technique is described in PCR Technology, Principles and Applications for DNA Amplification (Erlich ed. 1989) and U.S. Pat. No. 4,683,202, the teachings of which are hereby incorporated by reference.
[0093] Inventive pairs of nucleic acid primers for use in PCR are contemplated by the present invention. Each member of such primer pair has the characteristics of the above described hybridization probes, namely, each member of the primer pair has a nucleotide sequence that is selected from the group consisting of nucleotide sequences that code for polypeptide fragments that are (a) derived from AAR expressed by wild type C. albicans and (b) conserved among fungi, wherein neither member of such primer pairs is homologous to nor cross reacts with nucleotide sequences found in the human genome. These inventive primer pairs, generated based on the information provided herein, including but not limited to that set forth in Table I, are employed during gene amplification.
[0094] Appropriate primer pairs are then used to amplify genetic material by well known methods. For the purposes of the present invention, a portion of a gene shall be taken to mean any portion of an entire gene, including regulatory sequences. More than one set of primer pairs may be used in the inventive method to amplify multiple gene fragments. The invention thus enables in vitro amplification of portions of fungal genes, for example, the LYS2 gene, that can then be used in a screening procedure capable of identifying the presence of fungal pathogens in a biological sample.
[0095] It is also possible that the PCR method known as “Touchdown” PCR would be useful in the amplifying DNA from fungi when the primers to be used are degenerate. ‘Touchdown’ PCR, which circumvents spurious priming during gene amplification is described by Don, et al. (Nucleic Acids Research, 19:4008 (1991)), which is hereby incorporated by reference.
[0096] The gene portions so amplified may be transferred to filters or into solution in the manner described above. Reagents containing one or more hybridization probes are then applied to the samples of the amplified nucleic acids and allowed to anneal under stringency conditions as described above. Non-annealed probes are then removed by washing. Hybridization of the probes to the amplified DNA samples is then detected by means appropriate to probe label, such as by autoradiography.
[0097] The results of the hybridization experiments are then analyzed to determine the presence of a fungal pathogen in the biological sample. This information is then used in planning a course of antifungal treatment.
[0098] The present invention also provides methods for detecting antibody binding to epitopes contained in a biological sample. Such methods entail applying an antibody, preferably a monoclonal antibody, capable of binding selectively to an epitope of C. albicans derived &agr;-amino adipate reductase and detecting selective antibody binding. Such methods include immunoblotting procedures, wherein the proteins contained in a biological sample are separated by electrophoresis and transferred to a support. Preferred supports include but are not limited to nitrocellulose filters and activated paper.
[0099] Proteins can be transferred to the filter by simple diffusion, vacuum assisted solvent flow or electrophoretic elution. Antibodies (either labeled or unlabeled) are put into solution in a protein containing solvent such as BSA/PBS. The solution is then applied to the solid support harboring the blotted protein and incubated at room temperature. The blot is then washed, such as with a buffer. If the antibodies are labeled, such as with a radioactive isotope or fluorescent compound, antibody binding can then be detected. If the antibodies are unlabeled, a secondary reagent capable of disclosing bound antibody, such as avidin or streptavidin is then added. Such secondary reagents may be enzyme labeled secondary reagents, such as those commonly utilized in enzyme linked immunosorbent assays.
[0100] The inventive antibodies may also be used to detect a fungal pathogen in a sample by means of immunoprecipitation, such as an Odin single diffuision or Ouchterlony double diffusion test. Optionally, the proteins of the sample may be separated prior to exposure to the inventive antibodies. In an alternative embodiment, the sample may first be immunoprecipitated and subsequently separated by gel electrophoresis.
[0101] Antibodies capable of binding selectively to epitopes of C. albicans derived &agr;-amino adipate reductase are particularly desirable for use in detecting the presence of a fungus in a biological sample as such epitopes are not known to have counterparts among human proteins.
[0102] Antibodies, including but not limited to monoclonal antibodies, capable of selectively binding to AAR in a biological sample can be generated through the use of hybridoma technology and related technologies well known in the art. Generation of monoclonal antibodies is described in Antibodies: A Laboratory Manual, eds. Harlow and Lane, Cold Spring Harbor, 1988, which is hereby incorporated by reference. The region of binding of such antibodies may be determined by first subjecting the target protein to enzymatic or chemical degradation, separating the fragments using electrophoresis and then immunoblotting.
[0103] In a particularly advantageous embodiment of the present invention, the inventive antibodies are employed in an enzyme linked immunosorbent assay (ELISA). In such method, the inventive antibody (the primary antibody) is anchored to a support, such as a multi-well microtiter plate. A biological sample is then added to the support, after which unbound sample is removed by washing. A second antibody to which an enzyme has been linked is applied to the support. The second antibody is one that is capable of binding to a fungal protein, though not necessarily specifically. The linked enzyme is one capable of producing a change, such as a color change, in a solution containing its substrate, the rate of color change being proportional to the enzyme concentration.
[0104] After removal of the unbound secondary antibody, a solution of the enzyme substrate is added to the support and the rate of change, such as color change, of the solution is measured. Use of such a method allows for the detection and quantification of epitopes in the sample to which the primary inventive antibody selectively binds.
[0105] In an additional aspect, the inventive methods provide a sandwich binding assay. In such an assay, the biological sample is first applied to a support, such as a filter. A inventive antibody (a primary antibody) is then applied to the support, such as by diffusion. After unbound primary antibody is removed by washing, a second labeled antibody is applied to the support. This second labeled antibody is capable of binding to the primary antibody. Appropriate labels include but are not limited to radioactive isotopes, colored compounds and fluorescent compounds.
[0106] Unbound secondary antibody is then removed by washing. Detection of a fungal pathogen in the sample is then achieved by measuring the presence of the antibody label on the support visually, or by methods such as autoradiography or fluoroscopy.
[0107] The invention also provides novel epitopes comprising polypeptides having amino acid sequences characteristic of fungi. Such epitopes may be synthesized by methods well known in the art. Such methods include both manual and automated methods of polypeptide synthesis that may be conducted in solid phase or in solution.
[0108] In a further embodiment, the invention provides a method of detecting fungal pathogens in a biological sample by means of a radioimmunoassay (RIA). In such a method, a sample of radioactively labeled inventive epitopes of known concentration are combined with a sample of inventive antibodies, also of known concentration. The amount of unbound epitope contained in the solution is then measured (the first measurement). To a solution containing a known concentration of radioactively labeled inventive epitope and unlabeled inventive antibody is then added a biological sample suspected of harboring a fungus. The amount of unbound labeled epitope in the solution is then measured (the second measurement). The first measurement is then compared to the second measurement to detect the amount of labeled epitope displaced by epitope contained in the biological sample. These results can then be used to quantify the amount of epitope contained in the biological sample. Use of a radioimmunoassay to detect fungal pathogens in a biological sample is especially desirable as it is a particularly sensitive assay.
[0109] Certain embodiments of the present invention are illustrated by the following non-limiting examples.
EXAMPLE 1 Isolation and Characterization of LYS2 Gene of C. albicans[0110] A. Materials and Methods
[0111] 1. Strains, Plasmids, and Growth Conditions
[0112] The yeast, bacterial strains and plasmids used in this study are listed in Table 2. Yeast strains were maintained on yeast extract-peptone-dextrose medium (YEPD). Minimal medium (MM) consisted of 1% dextrose and 0.67% yeast nitrogen base without amino acid. Minimal medium was supplemented with L-lysine (50 &mgr;g/ml) where appropriate. Escherichia coli strains were maintained on Luria Bertani medium. Plasmid containing strains were maintained in L-agar containing ampicillin at a concentration of 50 &mgr;g/ml. 2 TABLE 2 Strains/ plasmids Genotype Source/Reference E. coli DH5aF′ F′ endA1 hsdR17(rk-mk-) supE44 ATCC thi-1 recA1 gryA (Nair) relAI D(lacZYA-argF)U169 deoR [F80dlacD(lacZ)M15] C. albicans WT9517 LYS Sarachek et al. (1981) WA153 LYS2 Sarachek et al. (1981 S. cerevisiae SR-36 his, ura3, LYS2 Yeast genetic stock culture Yeast genetic RC1 a, LYS stock culture Plasmids pUC18 Vector for cloning in E. coli and IBI sequencing pCaLYS2 LYS2 cloned into pEMBLYe23 Magee et al. (1988) pCaLYS2a EcoRI-PstI (2.0 kb) in pUC18 This study pCaLYS2b EcoRI-PstI (2.2 kb) in pUC18 This study
[0113] 2. Plasmid DNA Isolation
[0114] Large scale plasmid isolation from transformed E. coli were performed using the Qiagen kit (Qiagen) according to manufacturer's instruction. DNA manipulations were performed as described by Sambrook et al. (1989). E. coli strain DH5&agr; was transformed with plasmid DNA by the method of Chung et al. (1989).
[0115] Transformation of S. cerevisiae and C. albicans. S. cerevisiae LYS2 mutant cells transformed with the cloned C. albicans LYS2 gene using the lithium acetate method (Ito et al. 1984) were selected on minimal medium devoid of lysine. Plates were incubated at 30° C. for 5 to 7 days. C. albicans LYS2 mutant cells were transformed by the standard spheroplast transformation procedure of Sherman et aL (1986). The transformed cells were added to top agar (minimal medium devoid of lysine plus 1.2 M sorbitol) and poured over minimal medium with 1.2 M sorbitol minus lysine. The plates were incubated at 30° C. for 5 days. For the purpose of plasmid curing, yeast cells transformed with plasmid pCaLYS2 were plated on minimal medium and incubated at 30° C. These plates were then replica plated for 5 cycles on non-selective (YEPD) medium and selective (minimal) medium. The number of transformants that lost the plasmid in the 5 cycles and reverted to auxotrophy was determined.
[0116] 3. DNA Sequence Analysis
[0117] DNA sequences were determined by the dideoxynucleotide chain termination method (Sanger et al. 1977) by using the Sequenase 2.0 kit (US Biochemical) and [&agr;-35S]dATP or [&agr;32P]dATP (Dupont-New England Nuclear). To facilitate sequencing, a 2.0 kb and 2.2 kb EcoRI-PstI fragments from plasmid pCaLYS2 were subcloned into EcoRI-Pstl digested pUC 18 vector. Sequencing reactions were primed with universal, reverse, and sequence generated synthetic oligonucleotide primers synthesized on a Milligen 7500 DNA synthesizer. A 0.6 kb region upstream of the start site was sequenced using the dye terminator method on an automated sequencer by Molecular Resources. All nucleotide positions were confirmed by sequencing both strands on the insert. The sequence of the 3′ end of the LYS2 ORF was obtained by using the adaptor ligation PCR strategy described by Siebert et al. (1995). The adaptor oligonucleotide linker (5′CTA ATA CGA CTC ACT ATA GGG CTC GAG CGG CCG CCC GGG CAG GT 3′ and 5′ AC CTG CCC 3′) was ligated to EcoRV digeeted C. albicans genomic DNA. PCR amplifications were carried out using Clontech “Advantage” Genomic PCR kit (Clontech) as per manufacturer's instructions. The “LYS2 C” gene specific primer (5′ CCC AGC AGA CTA TCC AGT ATG GAC CAG TGC 3′) was used along with adaptor primer AP1 (5′ GGA TCC TAA TAC GAC TCA CTA TAG GGC 3′) to obtain the primary PCR product The primary PCR product (1 &mgr;l) was used as a template for secondary PCR reaction with adaptor primer AP2 (5′ AAT AGG GC CGA GCG GC 3′) and “LYS2 B” nested gene specific primer (5′ CAC AAG ACA CAA AGG CTC CCG AGT TAG ACG 3). The secondary PCR product was sequenced using the Promega fmol cycle sequencing kit (Promega). The DNA sequence and the deduced protein sequence were analysed by using various program available with the Genetics Computer Group software (Univ. of Wisconsin Biotechnology Center, Madison, Wis., USA) (Devereux et al. 1984). The GenBank accession number for the sequence reported in this paper is U58133.
[0118] 4. Northern Blot Analysis
[0119] Total RNA was isolated from C. albicans WA95 17 cells grown in different media according to the procedure described by Sherman et al. (1986). Total RNA (20 &mgr;g/lane) was fractionated by electrophoresis on a 1% agarose gel, transferred to nylon membranes, and hybridized to LYS2 gene and 18s rDNA radio-labelled probes. The 2.0 kb EcoRI PstI fragment of the LYS2 gene was labelled with [&agr;32P]dATP by a random primer kit (Gibco BRL) and used as a probe. A plasmid carrying the 18S rDNA was also labeled similarly and used as ribosomal probe. Hybridization was carried out at 60° C. in 0.5 M Sodium phosphate (pH 7.2), 7% SDS, 1% BSA, 1 mM EDTA (pH 8.0). The membrane was washed in 2×SSC and 0.1% SDS at room temperature for 30 min and followed by a wash in 0.5×SSC and 0.1% SDS at 60° C. for 30 min. The membrane was stripped by boiling in 0.1×SSC and 0.1% SDS for 30 min followed by washing with water at 65° C. for 30 min and then reprobed.
[0120] 5. Preparation of Cell Extract
[0121] Cells were grown in appropriate media at 30° C. with constant shaking and harvested during the late logarithmic phase. Crude enzyme preparations were obtained by disruption of the cells in a Braun homogenizer flask in the case of S. cerevisiae (Sinha and Bhattacharjee 1971), and by vortexing with glass beads for 30s with 30s intervals at 4° C. for a total of 5 mins in case of C. albicans. The crude extracts were dialyzed and used as the enzyme source for the AAR activity. The amount of protein in the dialyzed extracts was determined according to the procedure of Bradford (1976).
[0122] 6. Aminoadipate Reductase Activity
[0123] The AAR activity was assayed using previously described procedure (Sagisaka and Shimura 1962). The reaction mixture consisted of DL aminoadipate, 12.5 mM; ATP, 15 mM; MgCl2, 10 mM; reduced glutathione, 1 mM; &agr;-NADPH (tetra sodium salt), 0.625 mM; and Tris HCl, 250 mM (pH8.0). Dialysed cell extract was added to a final concentration of 0.02-1.0 mg of dialyzed protein. Tubes lacking aminoadipate were used as controls. The reaction mixtures were incubated at 30° C. for 1 h and terminated by the addition of I ml of 2% p-dimethylaminobenzaldehyde (PDAB) in 2-methoxyethanol. Activity of AAR was reported in units of A460 h-1 mg protein-1.
B. LYS 2 Characterization[0124] 1. Complementation of S. cerevesiae SR-36 and C. albicans WA153
[0125] The LYS2 gene of C. albicans was originally isolated by heterologous complementation of the S. cerevisiae LYS2 mutant with plasmid pCaLYS2 (Magee et al. 1988). The plasmid pCaLYS2 containing the 4.8 kb BamHI-HindIII insert (FIG. 2) was digested with six different restriction enzymes to obtain a restriction map. The LYS2 mutants of S. cerevisiae SR-36 lacked AAR activity. The plasmid pCaLYS2 transformed the LYS2 mutant of S. cerevisiae SR-36, and the C. albicans strain WA 153 and restored lysine prototrophy. In a previous study (Garrad and Bhattachajee 1992), the C. albicans strain WA153 was shown to be blocked in the synthesis of &agr;-aminoadipic semialdehyde. Lack of AAR activity in C. albicans WA153 and transformation of this strain with plasmid pCaLYS2 identified it to be a LYS2 mutant of C. albicans. The maintenance of pCaLYS2 in C. albicans transformants was shown to be non-integrative by plasmid loss experiments (data not shown). Wild type S. cerevisiae RC1, LYS2 mutant SR-36 and transformants were assayed for AAR activity (Table 5). Wild type C. albicans WT9517, LYS2 mutant WA153, and transformants were also assayed for AAR activity (Table 5).
[0126] The AAR activity of C. albicans WT 9517 cells was determined for cells grown in minimal medium, minimal medium supplemented with lysine, and YEPD. The AAR activity of cells grown in minimal medium supplemented with lysine was repressed by 40% and the activity of cells grown in YEPD was repressed by 66% compared to the activity of cells grown in minimal medium (Table 3). This further demonstrates that the AAR of C. albicans is repressed by excess lysine and by general amino acid control mechanisms.
[0127] Feedback inhibition by the end product, lysine, was determined by addition of various concentrations of lysine to the reaction mixture. 50 mM lysine inhibited the AAR activity by 70%. However, when a lysine analog, [S-(2-amino ethyl)] L-Cysteine L-thialysine), was used, 1 mM thialysine was sufficient to abolish 92% of the enzyme activity (Table 5). This demonstrates that the AAR of C. albicans in addition to being repressed at the transcriptional level is feedback inhibited by the end product, lysine and its analog, thialysine.
[0128] The Lys2+ transformants of S. cerevisiae and C. albicans showed a significantly higher activity compared to that of the wild type cells. Results of homologous and heterologous transformation along with the enzyme activities show that the insert in plasmid pCaLYS2 carries the functional LYS2 gene of C. albicans. 3 TABLE 3 &agr;-aminoapidate reductase (AAR) activity in S. cerevisae and C. albicans Strain AAR activitya % AAR activity of wild-type S. cerevisiae RC-1 (wild-type) 13.38 100 SR-36 (LYS2) 0.25 1.9 SR-36 (pCaLYS2) 18.47 138 C. albicans WT9517 (wild type) 6.73 100 WA153 (LYS2) 0.00 0 WA153 (pCaLYS2) 10.80 160 aAAR activity is reported as A460 h−1 mg protein−1. The results represent the average of three independent determinations.
[0129] Results of transformation, plasmid loss and enzyme activity confirm that the LYS2 gene is located in the 4.8 kb BamHI-HindIII insert of plasmid pCaLYS2 (FIG. 2; Table 3). Although the plasmid pCaLYS2 does not contain a C. albicans ARS, the plasmid loss experiment showed that the transformation was non-integrative. This suggests that an ARS is present in the insert of plasmid pCaLYS2 or that an ARS element was acquired by recombination. Non-ARS-dependent maintenance of plasmid has been described in S. pombe (Wright et al. 1986).
[0130] 2. Sequence Analysis of LYS2 Gene of C. albicans
[0131] The complete DNA sequence along with the deduced amino acid sequence of the LYS2 gene is shown in FIG. 2 and SEQ ID NO.: 5. Analysis of the sequence revealed a continuous ORF of 4173 nucleotide encoding 1391 amino acid residues with an estimated Mr of 154,644. The nucleotide sequence showed 63.0% identity to the LYS2 gene sequence of S. cerevisiae. In the 5′ region upstream of the LYS2 ATG start site is a potential TATA box with sequence TATATTAA (located 109 bp upstream of the start site). At position -3bp relative to the putative start is an adenosine residue, consistent with the Kozak model for translation initiation. There are several poly(dA-dT) regions and nine CAAT boxes in the 5′ upstream region. A potential GCN4 box (TGACTC) was located at postion 413-418. This suggests that the AAR of C. albicans is also under general amino acid control. The last 48 nucleotides of the ORF, stop codons (TAA. . . . TAA . . . TAG) and the subsequent nucleotides of the 3′ end were sequenced from genomic DNA (see materials and methods). An S. cerevesiae-type termination signal (TATG . . . TATG . . . TTT) is seen in the 3′ downstream region. Although the insert in plasmid pCaLYS2 is missing 48 bp of the LYS2 3′ end, it was able to complement the LYS2 mutants of S. cerevisiae and C. albicans. It was shown by Ohama et al (1993) that there is non universal decoding of CUG (leucine codon) to serine in C. albicans. These serine residues (coded by CTG) are shown with an asterisk (FIG. 3).
[0132] The LYS2 gene has been mapped to chromosome 1 by Chu et al. (1993). Although this gene has evolved only in fungi, the nucleotide sequence shows only 63.0% identity to the nucleotide sequence of LYS2 gene of S. cerevisiae and is not completely conserved. The presence of domains for AMP binding and &agr;-aminoadipate activation in the LYS2 gene-encoded polypeptide (by comparison with the &agr;-aminoadipate activation domain of ACV synthetase from Penicillium chrysogenum) strongly supports the observed adenyl-aminoadipate formation and validates the proposed mechanism for activation of aminoadipic acid. The predicted amino acid sequence of the Lys2p polypeptide of C. albicans is homologous to adenylate forming enzymes that activate and bind amino acids in antibiotic synthesis. The various domains in these peptide antibiotic synthetases were suggested to be involved in amino acid activation, ATP hydrolysis, and thioester formation. These domains were shown to have six core sequences spanning a region of 600 residues by Marahiel (1992). Core sequence 6 (sequence LGG(DIH)S*(I/L) is involved in thioester formation. This sequence resembles the 4-phosphopantetheine binding site consensus sequence with serine being the active residue (FIG. 4).
[0133] 3. Amino Acid Analysis and Homology to Peptide Antibiotic Synthetases
[0134] The deduced amino acid sequence has 56.2% identity with deduced amino acid sequence of S. cerevisiae Lys2p. Codon usage analysis revealed that 60 of the 61 non stop codons were being used. The codon adaptation index was 0.22. By comparison with other genes that are expressed at low levels which have a similar codon usage, the LYS2 gene is probably also lowly expressed, which might be expected for an amino acid biosynthetic gene that is tightly regulated (Hinnebusch 1992; Lloyd and Sharp 1992). A hydropathy plot revealed that the enzyme is membrane associated (data not shown).
[0135] Using motifs program in GCG, the AMP binding domain signature was located from amino acids 413 to 424 (FIG. 2). A conserved glycine is seen following the lysine residue of the signature. This sequence is identical to the sequence present in S. cerevisia. Additionally, a short chain alcohol dehydrogenase family signature sequence at position 1137-1165 DDLQGSAKGLGNGYGQSKWAAEYIIRRG) was found in the deduced Lys2p amino acid sequence of C. albicans (FIG. 2). The ACV synthetase catalyses the synthesis of the tripeptide &dgr;(L-&agr;-aminoadipyl) L-cysteinly-D-valine (ACV) in the synthesis of &bgr;-lactam antibiotics like penicillins and cephalosporins Marahiel, 1992). In an attempt to identify the binding site of the substrate L-&agr; aminoadipic acid, we compared the deduced amino acid sequence of Lys2p with the previously characterized aminoadipate activation domain in ACV synthetases (Diez et al. 1990; Needleman and Wunsch 1970). Residues Leu-351, Pro-462, Arg-465, Glu-513, and Thr-536 are conserved between AAR of C. albicans and ACV synthetases. These residues may play a role in &agr;-aminoadipate binding. The other residues that were highly conserved between ACV synthetase and AAR of yeast were found to be part of the domain structure seen in peptide antibiotic synthetases (Coque et al. 1991; Cosima et al. 1993; Diez et al. 1990; Hori et al. 1989; MacCabe et al. 1991; Marahiel 1992; Mittenhuber et al. 1989) of the adenylate-forming enzyme superfamily (FIG. 3). The conserved residues along with the six core sequences of the amino acid activation domains in this superfamily of peptide synthetases and AAR of S. cerevisiae and C. albicans are shown as shaded blocks. The regions of identity previously observed by Morris and Jinks-Robertson (Morris and Jinks-Robertson 1991) between tyrocidine synthetase 1 from Bacillus brevis and Lys2p of S. cerevisiae are part of the peptide antibiotic synthetase domain structure. The core sequences of the six domains are shown below the conserved block of residues (FIG. 3). The yeast AAR's showed 22-25% identity to the peptide antibiotic synthetases within the conserved amino acid activation domain.
[0136] It appears that &agr;-aminoadipate is first activated to its adenylate form, which is bound to the enzyme via a thioester bond by interaction of the carboxyl group with the thiol group in the enzyme. The co-factor, 4-phosphopantetheine, may be bound to the enzyme as in the peptide antibiotic synthetases and involved as a carrier of activated aminoadipate. The high degree of conservation in these six domains suggests that these enzymes may have a common ancestry and would be of use in elucidating the evolutionary relationship of this novel enzyme. Structural analysis of the protein and site directed mutagenesis of these regions would be worthwhile to elucidate the function of each of these domains including the biochemical mechanism of this enzyme reaction. Although AAR is a heterodimeric enzyme, a leucine zipper region, with a possible role in heterodimer formation seen in the S. cerevisiae Lys2p deduced aminoacid sequence, is absent in the Lys2p of C. albicans (Morris and JinksRobertson 1991). However, a short-chain alcohol dehydrogenase family signature sequence at position 1137-1165 (DDLQGSAKGLGNGYGQSKWAAEYIIRRAG) was found in the deduced Lys2p amino acid sequence of C. albicans (FIG. 3). There are two conserved residues, a tyrosine and a lysine residue, in the signature which have been shown to be important for catalytic activity and for subunit binding (Ensor and Tai 1991; Janyetal. 1984).
[0137] Little was previously known about the regulation of lysine biosynthesis in C. albicans. The expression of the LYS2 gene in S. cerevisiae is regulated by general amino acid control due to amino acid starvation and also to a lesser extent by lysine (3arnes and Thorner 1986; Ford and Bliattacharjee 1995). The higher repression of LYS2 mRNA and AAR in cells grown in YEPD medium compared to that of cells grown in minimal medium supplemented with lysine along with the presence of GCN4 box in the upstream region of the LYS2 gene of C. albicans suggests that the AAR of C. albicans is under general amino acid control and is also regulated to some extent by lysine. The repression in enzyme activity observed in the case of C. albicans was intermediary to the relative repression in AAR activity seen in S. pombe and S. cerevisiae under similar conditions (Bhattacharjee 1995). Additionally, the experiments described here provide strong evidence that AAR of C. albicans is also feedback inhibited by the end product lysine, as seen in S. pombe and P. chrysogenum (Table 4) (Affenzeller et al. 1989; Ford and Bhattacharjee 1995). The 92% inhibition by lysine analog, thialysine, suggests involvement of a -SH group in the enzyme important in catalysis. 4 TABLE 4 Effect of growth medium AAR activitya Minimal medium 19.79 Minimal medium + lysine 11.87 YEPD medium 6.74 Inhibition by lysine and the lysine analog, thialysine Cell extract 19.76 Cell extract + 1 mM lysine 19.34 Cell extract + 10 mM lysine 9.68 Cell extract + 50 mM lysine 5.92 Cell extract + 1 mM thialysine 3.58 Cell extract + 10 mM thialysine 1.78 aAAR activity is reported as A460 h−1 mg protein−1. The results represent the average of three independent determinations
[0138] 4. Expression of LYS2 mRNA
[0139] To determine if the LYS2 gene expression is controlled at the transcriptional level by lysine and by other amino acids in rich medium, total RNA was extracted from C. albicans WT9517 grown in minimal medium, minimal medium supplemented with lysine, and in YEPD medium. The blot was quantitated using a beta scanner and the AMBIS Image analysis software. The results indicate that the LYS2 transcript is 4.25 kb. The level of LYS2 mRNA from cells grown in minimial medium supplemented with lysine was significantly lower compared to the level of LYS2 mRNA in cells grown in minimal medium. The LYS2 mRNA level in YEPD grown cells could not be detected. This suggests that transcription of LYS2 gene is repressed by lysine. The 18s rRNA was used as control for the amount of RNA loaded and transferred to the membrane (FIG. 5).
[0140] The information obtained from this study can now be utilized to design specific probes for detection of C. albicans. Preliminary studies using unique sequences of the LYS2 gene of C. albicans have already showed promising results in detection of Candida species in laboratory cultures and simulated blood and tissue samples (Bhattacherjee and BharLachaijee 1996). This study also provides the basis for site-directed mutagenesis studies to enable us to determine the residues important in the catalytic activity and subunit binding for design of a potential antifungal agents.
EXAMPLE 2 PCR Amplification of LYS2 Sequences[0141] The nucleotide sequences described above do not appear to have significant homologs in any human gene based on a Genebank search. Thus, these regions of the LYS2 genes are particularly useful as starting points for constructing hybridization probes for the detection of fungal pathogens, including but not limited to C. albicans, in a biological sample.
[0142] The nucleotide sequencing data was also used to determine the putative amino acid sequence of the LYS2 gene.
[0143] Due to the high degree of homology between the above referenced amino acid sequences, these sequences are the most preferred starting point for generating the probes and primers of the present invention. Due to the degeneracy of the genetic code, the degree of homology between fungi of amino acid sequences may be significantly higher than the homology of the nucleic acids that encode the amino acid sequences. Thus, in the present invention, the sequences of inventive probes and primers are generally defined in terms of amino acid sequences that they encode. In preferred embodiments, the probes and primers are defined in terms of specific sequences that have shown homology between fungal species.
[0144] Two oligonucleotides coding for these two conserved amino acid sequences of which genes were then synthesized as slightly degenerate PCR primers having the sequences set forth below (both are provided in the 5′ to 3′ orientation):
VB21 5′-TTAACAAAGAGAGATTGTTT-3′ (SEQ ID NO.:2)
VB22 5′-CTGAAACCTCTAATCTT-3′ (SEQ ID NO.: 3)
[0145] These primers were used to amplify a nucleic acid 526 base pairs in length from a sample of genomic DNA isolated from C. albicans. The genomic DNA was isolated from C. albicans by the methods described by Minuth and coworkers (W. Minuth et al., Current Genetics 5:227-231 (1982)).
[0146] Amplification was conducted essentially as described in IIPCR Protocols; a Guide to Methods and Applications” (eds. M. A. Innis, D. H. Gelfand, J. J. Sninsky and T. J. White (1990), Academic Press, Inc., New York) which is hereby incorporated by reference. Specific reaction conditions for this amplification were as follows: 50 picomoles of each primer and 10 ng of C. albicans genomic DNA were used. 1-5 units of Taq polymerase and corresponding 10× buffer was obtained from Boehringer Mannheim. A 1× solution of the Taq polymerase in buffer was made for a total volume of 100 gL. The PCR reactions were incubated in a DNA Thermal Cycler (Perkin Elmer Cetus, Emeryville, Calif.) with the following cycle parameters:
[0147] One cycle was completed as follows: 5 stage 1 melting temperature: 94° C., one minute annealing temperature: 37° C., one minute extension temperature: 72° C., two minutes
[0148] Thirty cycles were then completed using the following parameters: 6 stage 2 melting temperature: 94° C., thirty seconds annealing temperature: 55° C., thirty seconds extension temperature: 72° C., thirty seconds.
[0149] The fragment so amplified was sequenced using the finol DNA Cycle Sequencing System (Promega, Inc., Madison, Wis.). The sequence of this 526 base pair fragment is shown as SEQ ID. NO.: 6.
[0150] It is believed that this 526 base pair nucleic acid is derived from the C. albicans gene for AAR.
EXAMPLE 3 PCR Amplification of LYS2 Sequences from a Biological Sample[0151] A. Synthesis of Primers
[0152] PCR primers were synthesized on a PerSeptive Biosystems (Campbridgem, Mass.) 8909 Expedite (™) Nucleic Acids Synthesis System using the “DNA 0.2 &mgr;mol” program. The deoxynucleotides and HPLC-grade acetonitrile (the solvent used) were obtained from Perceptive Biosystems. The oligonucleotides were synthesized bound to 200 nmol size Controlled Pore Glass (CPG) columns. When the synthesis was complete, the contents of the column was decanted into a polypropylene screw-capped microcentrifuge tube. 1 ml of concentrated ammonium hydroxide (Fisher Scientific) was added and the mixture was incubated for a minimum of 10 hours at 55° C. to cleave the oligonucleotides from the glass bead matrix. The supernatant was decanted into a fresh tube and the ammonium hydroxide was removed by vacuum drying. The oligonucleotides were dissolved in 1 ml of sterile distilled water and the concentration was found by measuring the absorbance at 260 mn on a spectrophotometer.
[0153] B. Preparation of Biological Samples
[0154] As biological samples from patients were unavailable, biological samples containing known concentrations of C. albicans cells were prepared. Cultures of C. albicans were prepared and resuspended. Using a haemocytometer to determine cellular concentration, stock suspensions of C. albicans were prepared by serial dilution having the following cellular numbers in 0.1 ml of sterile water: 1×105, 1×104, 1×103, 1×102, 1×101, 1×100, and 0. 0.1 ml of each of the stock suspensions was then added to 0.1 ml of human blood obtained from a male volunteer which had been collected in EDTA (Fisher Scientific) as an anticoagulant.
[0155] C. Preparation of DNA for Amplification
[0156] The blood/Candida mixtures thus prepared were then mixed with 0.1 ml of lysis buffer (10 mM Tris.Cl, pH 8 (Fisher Scientific); 320 mM sucrose (Fisher Scientific); 5 mM MgCl2 (Fisher Scientific); 1% Triton X-100 (Fisher Scientific). The final compositions of the blood/Candida mixtures used in the present investigation are set forth below in Table 5. 7 TABLE 5 C. albicans # of C. albicans Lysis buff. No susp. (vol.) cells Blood vol. Vol. Total Vol. 1 0.1 ml 1 × 105 0.1 ml 0.1 ml 0.3 ml 2 ″ 1 × 104 ″ ″ ″ 3 ″ 1 × 103 ″ ″ ″ 4 ″ 1 × 102 ″ ″ ″ 5 ″ 1 × 101 ″ ″ ″ 6 ″ 1 × 100 ″ ″ ″ 7 0 ml 0 ″ ″ 0.2 ml
[0157] The mixtures were left at room temperature for 10 minutes before being spun in an Eppendorf microcentrifuge at 14,000 rpm for 5 minutes. The supernatant was aspirated and the pellet was resuspended in another 0.5 ml of the lysis buffer described above. This step was repeated; during the final wash in lysis buffer, 7 &mgr;l of 1 mg/ml Dnase 1 (Sigma, St. Louis, Mo.) was added. This suspension was incubated at 37° C. for 30 min. followed by incubation at 100° C. for 10 min. The tubes were immediately cooled on ice. This suspension was centrifuged again for 5 minutes, the supernatant removed by aspiration and the pellet was resuspended in 0.1 ml of a solution containing 10 mM Tris.Cl pH 8.0 Fisher Scientific; 30 mM EDTA (Fisher Scientific) and 0.5% SDS (Fisher Scientific). The suspension thus prepared was incubated at 100° C. in a dry block incubator for 15 minutes after which 0.1 ml of 2.5M potassium acetate was added. The suspension was incubated on ice for 30 minutes after which precipitated debris was removed by centrifugation for 10 minutes at 14,000 rpm. The supernatant was transferred by pipetting to a fresh tube and 0.2 ml of isopropanol was added. The DNA was precipitated at −20° C. for 20 minutes and then centrifuged at 14,000 rpm for 10 minutes. The supernatant was aspirated and the pelleted DNA was resuspended in 70% ethanol cnetrifuged at 14,000 rpm and the supernatant was removed by aspiration. The pelleted DNA was then vacuum dried and resuspended in 50 &mgr;L dH2O.
[0158] D. Primer Design
[0159] The Lys1 gene of was sequenced. The putative amino acid sequence of this gene was compared to that of the LYS2 gene of Saccharomyces cerevisiae which encodes the same protein. Areas of conservation (both at the nucleotide and amino acid levels) were used to select possible PCR primer sites. A pair of primers were designed from two such conserved regions, VB17 (which is identical in sequence to a sequence found in the sense strand of this gene) and VB18 (which is identical in sequence to a sequence found in the antisense strand of this gene). The sequence of these primers is set forth below:
VB17: TT(G/A)AC(G/A)AAACGTGATTGTCT
VB18: TTC(G/T)GAA(C/A)CCACGAATTTT
[0160] The corresponding DNA sequence from C. albicans was obtained (Suvarna, et al. 1998) and the primers were redesigned to be specific to C. albicans at these two sites. These two redesigned primers were named VB21 (SEQ ID NO.:2) and VB22 (SEQ ID NO.:3), and are shown below:
VB21: TTAACAAAGAGATTGTTT
VB22: CTGAAACCTCTAATCTT
[0161] E. Amplification
[0162] 3 &mgr;L aliquots of sample DNA prepared in part C above were used as templates in the PCR reactions described below. The primer reaction mixtures were prepared with the following concentrations of materials in a final reaction volume of 20 &mgr;L: dATP, dCTP, dGTP at 0.2 mM each, 50 pmol of each of the primers prepared as described in Example 2, 2.5 mM MgCl2 and 2.5 units of Taq DNA polymerase (Promega, Wis.) in the magnesium free buffer supplied by the manufacturer (500 mM potassium chloride, 100 mM Tris-HCl pH 9.0, 1% Triton X-100). The reaction cycling conditions that were used are as follows: 94° C. for one minute, 55° C. for 1 minute, 72° C. for 1 minute; 72° C. for 5 minutes to complete unfinished PCR products.
[0163] The volumes required of sterile water, buffer, magnesium chloride, nucleotides, PCR primers and Taq DNA polymerase were calculated for the number of reactions to be carried out. The following reagents were combined per 100 &mgr;l of PCR mix:
[0164] 10 &mgr;l 10×reaction buffer;
[0165] 10 &mgr;l 25 mM magnesium chloride;
[0166] 5 &mgr;l of forward PCR primer (100 ng/&mgr;l)
[0167] 5 &mgr;l of reverse PCR primer (100 ng/&mgr;l)
[0168] 1 &mgr;l 20 nM dNTPs;
[0169] 0.4 &mgr;l of 5 units/&mgr;l Taq DNA polymerase
[0170] dH2O to make 100 &mgr;l.
[0171] These were all combined in the above referenced order in one tube. This “master-mix” was then divided among the individual reaction tubes. Then the DNA templates were added to each tube, followed by enough mineral oil to cover the surface of the reaction mix. The PCRs were carried out using a Perkin Elmer DNA Thermal Cycler. The machine was programmed with three linked programs: (1) a denaturation program of 94° C. for 3 min.; (2) a program of 35 amplifications using 94° C. for 1 min, 55° C. for 1 min and 72° C. for 1 min; (3) a primer extension program of 72° C. for 5 min.
[0172] PCR was carried out on the biological samples as described above, on positive controls (3 &mgr;l of one of the biological sample templates added together with 10 ng of C. albicans genomic DNA) and on negative controls (samples prepared from biological tissue with no. C. albicans cells added and PCRs with no DNA template added) and on genomic DNA derived from E. coli, Bacillus megaterium, S. pombe, S. cerevisiae, mouse and human.
[0173] The completed PCRs were electrophoresed in 1% agarose gels containing ethidium bromide at 250 ng/ml in a running buffer of 40 mM Tris base, 2 mM EDTA, and 20 mM sodium acetate at a constant voltage of 100V. Amplification of the 526 base pair oligonucleotide was detected through ethidium bromide staining and visualization.
[0174] The VB17/VB18 primer pair was able to strongly amplify a product of approximately 500 base pairs from S. cerevisiae and S. pombe when used as amplification primers in PCR reactions (and electrophoresed) as described herein. A similar product was also amplified from C. albicans genomic DNA (FIG. 7).
[0175] These VB21/VB22 primers, when used in PCR procedures such as those described herein, will strongly amplify a 526 base pair oligonucleotide from DNA of C. albicans. The sequence of the amplified oligonucleotide is set forth in FIG. 6.
[0176] Amplifications were obtained only from the genomic DNA of C. albicans. The sequence of the amplified product was confirmed through enzymatic dideoxy sequencing (Promega's fmol DNA Cycle Sequencing System) to verify that this oligonucleotide corresponded to the nucleotide sequence of the C. albicans gene for the large subunit of the aminoadipate reductase gene. All of the genomic DNAs used had previously been tested for their competence as PCR templates by amplification with a pair of primers from a conserved ribosomal DNA target sequence.
[0177] F. Sensitivity of Primers VB21 And VB22 to C. albicans and Clinical Samples
[0178] 1. Sensitivity to C. albicans
[0179] The sensitivity of the primers VB21 and VB22 in amplifying the 526 base pair oligonucleotide identified was first investigated using genomic DNA extracted from C. albicans cells alone. DNA was extracted from 106 cells and suspended in 50 &mgr;L of distilled water. A set of PCRs minus DNA template were prepared. 5 &mgr;l from the DNA extraction was added to the first PCR (providing this reaction with 105 genome equivalents). This DNA template was serially diluted 1 in 10 and the prepared series of reaction tubes producing a range of diluted DNA templates from 105 to 10−3 genome equivalents. After PCR amplification, the minimum amount of DNA which could provide visible amplification was 100-101 genome equivalents. By this method, it was determined that C. albicans can be detected in a biological sample having a cellular concentration of C. albicans of 10-100 cells/ml.
[0180] 2. Sensitivity of Primers in Screens of Clinical Samples
[0181] The inventive primers were tested for their sensitivity in amplifying the 526 base pair oligonucleotide from a biological sample containing C. albicans as follows:
VB21 5′-TTAACAAAGAGATTGTTT-3′ (SEQ ID NO.:2)
VB22 5′-CTGAAACCTCTAATCTT-3′ (SEQ ID NO.: 3)
[0182] Suspensions of C. albicans were prepared having the following cellular numbers in 0.1 ml of sterile water: 1×105, 1×104, 1×103, 1×102, 1×101, 1×100, and 0. To each of these preparations, 100 &mgr;L of whole human blood (obtained from a male volunteer and collected in EDTA as an anticoagulant) or homogenized mouse kidney tissue in saline (prepared by homogenized the kidney of a freshly sacrificed mouse in 5 ml of sterile saline). DNA was extracted from these preparations and PCR conducted as described herein. A photograph of the electrophoretic gel (following ethidium bromide staining) corresponding to the PCRs conducted using spiked mouse kidney tissue as the biological sample is provided in FIG. 3.
[0183] Primers VB21 and VB22 were reproducibly able to amplify the 526 base pair oligonucleotide from biological samples having Candida concentrations of approximately 526 cells/ml.
[0184] In the both of the above described sensitivity determinations, strong bands were visible at the level of 100 cells/ml by ethidium bromide staining without any requirement for Southern transfer and hybridization to a radioactive probe.
[0185] 3. Specificity of Primers VB21 and VB22
[0186] The primer pair VB21/VB22 were used in conducting PCR on DNA obtained from the following fungal species: S. pombe, S. cerevisiae, Aspergillus flavus, A. fumigatus, Coccidioides immitis, Histoplasma capsulatum, Pneumocysitis carinii, Candida tropicalis, C. krusei and C. glabrata. Of these fungi, positive amplifications were obtained only from C. tropicalis and C. krusei.
EXAMPLE 4[0187] PCR Amplification of LYS2 Sequences from a Biological Sample
[0188] DNA isolated from a blood sample obtained from a patient suspected of harboring a Candida infection is subjected to PCR amplification. Appropriate primer pairs are selected from the following sequences for use in amplifying genetic material contained in the blood sample by means of the polymerase chain reaction:
VB21 5′-TTAACAAAGAGATTGTTT-3′ (SEQ ID NO.:2)
VB22 5′-CTGAAACCTCTAATCTT-3′ (SEQ ID NO.: 3)
[0189] The amplified nucleic acids are transferred to a nitrocellulose filter and bound there. Fluorescently labeled nucleic acid hybridization probes homologous to at least a portion of the amplified genetic fragments are then applied in a hybridization buffer and are allowed to incubate with the DNA-harboring filter for 24 hours.
[0190] The filter is washed and probe binding is detected through fluoroscopy. Statistically significant probe binding is indicative of the presence of fungus in the biological sample.
[0191] Alternatively, the procedure described above may be conducted using primers included in the following description:
[0192] The nucleotide sequence of each member of the primer pair is a nucleotide sequence selected from the group consisting of nucleic acid sequences that code for polypeptides that are (a) derived from AAR expressed by wild type C. albicans and (b) are conserved among fungi, wherein the nucleotide sequences are not homologous to and do not cross react with nucleotide sequences found in the human genome and homologues thereof.
EXAMPLE 5[0193] A throat swab is obtained from a patient suspected of harboring a Candida infection. DNA is isolated from the sample and applied as a dot blot to a nitrocellulose filter. The filter is then treated with a high concentration salt solution and heated to bind the DNA. The filter so treated is placed in a plastic bag with prehybridization buffer.
[0194] Hybridization buffer containing radiolabeled nucleic acid hybridization probes having a sequence comprising that illustrated in SEQ ID NO.: 7 is then applied to the filter. The nucleic acid hybridization probes are not homologous to and do not cross react with nucleotide sequences found in the human genome. Homologs of the sequences set forth above that will remain hybridized under relatively high stingency conditions may also be utilized.
[0195] The filter is incubated in the bag for approximately 24 hours. Such probes bind specifically to fungi and binding is indicative of the presence of fungal nucleic acids in the blood sample. The filter is then washed to remove unannealed probe and dried. The filter so treated is then subjected to autoradiography. Statistically significant probe binding indicates the presence of a fungal pathogen in the sample; appropriate therapeutic intervention is then planned.
EXAMPLE 6[0196] The procedure carried out in Example 5 is conducted in an identical fashion, with the exception that the sample utilized is a vaginal swab.
[0197] It should be understood that the foregoing disclosure emphasizes certain specific embodiments of the invention and that all modifications or alternative equivalent thereto are within the spirit or scope of the invention as set forth in the appended claims.
Claims
1. A nucleic acid hybridization probe comprising an isolated and purified nucleic acid having a nucleotide sequence selected from the group consisting of nucleotide sequences coding for a polypeptide fragment wherein the isolated and purified nucleic acid is not homologous to and does not cross react with mammalian genetic material and wherein the polypeptide fragment is (a) derived from the &agr;-aminoapidate reductase molecule expressed by C. albicans and (b) conserved in fungi.
2. A nucleic acid of claim 1 wherein the hybridization probe has a nucleotide sequence that either is identical to a sequence contained in the LYS 2 gene of C. albicans or cross hybridizes with a portion of the LYS 2 gene of C. albicans under conditions of high stringency.
3. A hybridization probe of claim 1 wherein the probe has the nucleotide sequence illustrated in SEQ ID NO.: 7.
4. A hybridization probe of claim 1 wherein the probe is a labeled probe.
5. A hybridization probe of claim 1 wherein the probe is labeled with a radioactive label, a fluorescent label or an antigenic label.
6. A method of screening a biological sample for the presence of a fungal pathogen, the method comprising the step of hybridizing a nucleic acid isolated from the biological sample with a hybridization probe of claim 1.
7. A method of screening a biological sample for the presence of a fungal pathogen, the method comprising the step of hybridizing a nucleic acid isolated from the biological sample with a hybridization probe of claim 2.
8. A method of screening a biological sample for the presence of a fungal pathogen, the method comprising the step of hybridizing a nucleic acid isolated from the biological sample with a hybridization probe of claim 3.
9. A method of screening a biological sample for the presence of a fungal pathogen comprising detecting hybridization of a nucleic acid hybridization probe wherein the hybridization probe
- (a) comprises an isolated and purified nucleic acid having a nucleotide sequence selected from the group consisting of nucleotide sequences coding for polypeptide fragments that are (i) derived from the &agr;-aminoapidate reductase molecule expressed by C. albicans and (ii) conserved in fungi; and
- (b) is not homologous to and does not cross react with mammalian genetic material.
10. The method of claim 9 wherein the method is performed by machine.
11. The method of claim 9 wherein the hybridization is carried out on a filter.
12. The method of claim 9 wherein the hybridization is carried out in solution.
13. The method of claim 9 wherein hybridization is detected by autoradiography.
14. The method of claim 9 wherein the nucleic acid is isolated from the biological sample prior to hybridization with the hybridization probe.
15. The method of claim 9 wherein the hybridization probe is applied directly to a biological sample.
16. The method of claim 9 wherein the hybridization probe has a nucleotide sequence that either is identical to a sequence contained in the LYS 2 gene of C. albicans or cross hybridizes with a portion of the LYS 2 gene of C. albicans under conditions of high stringency.
17. The method of claim 9 wherein the nucleotide sequence of the nucleic acid hybridization probe comprises the sequence illustrated in SEQ ID NO.:7.
18. A kit for detecting a fungal pathogen in a biological sample comprising a hybridization probe of claim 1.
19. A kit for detecting a fungal pathogen in a biological sample comprising a hybridization probe of claim 2.
20. A kit for detecting a fungal pathogen in a biological sample comprising a hybridization probe of claim 3.
21. A reagent for detecting the presence of a fungal pathogen in a biological sample comprising a hybridization probe of claim 1.
22. A reagent for detecting the presence of a fungal pathogen in a biological sample comprising a hybridization probe of claim 2.
23. A reagent for detecting the presence of a fungal pathogen in a biological sample comprising a hybridization probe of claim 3.
24. A pair of nucleic acid primers, each member of the pair having a nucleotide sequence selected from the group consisting of nucleotide sequences coding for a polypeptide fragments wherein the primer is not homologous to and does not cross react with mammalian genetic material and wherein the polypeptide fragment is (a) derived from the &agr;-aminoapidate reductase molecule expressed by C. albicans and (b) conserved in fungi.
25. A pair of nucleic acid primers, each member of the pair having a nucleotide sequence selected from the group consisting of nucleotide sequences that either are identical to a sequences contained in the LYS 2 gene of C. albicans or cross hybridize with a portion of the LYS 2 gene of C. albicans under conditions of high stringency.
26. A nucleic acid primer of claim 24 wherein the nucleotide sequence either (a) is identical to, or (b) cross-hybridizes with under conditions of high stringency, nucleotide sequence selected from the group consisting of VB21 (SEQ ID NO.:2) and VB22 (SEQ ID NO.: 3).
27. A method of screening a biological sample for the presence of a fungal pathogen comprising detecting hybridization of a hybridization probe to an amplified sample of genetic material, wherein the genetic material is amplified using nucleic acid primer pairs each member of the pair having a nucleotide sequence selected from the group consisting of nucleotide sequences coding for a polypeptide (a) derived from the &agr;-aminoapidate reductase molecule expressed by C. albicans and (b) conserved in fungi, wherein neither member of the primer pair is homologous to or cross reacts with mammalian nucleic acids.
29. The method of claim 27 wherein each member of the nucleic acid primer pairs has a nucleotide sequence that either is identical to a sequence contained in the LYS 2 gene of C. albicans or cross hybridizes with a portion of the LYS 2 gene of C. albicans under conditions of high stringency.
30. The method of claim 27 wherein each member of the nucleic acid primer pair has a nucleic acid sequence selected from the group consisting of VB21 (SEQ ID NO.:2) and VB22 (SEQ ID NO.: 3).
31. The method of claim 27 wherein the hybridization is conducted on a filter.
32. The method of claim 27 wherein the hybridization is conducted in solution.
33. The method of claim 27 wherein hybridization is detected by autoradiography.
34. The method of claim 27 wherein the method is performed by machine.
35. A reagent for detecting the presence of a fungal pathogen in a biological sample comprising a nucleic acid primer of claim 24.
36. A reagent for detecting the presence of a fungal pathogen in a biological sample comprising a nucleic acid primer of claim 25.
37. A reagent for detecting the presence of a fungal pathogen in a biological sample comprising a nucleic acid primer of claim 26.
38. A kit for detecting the presence of a fungal pathogen in a biological sample comprising a nucleic acid primer of claim 24.
39. A kit for detecting the presence of a fungal pathogen in a biological sample comprising a nucleic acid primer of claim 25.
40. A kit for detecting the presence of a fungal pathogen in a biological sample comprising a nucleic acid primer of claim 26.
41. An antibody capable of binding to an epitope of &agr;-aminoapidate reductase expressed by wild type C. albicans.
42. An antibody of claim 41 wherein said epitope comprises the amino acid sequence LTKRDCLKIRGFT or a fragment thereof.
43. An antibody of claim 41 wherein the antibody is labeled.
44. An antibody of claim 43 wherein the antibody label is selected from the group consisting of a radioactive isotope, a fluorescent compound or an enzyme.
45. A method of screening a biological sample for the presence of a fungal pathogen, the method comprising detecting antibody binding to a biological sample, wherein the antibody binds selectively to &agr;-aminoapidate reductase expressed by wild type C. albicans.
46. The method of claim 45 wherein the method is an enzyme linked immunosorbent assay.
47. The method of claim 45 wherein the method is carried out by machine.
48. A kit for detecting a fungal pathogen in a biological sample wherein the kit comprises an antibody of claim 41.
49. A reagent comprising an antibody of claim 41.
50. An epitope comprising a polypeptide having an amino acid sequence homologous to the amino acid sequence LTKRDCLKIRGFT or fragment thereof.
51. A method of using the antibody of claim 41 comprising using the antibody to detect the presence of a fungal epitope in a biological sample wherein the antibody is used to immunoprecipitate the fungal epitope.
52. The method of claim 45 wherein the method is a radioimmunoassay.
53. The method of claim 45 wherein the method is an sandwich binding assay.
54. A reagent comprising the epitope of claim 50.
55. The epitope of claim 50 wherein the epitope is labeled.
56. A method of using the antibody of claim 41 wherein the antibody is used im a radioimmunoassay.
57. A method of using the epitope of claim 50 wherein the method comprises a radioimmunoassay.
58. A method of using the hybridization probe of claim 1, wherein the probe is used to identify restriction fragment length polymorphisms in nucleic acid isolated from a biological sample and digested.
Type: Application
Filed: Nov 27, 2001
Publication Date: Feb 27, 2003
Applicant: Miami University
Inventors: Jnanendra K. Bhattacharjee (Oxford, OH), Kalavati Suvarna (West Haven, CT), Vasker Bhattacherjee (Louisville, KY)
Application Number: 09994595
International Classification: C12Q001/68; C07H021/04;
