Identification and characterization of a phase-specific, nuclear DNA binding protein from the dimorphic pathogenic fungus Histoplasma capsulatum.

Genes expressed in the parasitic yeast (Y) phase of the dimorphic fungal pathogen Histoplasma capsulatum which are transcriptionally silent in the mycelial (M) phase have recently been cloned and analyzed. To understand the molecular regulation of genes involved in the transition to and maintenance of the Y phase, the presumptive 5' regulatory regions of two Y phase-specific genes (yps-3 and yps 21:E-9) were PCR amplified as labelled probes to identify nuclear DNA binding proteins which may influence phase-specific gene transcription. Protein-DNA interactions were assessed by Southwestern blot analysis in which sodium dodecyl sulfate-polyacrylamide gel electrophoresis-separated protein extracts from Y and M phases of the virulent G217B strain of H. capsulatum were visualized by their capability for in situ binding to the labelled 517-bp (G217B yps-3) or the 395-bp (G217B yps 21:E-9) putative 5' regulatory regions. A 30-kDa nuclear protein unique to the M-phase extracts of the highly virulent G217B strain, but absent in the Y phase of the same organism, was identified. In contrast, the low-virulence, thermal-sensitive Downs strain of H. capsulatum lacked detectable p30 binding activity in either yeast- or mycelial phase extracts, regardless of the source of labelled probe (395-bp G217B yps 21:E-9 probe or 512-bp HindIII-EcoRI-labelled Downs yps21:E-9). A decanucleotide motif, TCCTTTTTTT, was identified in the upstream regulatory regions of these yps genes, as well as in the putative alpha-tubulin promoter, and was conserved with 70 to 100% homology. This recognition sequence was sufficient for p30M binding with 32P-labelled ligated oligonucleotides when used in the Southwestern assay. These findings describe the first nuclear DNA binding factor identified in H. capsulatum which binds to target sequences in a phase-specific manner, suggesting that p30M may govern aspects of gene transcription in this pathogenic fungus, in which a temperature-sensitive switch influences morphology and virulence.

Molecular epidemiology of mucosal candidiasis in HIV-positive women.

Mucosal candidiasis is a common complication of HIV infection and HIV-positive women may develop both oropharyngeal and vaginal disease. Colonization with Candida albicans and related species at either site is a common preceding event in asymptomatic women. To examine the molecular epidemiology of colonizing yeast strains in HIV-positive women, concurrent oropharyngeal and vaginal cultures were obtained from 32 women (mean CD4 count 392 cells/mm3, range 0-1319). Positive oropharyngeal cultures were obtained in 18 (56%) and positive vaginal cultures in 10 (31%). Candida species were isolated from both sites simultaneously in nine (28%) women. All strains were evaluated for restriction fragment length polymorphisms (RFLPs) at the ribosomal DNA locus (using a heterologous 8.4-kb NotI probe from H. capsulatum) and with a C. albicans-specific repetitive DNA probe. Isolates were grouped into three classes by the NotI probe and then members of each class were evaluated with the C. albicans-specific probe. Isolates were subsequently evaluated by random amplified polymorphic DNA (RAPD) PCR with four arbitrary primers to detect strain-specific differences. All isolates tested were unique and could be discriminated by RFLP or RAPD PCR. Vaginal and oropharyngeal isolates from the same individual in all nine cases were dissimilar, suggesting that the dominant strain of Candida colonizing different body sites is different. These findings suggest that the epidemiology of Candida infection in HIV disease is complex, that the development of oropharyngeal and vaginal disease may be disassociated, and that HIV-positive patients are each infected by their own unique strains of Candida.

Localization of a yeast-phase-specific gene product to the cell wall in Histoplasma capsulatum.

A yeast-phase-specific gene, yps-3, has been identified in the virulent Histoplasma capsulatum strain, G217B. Although DNA sequencing of the genomic yps-3 gene from G217B failed to detect homologies with known proteins, the 5' end of a yps-3 cDNA contained a consensus signal sequence. A 519-bp fragment of the cDNA containing the translational stop codon was linker modified and inserted into the bacterial expression vector, pATH 1. Escherichia coli extracts containing the pATH 1 vector alone expressed a major 34-kDa TrpE polypeptide following induction with indoleacrylic acid, while the pATH 1/yps-3 construct produced a predominant 54-kDa TrpE/yps-3 fusion protein. Polyclonal rabbit sera directed against G217B reacted exclusively with the 54-kDa fusion protein in Western blots (immunoblots); serum samples from three patients with acute pulmonary or disseminated histoplasmosis were also positive. To localize the yps-3 protein within G217B, a monoclonal antibody (MAb 7.1) which recognized the yps-3 portion of the fusion protein was generated. A 17.4-kDa protein was detected with MAb 7.1 in Western blots prepared from cell wall fractions of G217B; cytoplasmic fractions were unreactive. No yps-3 antigen was detected in either fraction of the Downs strain, which fails to express the yps-3 gene. MAb 7.1 also detected a 17.4-kDa antigen in ethanol-precipitated culture supernatants derived from G217B. These findings localize the yps-3 gene product to the cell wall and culture supernatants, where the protein may influence the phase transition or the maintenance of the yeast state.

Genetic diversity in clinical isolates of the dimorphic fungus Blastomyces dermatitidis detected by a PCR-based random amplified polymorphic DNA assay.

Blastomyces dermatitidis is a dimorphic fungus causing localized or systemic infection in areas where the organism is endemic in the central and southeastern United States. In this study, 19 independent isolates of B. dermatitidis from Little Rock, Ark., were grouped into three classes based on restriction fragment length polymorphism patterns in mitochondrial DNA with a heterologous probe from Histoplasma capsulatum. One large class of 15 isolates and two smaller classes (classes 2 and 3), each consisting of two isolates, were observed in BglII digests. Strain-specific arrays of PCR-amplified DNA products were obtained with arbitrarily selected primers (18 to 29 nucleotides long; G+C contents, 33 to 56%). In the large class 1 group, 13 isolates could be differentiated by the random amplified polymorphic DNA (RAPD) method with various primers. The two remaining class 1 isolates were obtained from the same patients and produced identical RAPD arrays. Dissimilar RAPD patterns were obtained from the smaller class 2 group but not from the class 3 isolates. Significant genetic diversity in clinical isolates of B. dermatitidis was observed; this may underscore a similar environmental diversification. Further application of the typing techniques may provide significant insight into the epidemiology of blastomycosis and aid in the assessment of specific virulence phenotypes.

Molecular cloning and sequence analysis of yps-3, a yeast-phase-specific gene in the dimorphic fungal pathogen Histoplasma capsulatum.

Genes specifically expressed in the parasitic yeast phase of Histoplasma capsulatum have been cloned to clarify the mechanisms underlying both pathogenesis and morphogenesis in this human dimorphic fungal pathogen. Previous studies have determined that the yeast-phase-specific gene, yps-3, is expressed differentially in two non-isogenic strains which differ in their thermotolerance and virulence. We have cloned the yps-3 homologues from the high virulence (G217B) and low virulence (Downs) strains, and obtained a partial cDNA clone representing the expressed gene from H. capsulatum G217B. The Downs clone harbours a 287 bp insertion sequence that disrupts a long ORF defined by the yps-3 G217B cDNA. Although the insertion sequence contains features reminiscent of mobile genetic elements, including 15 bp direct repeats of flanking sequence, it is not randomly distributed in the H. capsulatum genome. S1 nuclease analysis was utilized to map the 5' end of the expressed yps-3 gene in G217B to potential regulatory regions which are largely homologous in both strains. This finding may point to a deficiency in a temperature inducible regulatory protein in the low virulence, temperature-sensitive Downs strain. The nucleotide sequence of the yps-3 gene and the predicted amino acid sequence of its product represents the first report of phase-specific gene and protein sequences in this widely distributed fungal pathogen. Further analysis of the product encoded by the yps-3 gene may provide significant insight into the pathogenic repertoire of H. capsulatum.

Molecular epidemiology of recurrent oral candidiasis in human immunodeficiency virus-positive patients: evidence for two patterns of recurrence.

The causative strains in 22 patients with recurrent oral candidiasis were examined using two DNA probes (a Histoplasma capsulatum DNA probe that cross-hybridizes with Candida albicans and a C. albicans strain-specific probe derived from repetitive sequence DNA). C. albicans was the causative organism in all 22 initial episodes of infection and was also obtained from 17 patients with recurrent oral disease. Molecular analysis showed that in 11 cases, the same isolate was identified in each episode. Six patients had a clearly different isolate of C. albicans causing a later episode of candidiasis. Five patients had different Candida species causing recurrent disease: 4, Torulopsis glabrata; 1, Candida parapsilosis. Patients with a new isolate (either new species or a new C. albicans strain) were more immunosuppressed and were significantly more likely (P < .001) than patients with the same recurrent strain to have received suppressive azole antifungal agents. These data indicate that the epidemiology of recurrent candidiasis in individual patients seropositive for the human immunodeficiency virus is complex and that both failure of eradication of Candida from the oral cavity and new infection occur.

Diversity among clinical isolates of Histoplasma capsulatum detected by polymerase chain reaction with arbitrary primers.

Clinical isolates of the fungal respiratory and systemic pathogen Histoplasma capsulatum have been placed in several different classes by using genomic restriction fragment length polymorphisms (RFLPs), but in general have not been distinguished further. We report here that a polymerase chain reaction (PCR)-based DNA fingerprinting method that has been termed arbitrary primer or random amplified polymorphic DNA (RAPD) PCR can distinguish among isolates in a single RFLP class. In this method, arbitrarily chosen oligonucleotides are used to prime DNA synthesis from genomic sites that they fortuitously match, or almost match, to generate strain-specific arrays of DNA fragments. Each of 29 isolates of RFLP class 2, the group endemic in the American Midwest, was distinguished by using just three arbitrary primers. In contrast, laboratory-derived S and E colony morphology variants of two strains were not distinguished from their R parents by using 18 such primers. Thus, the clinical isolates of H. capsulatum are quite diverse, but their genomes remain stable during laboratory culture. These outcomes suggest new possibilities for epidemiological analysis and studies of fungal populations in infected hosts.

Typing of Histoplasma capsulatum by restriction fragment length polymorphisms in a nuclear gene.

We previously described yps-3, a Histoplasma-specific nuclear gene probe useful in the identification of Histoplasma capsulatum. By using restriction fragment length polymorphisms (RFLPs) of DNA detected by the yps-3 gene and mitochondrial DNA, 76 clinical and soil isolates of H. capsulatum were classified. The majority of North American isolates obtained from endemic regions of the midwestern United States were members of the previously characterized class 2, although four clinical isolates from different patients with AIDS from that region were grouped in class 1 with the temperature-sensitive Downs strain. A Florida soil isolate (FLS1) was placed in class 4 on the basis of RFLP with both probes. Two American Type Culture Collection strains (G184B and G186B) from Panama were grouped into class 3 by this analysis. A group of five H. capsulatum isolates obtained from patients with AIDS in New York City were typed into a new class 5 on the basis of yps-3 polymorphisms; those organisms fell into two broad mitochondrial DNA patterns, designated 5b and 5c. Two new isolates from Panama were also members of this broad yps-3 class 5 group, but they exhibited a distinct mitochondrial DNA profile (class 5a). A sixth class was detected in DNA obtained from a patient with AIDS from Panama; that DNA had unique RFLP profiles with respect to both probes. These observations suggest that the Histoplasma-specific yps-3 gene probe is a sensitive tool for typing H. capsulatum in clinical specimens. Additionally, these studies provide molecular support for the hypothesis that AIDS-associated histoplasmosis in nonendemic areas is due to reactivation of a previously acquired infection.

Molecular typing of candida albicans isolated from oral lesions of HIV-infected individuals.

OBJECTIVE: To evaluate the epidemiology of Candida albicans infection in HIV-infected patients with oral lesions using molecular techniques. METHODS: Thirty-nine isolates from HIV-positive patients with oral candidiasis were examined using two DNA probes (a Histoplasma capsulatum ribosomal DNA probe that cross-hybridizes with C. albicans and a C. albicans strain-specific probe derived from repetitive sequence DNA). C. albicans obtained from the oral cavity of patients receiving cytotoxic chemotherapy was used as controls. RESULTS: Using the H. capsulatum ribosomal DNA probe, isolates were shown to members of many distinct classes of C. albicans. Forty-nine per cent (19 out of 39) of isolates were members of the same class; however, 46% (6 out of 13) of control C. albicans isolates were also members of this class. Further analysis of the class-restricted isolates from the HIV-infected patients using the C. albicans strain-specific probe showed that these could be further separated into distinct strains. CONCLUSIONS: These data indicate that strains of C. albicans that cause oral candidiasis in HIV-positive individuals are not clonally restricted and are similar to those colonizing the oral cavity of other severely immunocompromised hosts. Most patients appear to be infected with unique strains of C. albicans.

Two cases of blastomycosis from a common source: use of DNA restriction analysis to identify strains.

Two friends, one with AIDS, developed severe pulmonary blastomycosis but differed markedly in clinical course. The human immunodeficiency virus-negative patient responded completely to ketoconazole; the patient with AIDS died of progressive disseminated infection despite treatment with fluconazole and amphotericin B. Epidemiologic investigation suggested a common source of infection, but serologic evaluation and environmental cultures were unrevealing. EcoRI digestion of the Blastomyces dermatitidis isolates showed identical restriction fragment patterns that differed from patterns obtained from other clinical isolates. Analysis using a Histoplasma capsulatum ribosomal DNA probe that cross-hybridizes with B. dermatitidis showed that the isolates from the two patients were identical and different from others. Thus, the patients were probably infected with the same strain, possibly from a common source. These data indicate the critical role of cellular immunity in patients with blastomycosis, show that there are multiple genotypes of B. dermatitidis, and suggest that DNA restriction analysis is a useful epidemiologic tool.

Temperature-sensitive variants of Histoplasma capsulatum isolated from patients with acquired immunodeficiency syndrome.

Histoplasma capsulatum isolates from three St. Louis area AIDS patients with disseminated histoplasmosis were found to be closely related to the temperature-sensitive, previously unique, Downs strain based on growth phenotype and restriction fragment length polymorphisms (RFLP) involving mitochondrial DNA, ribosomal DNA, and the yps-3 gene. H. capsulatum isolates from five non-AIDS patients in the St. Louis area with disseminated histoplasmosis or chronic pulmonary histoplasmosis had the growth phenotype and RFLP pattern characteristic of most strains isolated from other regions of the USA.

DNA probe for the identification of Histoplasma capsulatum.

A 1.85-kilobase HindIII nuclear DNA probe from Histoplasma capsulatum G217B detected polymorphic restriction fragments within whole-cell DNA from different clinical isolates of H. capsulatum, consistent with the previous system of classification. The probe failed to hybridize to DNA from Blastomyces dermatitidis, Candida spp., Saccharomyces cerevisiae, Sepedonium chrysospermum, and Chrysosporium keratinophilum under low-stringency conditions and therefore may have value as a diagnostic reagent to identify H. capsulatum.

Characterization of alpha and beta tubulin genes in the dimorphic fungus Histoplasma capsulatum.

Evidence from our laboratory indicates that microtubules are involved in the differentiation of the dimorphic, pathogenic fungus Histoplasma capsulatum; therefore, we cloned the tubulin genes from a virulent strain of the organism. We report that the H. capsulatum genome contains a single alpha (TUB1) and a single beta (TUB2) tubulin gene rather than the more typical multigene family which is common in even the simplest eukaryotes. Sequence data from these genes reveal a high degree of nucleotide and protein sequence conservation relative to tubulins from other species. The coding regions of TUB1 and TUB2 contain five and eight intervening sequences, respectively. Field inversion gel electrophoresis of H. capsulatum chromosome-sized DNA fragments indicates that the TUB1 and TUB2 genes are unlinked. Potential regulatory elements common to both genes have been identified in the 5' promoter regions. These elements may direct the coordinate expression of TUB1 and TUB2 during differentiation. The cloning and characterization of alpha and beta tubulin genes from H. capsulatum provides the first description of gene structure in this widely distributed pathogenic fungus. Isolation of the tubulin genes will facilitate future studies of tubulin gene expression during the dimorphic phase transitions and clarify the role of microtubules in the differentiation process.

Variable expression of a yeast-phase-specific gene in Histoplasma capsulatum strains differing in thermotolerance and virulence.

By means of differential hybridization techniques, several yeast-phase-specific DNA sequences were identified in the dimorphic pathogenic fungus Histoplasma capsulatum. A 1.85-kilobase (kb) HindIII fragment from one genomic clone, yps-3, hybridized to at least three distinct yeast poly(A)+ RNAs of 1.3, 1.05, and 0.95 kb from the virulent strain G217B. These mRNAs were not detected in mycelia. When mycelia from G217B were induced to become yeast by transfer from 25 to 37 degrees C, a process requiring approximately 9 days, expression of yps-3 was detected within 24 h, although not in the initial 2 h following the temperature shift. In contrast, a low-virulence strain (Downs) which completes the transition in approximately 2 weeks failed to express the yps-3 gene during phase transitions. A third isolate, G186B, intermediate in its virulence properties and in the time required for the transition (11 days), expressed a single 1.25-kb mRNA but only at low levels in the yeast phase and only after 3 days following the 25-to-37 degrees C temperature shift. Although yps-3 expression does not appear to be essential for the transformation to the yeast phase, it may facilitate the early adaptive processes which permit the mycelium-to-yeast transition and survival of the yeast phase of H. capsulatum at elevated host temperatures. The phase-specific yps-3 nuclear gene is carried on highly polymorphic restriction fragments in all three strains, suggesting that this probe may provide a sensitive diagnostic tool for the classification of H. capsulatum isolates.

Expression of alpha- and beta-tubulin genes during dimorphic-phase transitions of Histoplasma capsulatum.

Recent investigations have confirmed the presence of one alpha-tubulin gene (TUB1) and one beta-tubulin gene (TUB2) in the dimorphic fungus Histoplasma capsulatum. In the present study, Northern blot (RNA blot) analyses revealed multiple alpha-tubulin transcripts and a single beta-tubulin transcript in the yeast and mycelial phases of the high-virulence 217B strain and low-virulence Downs strain. S1 nuclease protection assays demonstrated one initiation start site and two major stop sites for the TUB1 transcripts, suggesting that variations in 3' processing generate the alpha-tubulin messages of 2.5 and 2.0 kilobases. Dot blot hybridization experiments indicated that tubulin gene expression is developmentally regulated during the dimorphic phase transitions. alpha- and beta-tubulin mRNAs increased six- to eightfold during the yeast-to-mycelium conversion and decreased two- to threefold during the reverse transition. These changes in tubulin mRNA content coincided with major morphological events associated with H. capsulatum development. Western blots (immunoblots) of H. capsulatum yeast-specific proteins resolved by two-dimensional gel electrophoresis demonstrated a single alpha- and a single beta-tubulin isoform. Multiple tubulin polypeptides expressed in mycelia are probably products of posttranslational modifications.

A mouse c-myc retrovirus transforms established fibroblast lines in vitro and induces monocyte-macrophage tumors in vivo.

Activation of the c-myc proto-oncogene, in the form of DNA rearrangements that lead to constitutive expression, has been implicated in the genesis of a wide range of tumors. Therefore, it is of great interest to determine the influence of c-myc oncogene activation on cellular growth control, especially in primary cells. To facilitate the efficient transfer of an activated c-myc oncogene, we developed a mouse retrovirus that contains the c-myc protein-coding sequences and which can be transmitted in the presence of a Moloney murine leukemia virus helper or established as a helper-free stock with a retrovirus-packaging cell line. The virus can transform established lines of mouse fibroblasts to anchorage-independent growth; the transformed cells are tumorigenic in nude mice. However, the virus was not capable of inducing foci of transformed cells on confluent monolayers. In addition to studies on established cell lines, the effect of the c-myc retrovirus on primary cells was examined. Infection of bone marrow cells gave rise to partially transformed mononuclear phagocytes which were entirely dependent upon an exogenous supply of the monocyte-specific colony-stimulating factor CSF-1 for proliferation. Infection in vivo induced monocyte-macrophage tumors with a latency period of 8 to 10 weeks.

Fibroblast lines expressing activated c-myc oncogenes are tumorigenic in nude mice and syngeneic animals.

The influence of c-myc expression on fibroblast growth and morphology was investigated by transfection of c-myc genes linked to viral promoters. No foci were observed after transfection of either NIH/3T3 or Rat 2 cells. Cell lines containing activated c-myc genes were established using SV2-neo coselection and several growth parameters of the cells were studied. The cells showed a slight increase in refractility and formed colonies in soft agar with an efficiency of only 1%-2%. The c-myc-transfected cells grew well in 0.5% serum while the controls did not. The major difference in cell growth noted was that c-myc-transfected cells were tumorigenic when inoculated into nude mice or syngeneic rats. Analysis of RNA from the tumorigenic cells showed a level of c-myc expression from the transfected genes that was 2 to 6 fold higher than that from the endogenous gene. The level of c-myc RNA in the fibroblast tumors was similar to that found in mouse plasmacytomas. Expression of the endogenous c-myc gene was unaffected by the transfected genes for subconfluent cells in culture, but the gene was shut off in the nude mouse tumors. These results demonstrate that constitutive c-myc expression leads to tumorigenicity in immortalized cell lines.

Transcriptional activation of the translocated c-myc oncogene in mouse plasmacytomas: similar RNA levels in tumor and proliferating normal cells.

We examine the influence of the immunoglobulin locus on the expression of the translocated c-myc oncogene in mouse plasmacytomas. The level of c-myc RNA was 30- 35-fold greater in tumor cells than in normal, quiescent B cells. Mitogen stimulation of the lymphocytes with lipopolysaccharide induced a 15-fold increase in c-myc expression per cell to a level that was similar to that in the transcription of the translocated c-myc gene involved initiation from sequences in the first c-myc intron. Abundant RNA transcripts were also found from the noncoding strand of the c-myc intron in most tumor lines. S1 nuclease mapping was used to locate the intronic sequences that are used to initiate the tumor-specific c-myc RNAs. Six different initiation sites within the intron were mapped, none of which have the TATA sequence usually associated with eucaryotic RNA polymerase II promoters. The noncoding strand transcripts were also found to initiate in the c-myc intron. Transcription of the c-myc coding strand was independent of the position of the translocation breakpoint, even when the heavy chain switch and constant regions were deleted.

Novel myc oncogene RNA from abortive immunoglobulin-gene recombination in mouse plasmacytomas.

We have found that the myc oncogene has been modified by abortive recombination with the alpha heavy-chain immunoglobulin constant-region (C alpha) gene in five different mouse plasmacytoma lines. Recombination occurred approximately 0.8-2.0 kb to the 5' side of two distinct coding regions, defined by sequence homology between the chicken cellular and plasmacytoma myc genes. The myc and C alpha genes were always in opposite transcriptional orientation, with the recombination site within the C alpha switch region sequences. DNA recombination was found to correlate with the production of a novel 2.1 kb species of myc RNA that was 0.4 kb shorter than the normal cellular transcript. No elevated levels of myc RNA were evident, suggesting that DNA rearrangements have altered the myc oncogene product. This oncogene activation corresponds to the chromosomal translocations found in nearly all plasmacytomas.