Isolation and identification of six Pneumocystis carinii genes utilizing codon bias

Molecular characterization of recombinant Pneumocystis carinii topoisomerase I: differential interactions with human topoisomerase I poisons and pentamidine

The Pneumocystis carinii topoisomerase I-encoding gene has been cloned and sequenced, and the expressed enzyme interactions with several classes of topoisomerase I poisons have been characterized. The P. carinii topoisomerase I protein contains 763 amino acids and has a molecular mass of ca. 90 kDa. The expressed enzyme relaxes supercoiled DNA to completion and has no Mg2+ requirement. Cleavage assays reveal that both the human and P. carinii enzymes form covalent complexes in the presence of camptothecin, Hoechst 33342, and the terbenzimidazole QS-II-48. As with the human enzyme, no cleavage is stimulated in the presence of 4',6'-diamidino-2-phenylindole (DAPI) or berenil. A yeast cytotoxicity assay shows that P. carinii topoisomerase I is also a cytotoxic target for the mixed intercalative plus minor-groove binding drug nogalamycin. In contrast to the human enzyme, P. carinii topoisomerase I is resistant to both nitidine and potent protoberberine human topoisomerase I poisons. The differences in the sensitivities of P. carinii and human topoisomerase I to various topoisomerase I poisons support the use of the fungal enzyme as a molecular target for drug development. Additionally, we have characterized the interaction of pentamidine with P. carinii topoisomerase I. We show, by catalytic inhibition, cleavage, and yeast cytotoxicity assays, that pentamidine does not target topoisomerase I.

Cell wall assembly by Pneumocystis carinii. Evidence for a unique gsc-1 subunit mediating beta -1,3-glucan deposition

Pneumocystis carinii remains a persistent cause of severe pneumonia in immune compromised patients. Recent studies indicate that P. carinii is a fungal species possessing a glucan-rich cyst wall. Pneumocandin antagonists of beta-1,3-glucan synthesis rapidly suppress infection in animal models of P. carinii pneumonia. We, therefore, sought to define the molecular mechanisms of beta-glucan cell wall assembly by P. carinii. Membrane extracts derived from freshly purified P. carinii incorporate uridine 5'-diphosphoglucose into insoluble carbohydrate, in a manner that was completely inhibited by the pneumocandin L733-560, an antagonist of Gsc-1-type beta-glucan synthetases. Using degenerative polymerase chain reaction and library screening, the P. carinii Gsc-1 catalytic subunit of beta-1,3-glucan synthetase was cloned and characterized. P. carinii gsc1 exhibited homology to phylogenetically related fungal beta-1,3-glucan synthetases, encoding a predicted 214-kDa integral membrane protein with 12 transmembrane domain structure. Immunoprecipitation of P. carinii extracts, with a synthetic peptide anti-Gsc-1 antibody, specifically yielded a protein of 219.4 kDa, which was also capable of incorporating 5'-diphosphoglucose into insoluble glucan carbohydrate. As opposed to other fungi, the expression of gsc-1 mRNA is uniquely regulated over P. carinii's life cycle, having minimal expression in trophic forms, but substantial expression in the thick-walled cystic form of the organism. These results indicate that P. carinii contains a unique catalytic subunit of beta-1,3-glucan synthetase utilized in cyst wall formation. Because synthesis of beta-1,3-glucan is absent in mammalian cells, inhibition of the P. carinii Gsc-1 represents an attractive molecular target for therapeutic exploitation.

The HSP70 gene family in Pneumocystis carinii: molecular and phylogenetic characterization of cytoplasmic members

Pneumocystis carinii, a major opportunistic lung pathogen of AIDS patients, is found in a number of mammals and is proposed to be a member of the fungi. In this work, several members of the highly conserved HSP70 multigene family were characterized from rat-derived P. carinii. Previously, we reported characterization of the ER resident HSP70 homolog known as BiP from prototype (P.c. carinii) and variant (P. c. rattus) strains of the organism. We report here, from P. c. carinii, characterization of Pcsa1, an HSP70 homolog that encodes a cognate/stress-induced HSP70 homolog of the SSA subfamily in Saccharomyces cerevisiae. We also identify, from both rat strains and from a human isolate of P. carinii (P.c. hominis), a third set of HSP70 homologs that apparently encode a ribosome-associated cytoplasmic HSP70 homologous to the S. cerevisiae SSB subfamily. Our data indicate that Pcsal mRNA, like Pcbip mRNA, bears an intron in the 5' untranslated region, is induced by heat shock, and suggest that this gene undergoes alternative transcription and splicing. The SSB homologs display significant sequence heterogeneity between P. carinii source strains, supporting the genetic divergence and likely speciation of P. carinii isolates within and between host species. Phylogenetic analysis with the PcSA1 protein supports inclusion of P. carinii among the higher fungi.

The genome of Pneumocystis carinii

The best understood special form of P. carinii, P. carinii formae specialis (f.sp.) carinii, appears to be haploid and contains about 8 million base pairs of DNA (8.5 fg) per nucleus. The genome of P. carinii f.sp. carinii is divided into 13-15 linear chromosomes that range from 300 to 700 kb in size. Eight different P. carinii f.sp. carinii karyotypes have been observed. The karyotypes of P. carinii f.sp. carinii differ due to slight variations in the lengths of chromosomes, but the 8 karyotype-forms of P. carinii f.sp. carinii exhibit very little variation in DNA sequence. By contrast, the genome of P. carinii f.sp. carinii differs markedly in sequence from the genomes of P. carinii from other hosts, such as mouse, ferret and human. In addition, chromosomes and DNA sequences from P. carinii from mouse, ferret, and human also differ greatly from each other. The genome of a ferret P. carinii appears to be up to 1.7 times larger than those of P. carinii from other hosts. Nearly two dozen P. carinii genes have been cloned and sequenced. The typical P. carinii gene sequence is 60-65% A+T. P. carinii genes usually contain introns, which are typically less than 50 bp in length, but can be as numerous as 9 per gene. A system for naming P. carinii genes is proposed in which each gene would be designated by an italic three-letter lower case symbol. The first allele (i.e. sequence) that is found would have a superscript 1, such as xyz1(1). Any subsequent alleles would be designated as xyz1(2), etc. A protein would have the same symbol as the gene that produced it, but written in roman print with the first letter an uppercase, such as Msg1. Some of the P. carinii genome is comprised of DNA sequences that are present dozens of times. Three families of such repeated DNA sequences have been described. Two of these families (MSG and PRT) encode proteins. The third family is the telomere repeat, which is found at the ends of each chromosome, and sometimes at internal chromosomal sites, in which case it has been called the alpha repeat. Determination of the complete sequence of the P. carinii genome is both practicable and of primary importance to the understanding of this organism. The small size of the P. carinii genome and its packaging into chromosomes that are resolvable by PFGE will facilitate sequence analysis.

Molecular cloning and characterization of a superoxide dismutase (sod) gene in Pneumocystis carinii

This work reports the isolation and characterization of a gene encoding a superoxide dismutase (SOD, EC.1.15.1.1.) from Pneumocystis carinii derived from rat. Sense and antisense oligonucleotides, deduced from SOD amino acid sequences from a wide variety of organisms, allowed amplification of a 669 bp genomic DNA fragment specific to this P. carinii. RACE-PCR was used to obtain the major part of the complementary DNA; the 5'- and 3'-genomic regions were obtained respectively from a Mbol subgenomic library and from an amplified fragment using oligonucleotides designed from the cDNA sequence. Comparison of genomic and cDNA sequences showed an open reading frame of 660 bp interrupted by seven small introns. The deduced amino acid sequence contained 220 residues. Protein sequence alignment demonstrated the highest homology (50.5% identity; 70.3% similarity) with Saccharomyces cerevisiae manganese-SOD (MnSOD) suggesting that P. carinii SOD belongs to the mitochondrial MnSOD group. A putative targeting peptide found at the 5'-end of the P. carinii SOD sequence also suggested its mitochondrial localization.

Characterization of a mitogen-activated protein kinase from Pneumocystis carinii

The pathogenic fungus Pneumocystis carinii causes severe pneumonia in patients with impaired immunity, particularly patients with acquired immunodeficiency syndrome. The life cycle of P. carinii is poorly understood, and the inability to continuously culture P. carinii is a major limitation in understanding its cell biology. In fungi homologous to P. carinii, pheromone mating factors signal through a mitogen-activated protein kinase (MAPK) signal transduction cascade, resulting in mitotic cell cycle arrest and entry into a pathway of conjugation, cellular differentiation, and proliferation. Using degenerate PCR and library screening, we have identified a MAPK cDNA in P. carinii that is highly homologous to fungal MAPKs involved in the pheromone mating signal transduction cascade, and we demonstrate MAPK activity in P. carinii lysates with a specific antiserum derived from the translated P. carinii MAPK cDNA sequence.

Pneumocystis carinii pneumonia: the status of Pneumocystis biochemistry

Pneumocystis carinii pneumonia remains a prevalent opportunistic disease among immunocompromised individuals. Although aggressive prophylaxis has decreased the number of acute P. carinii pneumonia cases, many patients cannot tolerate the available drugs, and experience recurrence of the infection, which can be fatal. It is now generally agreed that the organism should be placed with the fungi, but the identification of extant fungal species representing its closest kins, remains debated. Most recent data indicate that P. carinii represents a diverse group of organisms. Since the lack of methods for the continuous subcultivation of this organism hampered P. carinii research, molecular cloning and nucleotide sequencing approaches led the way for understanding the biochemical nature of this pathogen. However, within the last 5 years, the development of improved protocols for isolating and purifying viable organisms from infected mammalian host lungs has enabled direct biochemical and metabolism studies on the organism. The protein moiety of the major high mol. wt surface antigen, represented by numerous isoforms, is encoded by different genes. These proteins are post-transcriptionally modified by carbohydrates and lipids. The organism has the shikimic acid pathway that leads to the formation of compounds which mammals cannot synthesise (e.g., folic acid), hence drugs that inhibit these pathways are effective against the pathogen. Ornithine decarboxylase has now been detected; rapid and complete depletion of polyamines occurs in response to difluoromethylornithine (DFMO). Instead of ergosterol (the major sterol of higher fungi), P. carinii synthesises distinct delta7, C-24-alkylated sterols. An unusual C32 sterol, pneumocysterol, has been identified in human-derived P. carinii. Another signature lipid discovered is cis-9,10-epoxy stearic acid. CoQ10, identified as the major ubiquinone homologue, is synthesised de novo by P. carinii. Atovaquone and other hydroxynaphthoquinone drugs with anti-P. carinii activity probably inhibit pathogen respiration as CoQ analogues. Unlike its effects on Plasmodium, atovaquone does not inhibit the P. carinii dihydroorotate dehydrogenase and pyrimidine metabolism.

Identification, characterization, and expression of the BiP endoplasmic reticulum resident chaperonins in Pneumocystis carinii

We have isolated, characterized, and examined the expression of the genes encoding BiP endoplasmic reticulum (ER) resident chaperonins responsible for transport, maturation, and proper folding of membrane and secreted proteins from two divergent strains of Pneumocystis carinii. The BiP genes, Pcbip and Prbip, from the P. c. carinii (prototype) strain and the P. c. rattus (variant) strain, respectively, are single-copy genes that reside on chromosomes of approximately 330 and approximately 350 kbp. Both genes encode approximately 72.5-kDa proteins that are most homologous to BiP genes from other organisms and exhibit the amino-terminal signal peptides and carboxyl-terminal ER retention sequences that are hallmarks of BiP proteins. We established short-term P. carinii cultures to examine expression and induction of Pcbip in response to heat shock, glucose starvation, inhibition of protein transport or N-linked glycosylation, and other conditions known to affect proper transport, glycosylation, and maturation of membrane and secreted proteins. These studies indicated that Pcbip mRNA is constitutively expressed but induced under conditions known to induce BiP expression in other organisms. In contrast to mammalian BiP genes but like other fungal BiP genes, P. carinii BiP mRNA levels are induced by heat shock. Finally, the Prbip and Pcbip coding sequences surprisingly exhibit only approximately 83% DNA and approximately 90% amino acid sequence identity and show only limited conservation in noncoding flanking and intron sequences. Analyses of the P. carinii BiP gene sequences support inclusion of P. carinii among the fungi but suggest a large divergence and possible speciation among P. carinii strains infecting a given host.

Pneumocystis carinii: an atypical fungal micro-organism

The purpose of this review is to assist mycologists in having a better understanding of Pneumocystis carinii and the disease that it causes. Now considered to be a fungus, P. carinii is unusual in its life cycle and relationship with the host. P. carinii pneumonia (PCP) pathogenesis, immunology and host defence mechanisms are examined, as well as epidemiological and control strategies. Most pneumocystosis pathophysiological changes result from the parasite's attachment and proliferation in the lungs, resulting in a filling of the alveoli with masses of the micro-organism. Pathological changes include an increase in alveolar capillary membrane permeability and injury to the alveolar epithelium, which may be mediated by the release of degradative enzymes from the pathogen. A host response takes place by hypertrophy, and hyperplasia involving type II epithelial alveolar cells. P carinii interacts with pulmonary surfactants by binding to the hydrophilic proteins A and D, and by modifying their phospholipid composition. Alveolar macrophages and CD4+ T cells play a key role in the host's defence against Pneumocystis. The epidemiology of PCP remains poorly understood. Airborne transmission has been established, but the actual infective form and its source remains unknown. Studies concerning P. carinii genetic diversity have shown that the parasite polymorphism is related, at least partially, to the host species. A strong host-species specificity in P. carinii has been found. From an epidemiological perspective, there appears to be no animal reservoir for the agent of human PCP. Thus, this disease should not be considered to be zoonotic. Although a significant decrease in the incidence of pneumocystosis has been obtained when employing chemoprophylaxis, anti-P. carinii drugs are not completely successful, often inducing deleterious side-effects. For these reasons, new prophylactic and therapeutic strategies need to be developed. One approach could be based on the anti-P. carinii effect of yeast killer toxins and antibiotic anti-idiotypic antibodies.

Comparison of six different PCR methods for detection of Pneumocystis carinii

We have recently developed a nested PCR method which amplifies internal transcribed spacers (ITS) of the ribosomal RNA genes of Pneumocystis carinii. To determine whether this PCR method can be used to diagnose P. carinii infections, we examined 30 bronchoalveolar lavage (BAL) specimens that were shown microscopically to contain P. carinii organisms by the P. carinii ITS PCR (Pc-ITS-PCR) and five other PCR methods that have been described for detecting P. carinii in clinical specimens. The targets of these PCR methods are portions of 18S rRNA, mitochondrial (mt) rRNA, 5S rRNA, thymidylate synthase (TS), and dihydrofolate reductase (DHFR). We also examined five different fungi, including Saccharomyces cerevisiae, Candida albicans, Histoplasma capsulatum, Cryptococcus neoformans, and Aspergillus fumigatus to determine the specificity of these six PCR methods for P. carinii. All 30 BAL specimens were positive by both the Pc-ITS-PCR and the 18S rRNA gene PCR, whereas only 26 (87%), 18 (60%), 10 (33%), and 7 (23%) of 30 BAL specimens were positive by mt rRNA gene PCR, TS gene PCR, 5S rRNA gene PCR, and DHFR gene PCR, respectively. Although the 18S rRNA gene PCR had the same sensitivity as the Pc-ITS-PCR, it nonspecifically amplified S. cerevisiae and C. albicans. The TS gene PCR also produced false-positive PCR results with C. albicans and C. neoformans. None of the other PCR methods (Pc-ITS-PCR, mt rRNA gene, 5S rRNA gene, and DHFR gene PCR) amplified the control fungal DNA. Considering both sensitivity and specificity, we conclude that Pc-ITS-PCR is the most effective of the six PCR methods evaluated in this study for the detection of P. carinii in BAL specimens.

Cloning and characterization of an ATPase gene from Pneumocystis carinii which closely resembles fungal H+ ATPases

A gene encoding a P-type cation translocating ATPase was cloned from a genomic library of rat-derived Pneumocystis carinii. The nucleotide sequence of the gene contains a 2781 base-pair open reading frame that is predicted to encode a 101,401 dalton protein composed of 927 amino acids. The P. carinii ATPase protein (pcal) is 69-75% identical when compared with eight proton pumps from six fungal species. The Pneumocystis ATPase is less than 34% identical to ATPase proteins from protozoans, vertebrates or the Ca++ ATPases of yeast. The P. carinii ATPase contains 115 of 121 residues previously identified as characteristic of H+ ATPases. Alignment of the Pneumocystis and fungal proton pumps reveals five homologous domains specific for fungal H+ ATPases.

Cloning and identification of Arp1, an actin-related protein from Pneumocystis carinii

The complete Pneumocystis carinii Arp1 gene has been sequenced from two cDNA clones. The gene encodes a protein 385 bp in length with an estimated size of 45,000 kD. The A + T% for the Arp1 gene and a 900-bp sequence upstream of the gene were 63.7% and 70.3%, respectively. These values are consistent with A + T codon preference displayed by P. carinii and are similar to values reported for other P. carinii genes. The predicted amino acid sequence of the P. carinii Arp1 protein had a similarity of 87.6% with Neurospora crassa Arp1, 82.1% similarity with vertebrate centractin, and 71.2% similarity with the Saccharomyces cerevisiae Act5p. Expression of Arp1 mRNA in P. carinii was detectable via synthesis of cDNA and subsequent PCR amplification. Affinity purified antibodies against S. cerevisiae Act5p, and canine centractin recognized both the recombinantly expressed protein and a 45,000 kD protein in P. carinii nuclear extracts. The Arp1 gene is the second member of the actin multigene family that has been identified in P. carinii.

Comparison of coding and spacer region sequences of chromosomal rRNA-coding genes of two sequevars of Pneumocystis carinii

Two distinct sequevars, denoted Pc1 and Pc2, of the opportunistic pathogen Pneumocystis carinii have been previously identified based on the sequence of their 26S rRNA genes, the location of group I self-splicing introns and pulsed field electrophoretic patterns of chromosomal DNA. This study shows that the sequences of 16S and 5.8S rRNA genes also vary between these sequevars, and that greater variation was seen in the internal transcribed spacer regions. Polymerase chain reaction and restriction analysis can distinguish between these sequevars.

Molecular characterization of clustered variants of genes encoding major surface antigens of human Pneumocystis carinii

A 13-kb genomic fragment from human Pneumocystis carinii was cloned as repetitive DNA. The fragment contains a cluster of three related genes, each 3 kb in size, and the 5' end of a fourth gene. The predicted polypeptide of the first gene in the cluster comprises 1,030 amino acid residues with a total molecular mass of 116 kDa. The gene's predicted amino acid sequence bears 32% identity to predicted sequences of recently described gene fragments of ferret P. carinii, which encode an immunodominant surface glycoprotein (gpA) (P. J. Haidaris, T. W. Wright, F. Gigliotti, and C. G. Haidaris, J. Infect. Dis. 166:1113-1123, 1992), and 36% identity to the predicted sequence of a rat P. carinii major surface glycoprotein gene (msg) (J. A. Kovacs, F. Powell, J. C. Edman, B. Lundgren, A. Martinez, B. Drew, and C. W. Angus, J. Biol. Chem. 268:6034-6040). DNA hybridization showed that sequences related to the cloned msg genes reside on at least 12 chromosomes of human P. carinii at various degrees of multiplicity and/or homology. Affinity-purified antibodies with specificity to a fusion protein made from the human P. carinii msgI gene recognized two bands on a Western immunoblot containing total human P. carinii protein; they also recognized fusion proteins derived from the other two genes of the cluster. Monoclonal antibodies with reactivity to Msg of human P. carinii recognized fusion proteins produced from two msg genes. Fusion proteins were also recognized by sera from healthy humans and from patients. The msg genes are candidates for the development of immunotherapy and subunit vaccines for the treatment and prevention of P. carinii pneumonia.

Cloning and characterization of the calmodulin-encoding gene from Pneumocystis carinii

Complete cDNA and genomic clones for the CaM gene encoding calmodulin (CaM) from Pneumocystis carinii have been isolated from rat and characterized. The nucleotide (nt) sequence contains an open reading frame interrupted by three introns, that encodes a protein of 152 amino acids. The predicted CaM protein of P. carinii shares a high degree of homology with other known CaM proteins.