Melanie T. Cushion

Pneumocystis carinii: sequence from ribosomal RNA implies a close relationship with fungi

Pneumocystis carinii is the etiologic agent of a lethal pneumonia which occurs in patients with the acquired immune deficiency syndrome (AIDS) and other immunocompromised hosts. The basic biochemical and genetic characteristics of P. carinii are poorly understood and its taxonomic classification as a protozoan is uncertain. To address the taxonomic question, a method was developed for the extraction of total RNA from P. carinii. Denaturing agarose gel electrophoresis showed the two ribosomal RNA species of P. carinii to be similar in size to those of other lower eukaryotes, including Saccharomyces cerevisiae. Three portions of the small ribosomal RNA of P. carinii were sequenced by reverse transcription from oligonucleotide primers. Three hundred seventy-two nucleotides of sequence were obtained. The sequence derived from P. carinii RNA contained regions that previous phylogenetic studies have shown to be highly variable among species, as well as regions that are highly conserved. Comparison of the P. carinii sequence to corresponding sequences of organisms from other taxa showed the P. carinii sequence to be more similar to sequences from the fungi (Saccharomyces cerevisiae, Neurospora crassa, Candida albicans, and Cryptococcus diffuens) than to protozoan sequences. These data suggest that P. carinii is more closely related to fungi than to protozoa.

Molecular Genetic Distinction of Pneumocystis carinii from Rats and Humans

Pneumocystis carinii from rats and from humans were compared with respect to electrophoretic karyotype, presence of DNA sequences known to be repeated in rat‐derived P. carinii, overall DNA sequence homology, and the sequences at two genetic loci. The organisms from each host species were different in each respect. Neither of two repeated DNAs from rat‐derived P. carinii was found in the genome of human‐derived organisms, and total DNA from rat‐derived P. carinii failed to hybridize to human‐derived P. carinii DNA. The sequences of the α‐tubulin genes from the two P. carinii were strikingly different and the base composition of the α‐tubulin gene from rat‐derived P. carinii was rich in adenine and thymine, while the base composition of this gene from human‐derived P. carinii was rich in guanine and cytosine. The sequence from the 18S rRNA gene of human‐derived P. carinii was twice as divergent from that of rat‐derived P. carinii as the sequence from the corresponding region of Candida albicans was from that of Candida tropicalis. These data show that rats and humans can harbor distinct types of P. carinii that are sufficiently different to suggest that P. carinii from the two hosts could be different species.

Pneumocystis activates human alveolar macrophage NF-kappaB signaling through mannose receptors.

ABSTRACT Alveolar macrophages (AM) represent important effector cells in the innate immune response to the AIDS-related pathogen Pneumocystis, but the early AM host defense signaling events are poorly defined. Using AM from healthy individuals, we showed in the present study that Pneumocystis organisms stimulate AM NF-κB p50 and p65 nuclear translocation in a time-dependent and multiplicity-of-infection-dependent manner as determined by electrophoretic mobility shift assay and immunofluorescence microscopy and that NF-κB nuclear translocation is associated with I-κB phosphorylation. Importantly, competitive inhibition of mannose receptor and targeted short interfering RNA-mediated gene suppression of mannose receptor mRNA and protein is associated with complete elimination of NF-κB nuclear translocation in response to Pneumocystis. Furthermore, human immunodeficiency virus (HIV) infection of AM (as a model human disease state of reduced AM mannose receptor expression and function) inhibits Pneumocystis-mediated NF-κB nuclear translocation and is associated with reduced I-κB phosphorylation and reduced interleukin-8 (IL-8) release. In contrast, NF-κB nuclear translocation and IL-8 release in response to lipopolysaccharide are intact in AM from both healthy and HIV-infected individuals, indicating that the observed impairment is not a global disturbance of the NF-κB pathway. Thus, in addition to phagocytic and endocytic effector functions, the present study identifies mannose receptors as pattern recognition receptors capable of NF-κB activation in response to infectious non-self challenge. AM mannose receptor-mediated NF-κB activation may represent an important mechanism of the host cell response to Pneumocystis, and altered NF-κB activation in the context of HIV infection may impair a critical innate immune signaling response and may contribute to pathogenesis of opportunistic lung infections.

Negative regulatory role of mannose receptors on human alveolar macrophage proinflammatory cytokine release in vitro.

Alveolar macrophages (AM) are critical components of lung innate immunity and contribute to an effective host response to Pneumocystis pneumonia. Recognition of unopsonized Pneumocystis organisms by human AM is mediated predominantly via mannose receptors and results in phagocytosis, release of reactive oxygen species, and activation of the nuclear transcription factor (NF)‐κB. However, the AM host defense genes activated by Pneumocystis have not been defined. In the present study, incubation of AM with unopsonized Pneumocystis organisms was not associated with release of interleukin (IL)‐1β, IL‐6, or tumor necrosis factor (TNF)‐α (important cytokines in the host response to Pneumocystis) and did not induce IL‐1β, IL‐6, or TNF‐α mRNA transcripts. These findings were not attributed to Pneumocystis‐induced cytopathic changes, as these same AM released IL‐8 and matrix metalloproteinase‐9 in response to Pneumocystis. NF‐κB‐mediated IL‐8 release was independent of Pneumocystis phagocytosis. The observed response was specific, as IL‐1β, IL‐6, and TNF‐α release and mRNA induction were preserved in response to lipopolysaccharide or serum‐opsonized Pneumocystis. The absence of IL‐1β, IL‐6, and TNF‐α release in response to Pneumocystis was predominately influenced by AM mannose receptors, as blocking mannose receptors or targeted mannose receptor small interfering RNA functional gene silencing resulted in TNF‐α release in response to unopsonized Pneumocystis organisms. Furthermore, ligation of AM mannose receptors by unopsonized Pneumocystis organisms reduced Toll‐like receptor 4‐mediated TNF‐α release. Taken together, these data suggest that mannose receptors on human AM may suppress select proinflammatory cytokine release and may serve to regulate the innate inflammatory responses to infectious challenge in the lungs.

The challenge of Pneumocystis carinii culture.

ABSTRACT. Published and unpublished data on the cultivation of P. carinii were reviewed by a panel of investigators convened by the National Institutes of Health. Although several cell culture systems allow propagation of P. carinii for a limited time with modest rates of replication, these have not proved adequate for isolation of P. carinii in sufficient quantity to explore important basic biological investigation. Attempts at cell‐free culture have yielded only transient proliferation. Because much of the unsuccessful work on cultivation of the organism has been unpublished, the panel agreed that these data may be useful to other investigators in designing experimental strategies for cultivation. Therefore, the purpose of this report is to make available this information to researchers, lest others unknowingly repeat unsuccessful methods. It is hoped that by documenting the history and the complexities of Pneumocystis culture, renewed interest and efforts will be directed toward this fundamental scientific challenge.

Phylogenomic Analyses Support the Monophyly of Taphrinomycotina, including Schizosaccharomyces Fission Yeasts

Several morphologically dissimilar ascomycete fungi including Schizosaccharomyces, Taphrina, Saitoella, Pneumocystis, and Neolecta have been grouped into the taxon Taphrinomycotina (Archiascomycota or Archiascomycotina), originally based on rRNA phylogeny. These analyses lack statistically significant support for the monophyly of this grouping, and although confirmed by more recent multigene analyses, this topology is contradicted by mitochondrial phylogenies. To resolve this inconsistency, we have assembled phylogenomic mitochondrial and nuclear data sets from four distantly related taphrinomycotina taxa: Schizosaccharomyces pombe, Pneumocystis carinii, Saitoella complicata, and Taphrina deformans. Our phylogenomic analyses based on nuclear data (113 proteins) conclusively support the monophyly of Taphrinomycotina, diverging as a sister group to Saccharomycotina + Pezizomycotina. However, despite the improved taxon sampling, Taphrinomycotina continue to be paraphyletic with the mitochondrial data set (13 proteins): Schizosaccharomyces species associate with budding yeasts (Saccharomycotina) and the other Taphrinomycotina group as a sister group to Saccharomycotina + Pezizomycotina. Yet, as Schizosaccharomyces and Saccharomycotina species are fast evolving, the mitochondrial phylogeny may be influenced by a long-branch attraction (LBA) artifact. After removal of fast-evolving sequence positions from the mitochondrial data set, we recover the monophyly of Taphrinomycotina. Our combined results suggest that Taphrinomycotina is a legitimate taxon, that this group of species diverges as a sister group to Saccharomycotina + Pezizomycotina, and that phylogenetic positioning of yeasts and fission yeasts with mitochondrial data is plagued by a strong LBA artifact.

New Nomenclature for the Genus Pneumocystis

Approximately 50 individuals attended the round-table discussion session on Pneumocystis nomenclature. The group discussed the desirability and appropriateness of retaining the currently used tripartite nomenclature system, as opposed to assigning new species names to organisms that seem to be too different to be accommodated within a single species. The group unanimously endorsed a proposal to rename organisms currently known as special forms of P. carinii as species in the genus fnewwcystis. Whereas the discussion at the round-table session led to a clear endorsement of the proposal to apply new species names, it should be noted that not all of the ideas and opinions expressed in this article were discussed during the meeting. Furthermore. time and distance prohibited providing every interested party the opportunities to either contribute to this text, or to critique it prior to publication. Therefore, the content of this article should not be viewed as having been explicitly endorsed by everyone at the meeting, or other interested individuals in the community of Pnewnocystis researchers. With this disclaimer in mind, the purposes of this article are confined to the following: 1) explain the rationale for changing the nomenclature, 2) provide guidelines for recognizing new species and assigning new species names. These guidelines may become conventions in the future. but it is more probable that modifications will be needed as the complexity of the genus becomes more completely described. Indeed, recent new data have already clouded the issue to some extent. Analysis of one genetic locus in Pnewnocystis organisms from a large number of primates (i.e., from a single taxonomic Order) showed that sequence divergence can be much less than it is when Pneumocystis organisms from hosts in different Orders of mammals are compared. Thus. the consensus in favor of recognizing new species emerged contemporaneously with new data showing that host specificity may be accompanied by relatively little DNA sequence divergence. This discovery poses a problem because host specificity has been the most clear and compelling discreet phenotypic characteristic for recognizing clades in this genus. This problem, however, does not apply to the best studied Pnewnocystis organisms, which are extremely divergent at the DNA level. It is still appropriate to proceed with renaming them. It is hoped that this article will be useful to those who will undertake this task.

Echinocandin treatment of pneumocystis pneumonia in rodent models depletes cysts leaving trophic burdens that cannot transmit the infection.

Fungi in the genus Pneumocystis cause pneumonia (PCP) in hosts with debilitated immune systems and are emerging as co-morbidity factors associated with chronic diseases such as COPD. Limited therapeutic choices and poor understanding of the life cycle are a result of the inability of these fungi to grow outside the mammalian lung. Within the alveolar lumen, Pneumocystis spp., appear to have a bi-phasic life cycle consisting of an asexual phase characterized by binary fission of trophic forms and a sexual cycle resulting in formation of cysts, but the life cycle stage that transmits the infection is not known. The cysts, but not the trophic forms, express β -1,3-D-glucan synthetase and contain abundant β -1,3-D-glucan. Here we show that therapeutic and prophylactic treatment of PCP with echinocandins, compounds which inhibit the synthesis of β -1,3-D-glucan, depleted cysts in rodent models of PCP, while sparing the trophic forms which remained in significant numbers. Survival was enhanced in the echincandin treated mice, likely due to the decreased β -1,3-D-glucan content in the lungs of treated mice and rats which coincided with reductions of cyst numbers, and dramatic remodeling of organism morphology. Strong evidence for the cyst as the agent of transmission was provided by the failure of anidulafungin-treated mice to transmit the infection. We show for the first time that withdrawal of anidulafungin treatment with continued immunosuppression permitted the repopulation of cyst forms. Treatment of PCP with an echinocandin alone will not likely result in eradication of infection and cessation of echinocandin treatment while the patient remains immunosuppressed could result in relapse. Importantly, the echinocandins provide novel and powerful chemical tools to probe the still poorly understood bi-phasic life cycle of this genus of fungal pathogens.

Pneumocystis-mediated IL-8 release by macrophages requires coexpression of mannose receptors and TLR2.

Interaction with the unique fungus Pneumocystis (Pc) promotes IL‐8 release by human alveolar macrophages (AM), although the receptor(s) mediating IL‐8 release have not been identified. TLR2 recognizes fungal components and mediates release of host defense cytokines and chemokines, although whether TLR2 mediates signaling in response to Pc is not known. In the current study, Pc induced IL‐8 release by human AM, and AM pretreatment with anti‐TLR2 neutralizing antibody reduced IL‐8 release. However, in nonphagocytic human embryonic kidney (HEK)293 cells transfected with human TLR2 cDNA, incubation with Pc did not induce IL‐8 release, whereas these same cells released IL‐8 in response to the TLR2 agonist lipoteichoic acid. Targeted gene silencing of AM mannose receptors (MR; phagocytic receptors for Pc) using small interfering RNA also reduced Pc‐mediated IL‐8 release in human AM. However, HEK293 cells transfected with human MR cDNA alone did not release IL‐8 in response to Pc. In contrast, HEK293 cells cotransfected with human TLR2 and human MR cDNA released IL‐8 in response to Pc. In human AM, Pc promoted direct interaction of MR and TLR2, IL‐8 release was reduced markedly upon simultaneous blocking of TLR2 and gene silencing of MR, and IL‐8 release was dependent in part on transcription factor NF‐κB and ERK1/2 and JNK MAPKs. These studies demonstrate that Pc‐mediated IL‐8 release by human AM requires the coexpression of MR and TLR2 and further supports the concept that combinatorial interactions of macrophage innate receptors provide specificity of host defense cell responses to infectious challenge.

Molecular and phenotypic description of Pneumocystis wakefieldiae sp. nov., a new species in rats

Organisms in the genus Pneumocystis are fungi that reside in the lungs of mammals that can cause a lethal pneumonia once the hosts lose immune function. The genus Pneumocystis contains many members, but only two species have been described formally to date, P. carinii, the type species found in rats, and P. jirovecii, resident in human beings. Rats have been shown to harbor another organism in addition to P. carinii, Pneumocystis wakefieldiae sp. nov., formerly known as Pneumocystis carinii f. sp. ratti, which is described here. Although often found together and morphologically similar, P. carinii and P. wakefieldiae are phenotypically and genetically divergent. We used the phylogenetic species recognition approach to distinguish these organisms as two distinct species and estimated the evolutionary time of their separation. Nucleotide sequence comparisons of seven homologous genes showed 4–7% divergence between the P. wakefieldiae and P. carinii sequences, which was in contrast to the 0–0.8% divergence observed within P. carinii species. Even greater divergence (30%) occurred in sequences located between genes. The MSG (major surface glycoprotein) gene families of P. carinii and P. wakefieldiae are 35% divergent from one another and differ with respect to sequence elements associated with regulation of their transcription. Differences in reactivity of monoclonal antibodies and polyclonal antisera reflected these genetically distinct surface antigens. Karyotypic analysis of P. wakefieldiae produced a single profile that was distinct from all 12 profiles known for P. carinii. Eight homologous genes were localized to chromosomes of different sizes in the two species. The cumulative genotypic and phenotypic data support a species distinction between these two organisms.