Organisms collectively known as Pneumocystis carinii (Pc) are eukaryotic extracellular lung pathogens that have been detected in almost every mammalian species evaluated for their presence. A compromised immune status due to malnutrition, disease, or in human beings, infection with the human immunodeficiency virus, can lead to development of a lethal pneumonia caused by Pc (PcP). In AIDS patients, PcP remains a problem because of limited therapeutic choices and adverse reactions to the 2 standard treatment regimens, trimethoprim-sulfamethoxazole and pentamidine isethionate.

Pc are unusual for a variety of reasons. Although first identified in 1909 by Carlos Chagas, a long term in vitro culture system remains elusive. The lack of a culture system has hindered progress in understanding their basic biological processes resulting in an incomplete understanding of the Pc life cycle, mode of transmission, and metabolic function. Organisms intractable to in vitro culture provide few opportunities for large scale drug development as evidenced by the limited therapeutic repertoire with which to treat PcP. Likewise, rational control of infection in susceptible populations is hindered by a lack of known reservoirs, unidentified infective form, and method of communicating the infection. Unlike any extant fungus, Pc possesses only 1-2 copies of the nuclear ribosomal RNA locus and has little to no ergosterol. The characteristics of the rDNA locus as well as insights into what constitutes an essential core of a eukaryotic genome will be revealed by the proposed genome project. Essential metabolic requirements will be elucidated by a gene inventory, perhaps affording the critical components of a medium for long term maintenance outside the mammalian host.

The phylogenetic placement of Pc in the fungal Kingdom has been a relatively recent event, occurring in the late 1980s, and the precise assignment to Order and Family remains controversial. Construction of phylogenetic trees based on nuclear 16S-like RNA have not identified any close relatives; fungal organisms on neighboring branches include the fission yeast, Schizosaccharomyces pombe, and Taphrina deformans, both of which are significantly different in gene sequence and morphology. Recently, Pc and these 2 fungi were placed in a diverse group of fungi called the Archiascomycetes, the 5 members of which share few biochemical or morphological similarities. It has been suggested that the Pneumocystis spp. represent an early divergent line in the fungal kingdom which may have branched coincident with the bifurcation of the Basidiomycete and Ascomycete lineages. This early divergence creates an opportunity to study evolutionary processes in these phylogenetically unique organisms.

A striking feature of Pneumocystis biology and genetic structure is the mannosylated surface antigens, referred to as the major surface glycoproteins (MSGs), which are a research focus of the Co-investigator, Dr. James Stringer (University of Cincinnati) and collaborator, Dr. Yoshi Nakamura. These molecules are the predominant antigenic species found on all Pc populations and are encoded by a gene family containing approximately 100 members that are organized in clusters in subtelomeric locations. The MSGs have been implicated as a means of attachment to host cells or as a mechanism to circumvent immune surveillance via antigenic variation, although they likely contribute to other life cycle processes. The MSG genes appear to be linked to another family of genes encoding subtilisin-like serine proteases that may be involved in the proteolytic cleavage of a precursor MSG to yield the surface form. Evidence supporting the expression of MSG genes by genetic rearrangements resulting in placement of one of the MSG genes in a unique expression site located at the end of a single chromosome has recently been described. Pc organisms have dedicated approximately 10% of their genome to this family of genes, which is striking when compared to the 1-2 genes dedicated to encoding ribosomal RNA (19). Analysis of the Pc genome is likely to reveal novel insights into chromosome evolution and the underlying processes causing it as well as the genomic basis of its pathogenicity.