Pneumocystis are eukaryotic, fungal, extracellular lung pathogens that have been detected in almost every mammalian species evaluated for their presence. Since the initiation of the Pneumocystis Genome Project in 1998, 4 distinct species within the genus Pneumocystis have been described and named in accordance with the International Code of Botanical Nomenclature. In 1999, Frenkel described the species which infects human beings as Pneumocystis jirovecii and retained the name of the species first identified in rats as Pneumocystis carinii. In 2004, Keely et al. and Cushion et al. described the species harbored by mice as Pneumocystis murina and another species found in rats as Pneumocystis wakefieldiae. P. jirovecii as the name for the human species is controversial and its validity will be decided by the International Botanical Congress in 2005. Pneumocystis carinii (Pc) was the species used for this genome project and when used in the text specifically refers to this species. The term "Pneumocystis" is used when referring to the organisms in general or when the host of origin is not known.

The Pneumocystis carinii genome is approximately 7.7 Mb, a small genome for a fungus, when compared to the 16 Mb S. cerevisiae genome. Chromosome organization is yet to be determined, since extensive chromosome polymorphism has been characterized in P. carinii strains. One interesting fact is that the Pneumocystis carinii genome size is susceptible to variations, depending on the host background. In fact, Pneumocystis carinii does not represent one single genus- single species but a variety of different organisms, which are collectively called special forms or formae specialis. This has implications on the expected variable chromosome size and diverse structure.

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 Pneumocystis 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 are linked to another family of genes encoding subtilisin-like serine proteases (PRT) that may be involved in the proteolytic cleavage of a precursor MSG to yield the surface form. Another member of these subtelomeric gene families is the MSR genes (MSG-related), of which the function of the encoded proteins is not known. 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 been described. Pneumocystis have dedicated approximately 10% of their genome to this family of genes, which is striking when compared to the single locus dedicated to encoding ribosomal RNA. Analysis of the Pc genome is likely to reveal novel insights into chromosome evolution and the underlying processes.

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 P. jirovecii (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.

Pneumocystis 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 a single copy 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 an 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 Pneumocystis in the fungal Kingdom has been a relatively recent event, occurring in the late 1980s. Erikkson proposed creation of a new Family and Order for the Pneumocystis group: Pneumocystidaceae, Pneumocystidales. 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.

The goals of this project, the Pneumocystis Genome Project (funded by the NIH NIAID), are to provide a physical map, gene sequence, and an expressed gene inventory for Pneumocystis carinii as a means to better understand their molecular structure and develop publicly available, centralized information and reagents that will be used to expedite research. This project will accomplish the following specific goals over a 5 year period starting February 15, 1999 through February 14, 2005:

1.      Construct cosmid libraries of the rat P. carinii genome in at least 2 vector systems.

2.      Sequence cDNAs of rat Pc for creation of expression sequence tags (ESTs).

3.      Create chromosome-specific libraries.

4.      Order the clones containing the rat P. carinii DNA along the chromosome of origin to create an in vitro reconstruction of each chromosome.

5.      Sequence the entire genome of P. carinii.

6.      Perform concurrent functional genomic studies to address basic biological questions in Pneumocystis research

So good luck! And have a good job for research and medical care!

Information:

Lineage( full ): cellular organisms; Eukaryota; Fungi/Metazoa group; Fungi; Ascomycota; Pneumocystidomycetes; Pneumocystidales; Pneumocystidaceae; Pneumocystis

                                                                                                      May 2005

                                                                                                 Barbara Colacchia

References

1)      Cushion MT. Pneumocystis: unraveling the cloak of obscurity.Trends Microbiol. 2004 May;12(5):243-9. Review.

2)      Cushion MT. Comparative genomics of Pneumocystis carinii with other protists: implications for life style.J Eukaryot Microbiol. 2004 Jan-Feb;51(1):30-7. Review.

3)      Cornillot E, Keller B, Cushion MT, Metenier G, Vivares CP. Fine analysis of the Pneumocystis carinii f. sp. carinii genome by two-dimensional pulsed-field gel electrophoresis.Gene. 2002 Jun 26;293(1-2):87-95.

4)      Stringer JR, Cushion MT. The genome of Pneumocystis carinii. FEMS Immunol Med Microbiol. 1998 Sep;22(1-2):15-26. Review.

These sequence data were produced by the Pneumocystis Genome Project (funded by the NIH NIAID) and can be obtained from http://pgp.cchmc.org/".

Information from: "The Pneumocystis Genome Project. http://pgp.cchmc.org/".