Genomics is the study of the structure, function, and evolution of genomes (2). Genomics is differentiated from traditional genetics by the application of computational biologic and robotics technologies that permits the simultaneous analysis of 1000 or more genes. This approach allows the study of large numbers of genes expressed during a variety of fundamental biologic processes such as meiosis, development, infection, or virulence. These data are able to be disseminated to the scientific community and immediately utilized in research strategies encompassing purely computer generated searches for gene homologies or genetic comparisons, or for unique in vivo approaches to identify genes involved in pathogenesis or virulence. The group of organisms known as Pneumocystis carinii is an especially attractive target for a genome project. There is a dearth of basic biologic information about these opportunistic pathogens that are a major cause of pneumonia in patients with AIDS, as well as pathogens of concern in commercial animal colonies. The lack of a continuous in vitro cultivation system for any member of this family has largely contributed to the scientific ignorance concerning its life cycle, mode of transmission, infective form and poor understanding of its metabolic processes. Pneumocystis has only recently been shown to be a member of the fungi by genetic sequence analysis of the nuclear 16S-like gene and other genes. It is a unique member of the fungal kingdom distinguished by its phylogenetic isolation; lack of ergosterol and insensitivity to standard anti-fungal therapies; paucity of nuclear ribosomal genes (1-2 copies); presence of a highly repeated gene family encoding surface antigens; and relatively delicate cell wall. Because of its compact genome size, 7.7 Mbp, and the availability of clearly resolved chromosomes by pulsed field gel electrophoresis, it is now possible to address basic biological questions by application of genomic technologies. The goals of the present proposal are to produce physical maps and gene inventories for Pneumocystis populations form the rat and human being. This project represents the first time a non- culturable microbe will be the subject of a genomics project. It is a unique opportunity to make a dramatic difference in the progress of Pneumocystis research and to concurrently broaden our understanding of that group of organisms known as the Fungi. Benefits from such a project include construction of a physical map that will provide structural information of the Pneumocystis genome; identification of gene networks involved in metabolism and virulence; determination of the genetic relatedness of Pneumocystis with extant fungi; insights into the mechanisms for host specificity demonstrated by different populations of Pneumocystis; identification of potential drug targets; and possible strategies leading to establishment of a continuous culture system.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI044651-02
Application #
6149902
Study Section
Special Emphasis Panel (ZRG5-AARR-1 (04))
Program Officer
Dixon (Dmid), Dennis M
Project Start
1999-02-15
Project End
2004-01-31
Budget Start
2000-02-01
Budget End
2001-01-31
Support Year
2
Fiscal Year
2000
Total Cost
$557,544
Indirect Cost
Name
University of Cincinnati
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
City
Cincinnati
State
OH
Country
United States
Zip Code
45221
Sesterhenn, Thomas M; Slaven, Bradley E; Keely, Scott P et al. (2010) Sequence and structure of the linear mitochondrial genome of Pneumocystis carinii. Mol Genet Genomics 283:63-72
Cushion, Melanie T; Walzer, Peter D (2009) Preclinical drug discovery for new anti-pneumocystis compounds. Curr Med Chem 16:2514-30
Cushion, Melanie T; Smulian, A George; Slaven, Bradley E et al. (2007) Transcriptome of Pneumocystis carinii during fulminate infection: carbohydrate metabolism and the concept of a compatible parasite. PLoS One 2:e423
Keely, Scott P; Renauld, Hubert; Wakefield, Ann E et al. (2005) Gene arrays at Pneumocystis carinii telomeres. Genetics 170:1589-600
Strobel, George L; Arnold, Jonathan (2004) Essential eukaryotic core. Evolution 58:441-6
Cushion, Melanie T (2004) Comparative genomics of Pneumocystis carinii with other protists: implications for life style. J Eukaryot Microbiol 51:30-7
Xu, Zheng; Lance, Britton; Vargas, Claudia et al. (2003) Mapping by sequencing the Pneumocystis genome using the ordering DNA sequences V3 tool. Genetics 163:1299-313
Milla, P; Viola, F; Oliaro Bosso, S et al. (2002) Subcellular localization of oxidosqualene cyclases from Arabidopsis thaliana, Trypanosoma cruzi, and Pneumocystis carinii expressed in yeast. Lipids 37:1171-6
Rebholz, S L; Cushion, M T (2001) Three new karyotype forms of Pneumocystis carinii f. sp. carinii identified by contoured clamped homogeneous electrical field (CHEF) electrophoresis. J Eukaryot Microbiol Suppl:109S-110S
Keely, S P; Wakefield, A E; Cushion, M T et al. (2001) Detailed structure of Pneumocystis carinii chromosome ends. J Eukaryot Microbiol Suppl:118S-120S