Essential Eukaryotic Core

Abstract

Abstract. The AIDs-related fungal pathogen Pneumocystis carinii is unusual in having a remarkably compact genome of 7.7 megabase pairs (mbp) whose small size presents the opportunity to identify the essential eukaryotic core of genes. The essential eukaryotic core is defined to be a collection of essential genes shared by all eukaryotes. Sequencing the 3Ј ends of more than 5500 cDNAs from P. carinii allowed us to identify about 200 genes shared with its nearest known but distant relative, Schizosaccharomyces pombe and also Saccharomyces cerevisiae, and with homologs known to be essential in S. pombe or S. cerevisae. As the cDNA library contains about one half of the P. carinii genes, the size of the essential eukaryotic core (ϳ400) is slightly larger than the prokaryotic core (265-350) being identified by studies of the bacterial pathogen Mycoplasma genitalium. The collection of genes in the essential eukaryotic core may prove useful in identifying new broad spectrum antifungal drug targets. The minimal gene complement of 256 genes essential to a bacterium, Mycoplasma genitalium with its about 700 kbp genome (one of the smallest), was recently identified by insertional mutagenesis (Hutchison et al. 1999). The question is whether or not there is a counterpart to Mycoplasma among eukaryotes that could be exploited to identify the minimal complement of genes shared by most eukaryotes and necessary to build a eukaryotic system, i.e., the essential eukaryotic core (Bennett and Arnold 2001). Pneumocystis, the major AIDs-related pathogen, is unusual in its biology in several respects, and having a list of its essential genes would be useful in selecting new drug targets (Cushion 1998). It has a compact genome of 7.7 mbp (Cushion et al. 1993) and no close relatives outside the genus to highlight shared features with other fungi (Cushion 1998). Extensive sequence of this genome is accumulating as part of the Pneumocystis Genome project (Xu et al. 2003). The sequence of Pneumocystis carinii can be compared with several nearly fully sequenced fungal genomes (Goffeau et al. 1996;Galagan et al. 2003). Two of these relatives of P. carinii, Schizosaccharomyces pombe and S. cerevisiae, have extensive data identifying their essential fungal genes (Winzeler et al. 1999). In this report we infer the essential eukaryotic core by utilizing the small genome size of P. carinii, its isolated phylogenetic position as a basal ascomycete (Edman et al. 1988) and the partial sequences of about one half of its genes having homologs to essential genes in S. pombe or S. cerevisiae. MATERIALS AND METHODSBecause P. carinii is uncultivable, cosmid and cDNA libraries were derived from the karyotype of P. carinii form 1, extracted from the lungs of immunologically suppressed rats during fulminate infection (Xu et al. 2003). Library construction from this karyotype is detailed in Smulian et al. (2001) and at http://pneumocystis.uc.edu. The cDNA library used in this study is in the vector pSK11, and the entire cDNA library is available from the Ameri...

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