ABSTRACTIn the context of deciphering the metabolic strategies of the obligate pathogenic fungi in the genusPneumocystis, the genomes of three species (P. carinii,P. murina, andP. jirovecii) were compared among themselves and with the free-living, phylogenetically related fission yeast (Schizosaccharomyces pombe). The underrepresentation of amino acid metabolism pathways compared to those inS. pombe, as well as the incomplete steroid biosynthesis pathway, were confirmed forP. cariniiandP. jiroveciiand extended toP. murina. All threePneumocystisspecies showed overrepresentation of the inositol phosphate metabolism pathway compared to that in the fission yeast. In addition to those known inS. pombe, four genes, encoding inositol-polyphosphate multikinase (EC 2.7.1.151), inositol-pentakisphosphate 2-kinase (EC 2.7.1.158), phosphoinositide 5-phosphatase (EC 3.1.3.36), and inositol-1,4-bisphosphate 1-phosphatase (EC 3.1.3.57), were identified in the two rodentPneumocystisgenomes,P. cariniiandP. murina. TheP. jiroveciigenome appeared to contain three of these genes but lacked phosphoinositide 5-phosphatase. Notably, two genes encoding enzymes essential formyo-inositol synthesis, inositol-1-phosphate synthase (INO1) and inositol monophosphatase (INM1), were absent from all three genomes, suggesting thatPneumocystisspecies are inositol auxotrophs. In keeping with the need to acquire exogenous inositol, two genes with products homologous to fungal inositol transporters, ITR1 and ITR2, were identified inP. cariniiandP. murina, whileP. jiroveciicontained only the ITR1 homolog. The ITR and inositol metabolism genes inP. murinaandP. cariniiwere expressed during fulminant infection as determined by reverse transcriptase real-time PCR of cDNA from infected lung tissue. Supplementation ofin vitroculture with inositol yielded significant improvement of the viability ofP. cariniifor days 7 through 14.IMPORTANCEMicrobes in the genusPneumocystisare obligate pathogenic fungi that reside in mammalian lungs and causePneumocystispneumonia in hosts with weakened immune systems. These fungal infections are not responsive to standard antifungal therapy. A long-termin vitroculture system is not available for these fungi, impeding the study of their biology and genetics and new drug development. Given that all genomes of thePneumocystisspecies analyzed lack the genes for inositol synthesis and contain inositol transporters,Pneumocystisfungi, likeS. pombe, appear to be inositol auxotrophs. Inositol is important for the pathogenesis, virulence, and mating processes inCandida albicansandCryptococcus neoformans, suggesting similar importance within thePneumocystisspecies as well. This is the first report to (i) characterize genes in the inositol phosphate metabolism and transport pathways inPneumocystisspecies and (ii) identify inositol as a supplement that improved the viability ofP. cariniiinin vitroculture.
Comparative Genomics of Pneumocystis Species Suggests the Absence of Genes for myo-Inositol Synthesis and Reliance on Inositol Transport and Metabolism
