Comparative Genomics of
Pneumocystis
Species Suggests the Absence of Genes for
myo-
Inositol Synthesis and Reliance on Inositol Transport and Metabolism
Authors: Porollo Aleksey , Sesterhenn Thomas M. , Collins Margaret S. , Welge Jeffrey A. , Cushion Melanie T. 
Published: November 2014

In the context of deciphering the metabolic strategies of the obligate pathogenic fungi in the genus
Pneumocystis
, the genomes of three species (
P. carinii
,
P. murina
, and
P. 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 in
S. pombe
, as well as the incomplete steroid biosynthesis pathway, were confirmed for
P. carinii
and
P. jirovecii
and extended to
P. murina
. All three
Pneumocystis
species showed overrepresentation of the inositol phosphate metabolism pathway compared to that in the fission yeast. In addition to those known in
S. 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 rodent
Pneumocystis
genomes,
P. carinii
and
P. murina
. The
P. jirovecii
genome appeared to contain three of these genes but lacked phosphoinositide 5-phosphatase. Notably, two genes encoding enzymes essential for
myo-
inositol synthesis, inositol-1-phosphate synthase (INO1) and inositol monophosphatase (INM1), were absent from all three genomes, suggesting that
Pneumocystis
species 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 in
P. carinii
and
P. murina
, while
P. jirovecii
contained only the ITR1 homolog. The ITR and inositol metabolism genes in
P. murina
and
P. carinii
were expressed during fulminant infection as determined by reverse transcriptase real-time PCR of cDNA from infected lung tissue. Supplementation of
in vitro
culture with inositol yielded significant improvement of the viability of
P. carinii
for days 7 through 14.

IMPORTANCE
Microbes in the genus
Pneumocystis
are obligate pathogenic fungi that reside in mammalian lungs and cause
Pneumocystis
pneumonia in hosts with weakened immune systems. These fungal infections are not responsive to standard antifungal therapy. A long-term
in vitro
culture system is not available for these fungi, impeding the study of their biology and genetics and new drug development. Given that all genomes of the
Pneumocystis
species analyzed lack the genes for inositol synthesis and contain inositol transporters,
Pneumocystis
fungi, like
S. pombe
, appear to be inositol auxotrophs. Inositol is important for the pathogenesis, virulence, and mating processes in
Candida albicans
and
Cryptococcus neoformans
, suggesting similar importance within the
Pneumocystis
species as well. This is the first report to (i) characterize genes in the inositol phosphate metabolism and transport pathways in
Pneumocystis
species and (ii) identify inositol as a supplement that improved the viability of
P. carinii
in
in vitro
culture.