Comparative genomics suggests that the fungal pathogen pneumocystis is an obligate parasite scavenging amino acids from its host's lungs

Abstract

Pneumocystis jirovecii is a fungus causing severe pneumonia in immuno-compromised patients. Progress in understanding its pathogenicity and epidemiology has been hampered by the lack of a long-term in vitro culture method. Obligate parasitism of this pathogen has been suggested on the basis of various features but remains controversial. We analysed the 7.0 Mb draft genome sequence of the closely related species Pneumocystis carinii infecting rats, which is a well established experimental model of the disease. We predicted 8'085 (redundant) peptides and 14.9% of them were mapped onto the KEGG biochemical pathways. The proteome of the closely related yeast Schizosaccharomyces pombe was used as a control for the annotation procedure (4'974 genes, 14.1% mapped). About two thirds of the mapped peptides of each organism (65.7% and 73.2%, respectively) corresponded to crucial enzymes for the basal metabolism and standard cellular processes. However, the proportion of P. carinii genes relative to those of S. pombe was significantly smaller for the "amino acid metabolism" category of pathways than for all other categories taken together (40 versus 114 against 278 versus 427, P<0.002). Importantly, we identified in P. carinii only 2 enzymes specifically dedicated to the synthesis of the 20 standard amino acids. By contrast all the 54 enzymes dedicated to this synthesis reported in the KEGG atlas for S. pombe were detected upon reannotation of S. pombe proteome (2 versus 54 against 278 versus 427, P<0.0001). This finding strongly suggests that species of the genus Pneumocystis are scavenging amino acids from their host's lung environment. Consequently, they would have no form able to live independently from another organism, and these parasites would be obligate in addition to being opportunistic. These findings have implications for the management of patients susceptible to P. jirovecii infection given that the only source of infection would be other humans.

Figure 1. Principle of the numerical experience used to optimize the precision and recall of the annotation predictions.

The S. pombe proteome (right box) was blasted against an intermediary set of fungal proteins, i.e. the proteome of S. cerevisiae in this example (middle box), and only the highest scoring blast matches were retained. By utilizing the S. cerevisiae mapping to the KEGG Orthologs (between the middle and left boxes), one can produce a mapping through S. cerevisiae of the S. pombe proteins to the KEGG Orthologs. The latter mapping can then be compared with the one that is actually provided by KEGG to compute precision and recall values. The experience was systematically repeated using different proteomes as intermediary data sets (or several proteomes at once), to eventually determine the optimal one.

Figure 2. Estimation of the quality of the mapping onto KEGG maps by performing a re-prediction of the annotation of S. pombe proteome through intermediary data set consisting of one, two, three, or 18 fungal proteomes.

The KO - S. pombe association pairs obtained by “blasting” an intermediary data set were evaluated a posteriori as true positive (TP) or false positive (FP) according to the KO - S. pombe mapping which is provided by KEGG. Those missed KO - S. pombe pairs existing in KEGG were taken as false negatives (FN). The overall quality of the obtained mapping can be expressed in terms of precision TP/(TP+FP) and recall TP/(TP+FN).