Comparative genomics suggests primary homothallism of Pneumocystis species

Abstract

Pneumocystis species are fungal parasites of mammal lungs showing host specificity. Pneumocystis jirovecii colonizes humans and causes severe pneumonia in immunosuppressed individuals. In the absence of in vitro cultures, the life cycle of these fungi remains poorly known. Sexual reproduction probably occurs, but the system of this process and the mating type (MAT) genes involved are not characterized. In the present study, we used comparative genomics to investigate the issue in P. jirovecii and Pneumocystis carinii, the species infecting rats, as well as in their relative Taphrina deformans. We searched sex-related genes using 103 sequences from the relative Schizosaccharomyces pombe as queries. Genes homologous to several sex-related role categories were identified in all species investigated, further supporting sexuality in these organisms. Extensive in silico searches identified only three putative MAT genes in each species investigated (matMc, matMi, and matPi). In P. jirovecii, these genes clustered on the same contig, proving their contiguity in the genome. This organization seems compatible neither with heterothallism, because two different MAT loci on separate DNA molecules would have been detected, nor with secondary homothallism, because the latter involves generally more MAT genes. Consistently, we did not detect cis-acting sequences for mating type switching in secondary homothallism, and PCR revealed identical MAT genes in P. jirovecii isolates from six patients. A strong synteny of the genomic region surrounding the putative MAT genes exists between the two Pneumocystis species. Our results suggest the hypothesis that primary homothallism is the system of reproduction of Pneumocystis species and T. deformans.

Importance: Sexual reproduction among fungi can involve a single partner (homothallism) or two compatible partners (heterothallism). We investigated the issue in three pathogenic fungal relatives: Pneumocystis jirovecii, which causes severe pneumonia in immunocompromised humans; Pneumocystis carinii, which infects rats; and the plant pathogen Taphrina deformans. The nature, the number, and the organization within the genome of the genes involved in sexual reproduction were determined. The three species appeared to harbor a single genomic region gathering only three genes involved in sexual differentiation, an organization which is compatible with sexual reproduction involving a single partner. These findings illuminate the strategy adopted by fungal pathogens to infect their hosts.

FIG 1

Multiple sequence alignment of S. pombe matMc (A) and matPi (B) proteins against homologs identified in P. carinii, P. jirovecii, and T. deformans. The identical, strongly, and weakly conserved residues identified using T-Coffee (47) are indicated by asterisks, double points, and single points, respectively. Dashes indicate gaps. The high-mobility group and homeobox domains are shown in panels A and B, respectively.

FIG 2

Phylogeny of the MAT genes of S. pombe, P. jirovecii, P. carinii, and T. deformans. The maximum likelihood method based on the JTT matrix-based model (48) was used to infer the evolutionary history of matMc, matMi, and matPi genes.

FIG 3

Schematic representation of the MAT loci of S. pombe, P. jirovecii, P. carinii, and T. deformans. Genes are shown in green, and their synteny with those of the other species is shown by the yellow rectangles. The sequence contigs carrying the genes are shown as gray lines. The centromere-homologous sequence (cenH) is shown in blue. The cis-acting sequence motifs H1, H2, and H3 involved in mating type switching in S. pombe are shown in light brown. The gene name or detected domain name is indicated for each identified open reading frame.