Sequence and structure of the linear mitochondrial genome of Pneumocystis carinii

Abstract

With the exception of a few genes, most of the mitochondrial (mt) genome of Pneumocystis carinii has not previously been sequenced. Shotgun sequences generated as a result of the Pneumocystis Genome Project (PGP) were assembled with the gap4 assembly program into a 23-kb contig. Annotation of the mt genome identified 4 open reading frames and 20 tRNAs in addition to 17 other genes: ATP synthase, subunits 6, 8, and 9; cytochrome c oxidase, subunits 1, 2, and 3; NADH dehydrogenase, subunits 1, 2, 3, 4, 4L, 5, and 6; apocytochrome b; RNase P RNA gene; and the mitochondrial large and small ribosomal RNA subunits. A 24-bp unit that repeated from one to five times was identified interior to the ends of the mt genome. Migration of the genome on CHEF gels was consistent with that of linear DNA and digestion with BAL31 showed a concomitant reduction in size of the genome, a characteristic of linear DNA. Together with the identification of terminal repeats similar to those found in other linear fungal mt genomes and the inability to join the ends by PCR, these data provide strong evidence that the mt genome of P. carinii is linear.

Ploidy of Cell-Sorted Trophic and Cystic Forms of Pneumocystis carinii

“…Nonetheless, we could not rule out the staining of mitochondrial DNA by the dye. As mitochondrial DNA is small (23 kb, [29]), its relative contribution to nuclear fluorescence intensity remains negligible. Moreover, computer-aided three-dimensional reconstruction showed that a unique mitochondrion is present in the studied life cycle parasite stages [30], [31], thus keeping the ratio mitochondrial-to-nuclear DNA content to one in these forms.…”

Characterizing Pneumocystis in the Lungs of Bats: Understanding Pneumocystis Evolution and the Spread of Pneumocystis Organisms in Mammal Populations

“…PCR products ranged from 252 to 333 bp (nested PCR at the mtLSU rRNA gene) and from 334 to 480 bp (nested PCR at the mtSSU rRNA gene). The sequences under analysis are part of the ribosome and are coded by the mitochondrial genome, and no introns were detected in the mitochondrial genome (82). Direct sequencing of PCR products revealed that each Pneumocystis mtLSU rDNA or mtSSU rDNA sequence could be associated with a unique bat species (Tables 9 and 10; Fig.…”

Genomic Insights into the Fungal Pathogens of the Genus Pneumocystis: Obligate Biotrophs of Humans and Other Mammals

“…Because of the low DNA purity, the assembly necessitated an innovative approach using iterative identification of the fungal homologies among the reads from the host and lung microbiota. The genome sequences of the mitochondria were also obtained from the same sequencings, as well as by PCR [4], [5].…”

“…The data of the mitochondrial genomes are from Sesterhenn et al [4] and Ma et al [5].bThe nuclear assemblies of the three species are considered to be incomplete and do not include repetitive elements.cThe numbers for P. jirovecii and P. carinii overestimate proteome size because some peptides are from incomplete coding DNA sequences at ends of contigs.dOnly complete copies in P. carinii assembly were considered.…”