Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts

Nature Communications
Liang MaJ A Kovacs

Abstract

Pneumocystis jirovecii is a major cause of life-threatening pneumonia in immunosuppressed patients including transplant recipients and those with HIV/AIDS, yet surprisingly little is known about the biology of this fungal pathogen. Here we report near complete genome assemblies for three Pneumocystis species that infect humans, rats and mice. Pneumocystis genomes are highly compact relative to other fungi, with substantial reductions of ribosomal RNA genes, transporters, transcription factors and many metabolic pathways, but contain expansions of surface proteins, especially a unique and complex surface glycoprotein superfamily, as well as proteases and RNA processing proteins. Unexpectedly, the key fungal cell wall components chitin and outer chain N-mannans are absent, based on genome content and experimental validation. Our findings suggest that Pneumocystis has developed unique mechanisms of adaptation to life exclusively in mammalian hosts, including dependence on the lungs for gas and nutrients and highly efficient strategies to escape both host innate and acquired immune defenses.

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Datasets Mentioned

BETA
ERR135863
M57601.1
SRX248091
SRX1435036
SRX387635
SRX387636
SRX387638
PRJNA292577
PRJNA70803
PRJNA223511

Methods Mentioned

BETA
RNA-Seq
glycosylation
genotyping
PCR
454 sequencing
electrophoresis
chip
density gradient centrifugation 60
acetylation

Software Mentioned

GATK UnifiedGenotyper
PrintReads
IndelRealigner
CreateSequenceDictionary
BWA
LG
GSEA
UnifiedGenotyper
BaseRecalibrator
Byonic Protein Metrics

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