Journal Article

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

Walsh, Laura, Zeng, Qiandong, Ma, Liang, Bishop, Lisa, Lempicki, Richard A., Hu, Xiaojun, Kovacs, Joseph A., Raley, Castle, Huang, Da Wei, Gogineni, Emile, Levin, Joshua Z., Huber, Charles, Song, Xiaohong, Birren, Bruce W., Nusbaum, Chad, Fan, Lin, Young, Sarah, Cuomo, Christina A., Deng, Rebecca, Xia, Yun, Fitzgerald, Michael, Zheng, Xin, Wang, Honghui, Sykes, Sean, Chen, Zehua, Yang, Jun, Macdonald, Pendexter, Sherman, Brad T., Goldberg, Jonathan M., Stephens, Robert, Sassi, Monica, Fantoni, Giovanna, Jones, Kristine, Ishihara, Mayumi, Abouelleil, Amr, Handley, Grace, Tran, Bao, Deng, Xilong, Liu, Yueqin, Melnikov, Alexandre, Davey, Emma, Azadi, Parastoo, Kutty, Geetha, Jiao, Xiaoli

2016

Overview

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. Pneumocystis jirovecii is a fungus that can cause life-threatening pneumonia in immunocompromised patients. Here, the authors sequence the genomes of P. jirovecii and two other Pneumocystis species, and show the unexpected absence of chitin (a near universal fungal cell wall component).

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 631/208/212 / 631/326/193/2484 / 692/699/255/1672 / 82 / 82/58 / Adaptation, Biological / Animals / Cell Wall - metabolism / Chitin / Genome, Fungal / Host-Pathogen Interactions - genetics / Humanities and Social Sciences / Humans / Lung - microbiology / Mammals / Metabolic Networks and Pathways - genetics / Mice / multidisciplinary / Multigene Family / Pneumocystis carinii - genetics / Pneumocystis carinii - metabolism / Rats / Science / Science (multidisciplinary) / Synteny