Diversity and complexity of the large surface protein family in the compacted genomes of variousPneumocystisspecies

Abstract

Supplemental Materials: 1 Text file (Text S1) 43 2 Tables (S1-S2) 44 13 Figures (S1-S13) 45 8 Data Sets (Msg sequences for different families) 46 47 48 Pneumocystis, a major opportunistic pathogen in patients with a broad range of 49 immunodeficiencies, contains abundant surface proteins encoded by a multi-copy gene family, 50 termed the major surface glycoprotein (Msg) gene superfamily. This superfamily has been 51 identified in all Pneumocystis species characterized to date, highlighting its important role in 52 Pneumocystis biology. In this report, through a comprehensive and in-depth characterization of 53 459 msg genes from 7 Pneumocystis species, we demonstrate, for the first time, the phylogeny 54 and evolution of conserved domains in Msg proteins, and provide detailed description of the 55 classification, unique characteristics and phylogenetic relatedness of five Msg families. We 56 further describe the relative expression levels of individual msg families in two rodent 57 Pneumocystis species, the substantial variability of the msg repertoires in P. carinii from 58 laboratory and wild rats, and the distinct features of the expression site for the classic msg 59 genes in Pneumocystis from 8 mammalian host species. Our analysis suggests a wide variety 60 of functions for this superfamily, not only conferring antigenic variation to allow immune evasion 61 but also mediating life-stage development, optimizing cell mobility and adhesion, and adapting 62 to specific host niches or environmental conditions. This study provides a rich source of 63 information that lays the foundation for the continued experimental exploration of the functions 64 of the Msg superfamily in Pneumocystis biology. 66Pneumocystis continues to be a major cause of disease in humans with 67 immunodeficiencies, especially those with HIV/AIDS and organ transplants, and is being seen 68 with increasing frequency in patients treated with immunodepleting monoclonal antibodies. As 69 an atypical fungus, Pneumocystis has highly adapted to the mammalian lung environment (1), 70 with a high level of host specificity; P. jirovecii infects humans, P. carinii infects Norway rats 71 (Rattus norvegicus), and P. murina infects house mice (Mus musculus). In addition, 72Pneumocystis cell walls are structurally unique and differ significantly from typical fungal cell 73 walls that are comprised of polysaccharides (mainly glucan and chitin) and highly mannosylated 74 proteins. Both genomic and experimental analyses have shown the absence of chitin and outer 75 chain N-mannans in Pneumocystis cell walls (1). Furthermore, beta-1,3-glucan is absent in the 76 trophic form while present but masked in the cyst form of Pneumocystis (2). 77An integral component of the Pneumocystis cell wall in both the cyst and trophic forms is 78 the major surface glycoprotein (Msg) (also known as gp95, gp115, gp120 and gpA) (3-8). Ever 79 since its identification in 1982 (9), Msg has been a focus of research, in part because it is the 80 most abundant Pneumocystis protein as as...