Mechanisms of surface antigenic variation in the 2 human pathogenic fungus Pneumocystis jirovecii

36 Microbial pathogens commonly escape the human immune system by varying surface proteins. 37 We investigated the mechanisms used for that purpose by Pneumocystis jirovecii. This 38 uncultivable fungus is an obligate pulmonary pathogen which causes pneumonia in immuno39 compromised individuals, a major life-threatening infection. Long-read PacBio sequencing was 40 used to assemble a core of subtelomeres of a single P. jirovecii strain from a bronchoalveolar 41 lavage fluid specimen of a single patient. A total of 113 genes encoding surface proteins were 42 identified, including 28 pseudogenes. These genes formed a subtelomeric gene superfamily 43 which included five families encoding adhesive GPI-anchored glycoproteins, and one family 44 encoding excreted glycoproteins. Numerical analyses suggested that diversification of the 45 glycoproteins relies on mosaic genes created by ectopic recombination, and occurs only within 46 each family. DNA motifs suggested that all genes are expressed independently, except those of 47 the family encoding the most abundant surface glycoproteins which are subject to mutually 48 exclusive expression. PCR analyses showed that exchange of the expressed gene of the latter 49 family occurs frequently, possibly favoured by the location of the genes proximal to the telomere 50 because this allows concomitant telomere exchange. Our observations suggest that (i) P. jirovecii 51 cell surface is made of a complex mixture of different surface proteins, with a majority of a 52 single isoform of the most abundant glycoprotein, (ii) genetic mosaicism within each family 53 ensures variation of the glycoproteins, and (iii) the strategy of the fungus consists in the 54 continuous production of new subpopulations composed of cells which are antigenically 55 different. 56 peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/158881 doi: bioRxiv preprint first posted online Jul. 3, 2017;