How host-like signals drive gene expression and gene expression drives capsule expansion in Cryptococcus neoformans .

Cryptococcus neoformans is an opportunistic fungal pathogen with a polysaccharide capsule that becomes greatly enlarged in the mammalian host and during in vitro growth in response to host-like conditions. To understand how individual host-like signals affect capsule size and gene expression, we grew cells with and without all combinations of 5 signals suspected of affecting capsule size and systematically measured cell and capsule sizes of 47,458 cells. We also collected samples for RNA-Seq at 30, 90, 180, and 1440 minutes and carried out RNA-Seq in quadruplicate, yielding 881 RNA-Seq samples. This massive, uniformly collected dataset will be a significant resource for the research community. Analysis revealed that capsule induction requires both tissue culture medium and either CO 2 or exogenous cyclic AMP, a second messenger. Rich medium (YPD) blocks capsule growth completely, DMEM permits it, and RPMI yields the largest capsules. Medium has the biggest impact on overall gene expression, followed by CO 2 , mammalian body temperature (37° compared to 30°), and then cAMP. Surprisingly, adding CO 2 or cAMP pushes overall gene expression in the opposite direction from tissue culture media, even though both tissue culture medium and CO 2 or cAMP are required for capsule development. By modeling the relationship between gene expression and capsule size, we identified novel genes whose deletion affects capsule size.