Systematic profiling of WD40 proteins reveals Wcp1, a cyclophilin linking CO 2 /heat tolerance to acidic pH adaptation in Cryptococcus neoformans

Abstract WD40 domains are major protein–protein interaction (PPI) scaffolds, yet their contributions to fungal pathogenicity remain poorly defined. We systematically analysed 94 canonical WD40 proteins in Cryptococcus neoformans. Conditional knockdown and sporulation identified 36 essential WD40 proteins, while in vitro and in vivo profiling of 103 signature-tagged deletion strains spanning 52 genes uncovered 31 pathogenicity-related WD40 proteins, including epigenetic and post-transcriptional regulators. We identified Wcp1, a dual-domain protein whose WD40-repeat and cyclophilin domains are required for growth at 37°C under 5% CO2. Its WD40 scaffold and PPIase domain supported CO2/heat tolerance and virulence. Notably, Wcp1 couples these functions to acidic pH adaptation: wcp1Δ failed to grow under elevated temperature and CO2 at acidic pH, exhibited enhanced intracellular acidification, reduced macrophage survival and attenuated virulence in Drosophila and mice. Integrated transcriptomic and proteomic analyses place Wcp1 at the centre of intracellular pH homeostasis, coordinating proton transport, metabolic adaptation and stress-buffering networks. Competing Interest Statement Industry-Academic Cooperation Foundation of Yonsei University, AmtixBio Co., Ltd. and Industry Cooperation Foundation of Jeonbuk National University have filed patent applications related to the WD40 proteins of Cryptococcus neoformans and their uses described in this manuscript (Korean patent application no. 10-2025-0039994; PCT application no. PCT/KR2025/003983), on which J.-T.C., S.-R.Y., J.O., Y.-B.J., Y.L., J.-S.L., K.-T.L., and Y.-S.B. are listed as inventors. Y.-S.B. and J.-S.L. are scientific co-founder and chief executive officer, respectively, of AmtixBio, Co., Ltd. Y.-S.B. and J.-S.L. are stock holders of AmtixBio, Co., Ltd. AmtixBio, one of the funders, played a role in the conceptualisation of this manuscript. All other authors declare no competing interests.