Here, we used a <i>vam6</i> deletion mutant to investigate the role of the homotypic fusion and vacuole protein sorting (HOPS) complex in mitochondrial functions and polyphosphate homeostasis in <i>Cryptococcus neoformans</i>, an important fungal pathogen of immunocompromised people including those suffering from HIV/AIDS. Here, VPS39 is linked to AIDS.