Prions are self-propagating amyloids. Yeast prion [PSI+] is a protein-based heritable element, in which amyloid aggregates of the Sup35 protein are transmitted to daughter cells. Hsp104, an ATP-dependent disaggregase, and other chaperones are essential to maintain [PSI+] Although previous reports have demonstrated the physical interactions of Hsp104 and Sup35 amyloids, the mechanism how Hsp104 interacts with Sup35 amyloids remains to be elucidated. Here we investigated the interaction between Hsp104 and Sup35 in the lysates of [PSI+] cells using fluorescence cross-correlation spectroscopy (FCCS), which can analyze the codiffusion events of different fluorophores. FCCS analysis showed a strong interaction between Hsp104 and Sup35 in [PSI+] lysates, but not in [psi(-)] lysates, suggesting that Hsp104 recognizes the amyloid aggregates of Sup35. Although the interaction was retained in ATP-depleted [PSI+] lysates, addition of ATP or guanidine hydrochloride, which is an inhibitor of Hspl 04, to [PSI+] lysates weakened the interaction. (C) 2013 Elsevier Inc. All rights reserved.