Before revision:  Among the few genes lost are both eukaryotic clpB orthologs, HSP104 and HSP78  , which encode amyloid disaggregases. Despite their ancient origins in the eukaryotic and mitochondrial primogenitors, we find that both clpB loci of Saccharomyces share a promoter signature that is specific to 7 genes involved in prion homeostasis.
After revision:  Among the few genes lost are both eukaryotic clpB orthologs, HSP104 and HSP78 , which encode protein disaggregase type chaperones. Finally, we find that in choanoflagellates and fungi the clpB genes and a small repertoire of refolding chaperones are co-regulated by the heat shock element HSE4 that can be bound by two Hsf1 trimers. Based on these findings, we propose that loss of branched chain biosynthetic genes in the holozoan radiation represents an initial pattern of loss that foreshadows the wholesale loss of metabolic genes in the eukaryotic and mitochondrial primogenitors, we find that both clpB loci of Saccharomyces share a promoter signature that is specific to 7 genes involved in prion homeostasis.