Proteomic analysis of Dhh1 complexes reveals a role for Hsp40 chaperone Ydj1 in yeast P-body assembly

P-bodies (PB) are ribonucleoprotein (RNP) complexes that aggregate into cytoplasmic foci
when cells are exposed to stress. While the conserved mRNA decay and translational
repression machineries are known components of PB, how and why cells assemble RNP
complexes into large foci remain unclear. Using mass spectrometry to analyze proteins
immunoisolated with the core PB protein Dhh1, we show that a considerable number of
proteins contain low-complexity (LC) sequences, similar to proteins highly represented in
mammalian RNP granules. We also show that the Hsp40 chaperone Ydj1, which contains
an LC domain and controls prion protein aggregation, is required for the formation of
Dhh1-GFP foci upon glucose depletion. New classes of proteins that reproducibly coenrich
with Dhh1-GFP during PB induction include proteins involved in nucleotide or
amino acid metabolism, glycolysis, tRNA aminoacylation, and protein folding. Many of
these proteins have been shown to form foci in response to other stresses. Finally,
analysis of RNA associated with Dhh1-GFP shows enrichment of mRNA encoding the PB
protein Pat1 and catalytic RNAs along with their associated mitochondrial RNA-binding
proteins. Thus, global characterization of PB composition has uncovered proteins
important for PB assembly and evidence suggesting an active role for RNA in PB function.