A fusion protein of polyphosphate kinase 1 (PPK1) and a Nudix hydrolase is involved in inorganic polyphosphate accumulation in the unicellular red alga Cyanidioschyzon merolae.

Inorganic polyphosphate (polyP) is a linear polymer of phosphate that plays various roles in cells, including in phosphate and metal homeostasis. Homologs of the vacuolar transporter chaperone 4 (VTC4), catalyzing polyP synthesis in many eukaryotes, are absent in red algae, which are among the earliest divergent plant lineages. We identified homologs of polyphosphate kinase 1 (PPK1), a conserved polyP synthase in bacteria, in 42 eukaryotic genomes, including 31 species detected in this study and 12 species of red algae. Phylogenetic analysis suggested that most eukaryotic PPK1 homologs originated from horizontal gene transfer from a prokaryote to a plant before the divergence of red algae and Viridiplantae. In red algae, the homologs were fused to a nucleoside diphosphate-linked moiety X (Nudix) hydrolase of the diphosphoinositol polyphosphate phosphohydrolase (DIPP) family. We characterized the fusion protein CmPPK1 in the unicellular red alga Cyanidioschyzon merolae, which has been used in studies on basic features of eukaryotes. In the knockout strain ∆CmPPK1, polyP was undetectable, suggesting a primary role for CmPPK1 in polyP synthesis. In addition, ∆CmPPK1 showed altered metal balance. Mutations in the catalytically important residues of the Nudix hydrolase domain (NHD) either increased or decreased polyP contents. Both high and low polyP NHD mutants were susceptible to phosphate deprivation, indicating that adequate NHD function is necessary for normal phosphate starvation responses. The results reveal the unique features of PPK1 in red algae and promote further investigation of polyP metabolism and functions in red algae and eukaryotic evolution.