Flexible phosphorus allocation to the phosphoproteome underpins diatom regulatory adaptations to fluctuating phosphate supply

Diatoms are major drivers of marine phosphorus (P) cycling and are highly adapted to cope with variable P supply. P-starved diatoms can sense increases in P availability within seconds, accumulating this limiting resource through luxury polyphosphate (polyP) storage. Yet, how diatoms coordinate such responses is unknown. Protein phosphorylation is a core mechanism for environmental signal transduction in eukaryotes, but how cells balance investment in protein phosphorylation against competing physiological demands during P limitation is poorly understood. Here, we characterise system-wide remodelling of the Phaeodactylum tricornutum phosphoproteome in response to P deficiency and subsequent resupply. We identify widespread proteome dephosphorylation across 44% of phosphosites, revealing a previously unrecognised P-sparing strategy in marine phytoplankton. Following P resupply, diatoms orchestrate extensive phosphoproteome reprogramming within minutes. We characterise previously unrecognized components for early recovery from P limitation, including a novel environmentally prevalent intracellular H+/phosphate transporter strongly conserved in diverse diatoms. We also identify a vacuolar Ca2+-dependent protein kinase (CDPK) associated with polyP-storage granules. Mutant and inhibitor analyses demonstrate a role for Ca2+- and CDPK-signalling in the regulation of luxury polyP accumulation. Our findings reveal that recovery from P starvation is mediated by rapid phosphoregulatory control of intracellular P trafficking, organellar ATP generation coupled with luxury P storage, enabling diatoms to exploit newly available P and thrive in fluctuating P regimes. Collectively, our study uncovers the phosphoproteome as a flexible intracellular P reservoir and establishes mechanistic links between intracellular P budgeting, signalling and the marine P cycle.