A photoprotection dial maps holistic light-stress response in diatoms

Cellular responses to light stress operate on two timescales: short-term responses, driven by dynamic photosynthetic mechanisms such as non-photochemical quenching (NPQ), and long-term responses, characterized by various physiological and metabolic shifts driven by changes in gene expression. Understanding the coordination within and between these layers represents a major challenge in photosynthesis research. We achieved this in the diatom Phaeodactylum tricornutum using an adjustable "photoprotection dial" across 10 mutant strains expressing different constitutive levels of the Lhcx1 protein, which determine their latent NPQ capacity. Crucially, a near-identical initial state is preserved among strains, which allows a precise mapping of the causal chain of events initiated by NPQ induction under high light. This unlocks exceptional leverage to examine holistic interactions between functional photosynthesis and gene expression within their natural regulatory architecture. We observe that increasing NPQ maintains the PSII primary acceptor QA in a more oxidized state with little effect on linear electron flow. This oxidation limits PSII photodamage and promotes cyclic electron flow around PSI, which in turn is consistent with enhanced ATP production supporting PSII repair. Moreover, transcriptomic analysis across high-light exposure time suggests that the expression of nearly half of the genome is modulated via NPQ-driven effects. Gene expression profile clustering reveals distinct and coherent transcriptomic regulatory networks. The short-term response is characterized by a strong downregulation of light-harvesting-related genes -- independently of NPQ -- and an upregulation of oxidative stress response genes that scales inversely with NPQ magnitude. In the long term, most of the transcriptome is deeply impacted by high-light stress in a widely NPQ-dependent manner, highlighting the critical role of this process in shaping photophysiology, which in turn influences gene expression. By engineering a native functional feedback loop into an experimental dial, our approach establishes a generalizable framework for studying the complex interplay between physiology and system-wide biological regulation.