Plants must acclimate to dynamic light environments to maintain photosynthetic efficiency. Under high-light conditions, the rapid induction of NPQ is essential for the dissipation of excess excitation energy. Understanding the molecular mechanism of NPQ is a prerequisite for engineering crops with optimised photoprotective responses. Although the PsbS protein has been identified as a key pH-sensor for NPQ, its precise mechanism of action remains debated despite more than two decades of research. This thesis investigates the molecular interactions of NPQ components to clarify some of the unresolved aspects of the NPQ mechanism. In Chapter 2, we examine the differences in NPQ mechanisms between Chlamydomonas and Arabidopsis. We show that LHCII trimers do not switch into a quenched state after protonation, either in detergent or in a more native lipid environment within liposomes. Furthermore, we demonstrate that protonation of the possible pH-sensing amino acids in Lhcb1 is not required to restore NPQ in vivo, suggesting that LHCII is not able to sense low pH by itself. In Chapter 3, we extend our analysis beyond LHCII trimers to include monomeric Lhcb proteins. We investigate pH-induced quenching changes in these complexes and evaluate how the surrounding lipid environment influences their quenching behaviour. In Chapter 4, we explore potential interaction partners of PsbS. Using a chemical crosslinker, we compare thylakoid protein interactions under dark and NPQ conditions to identify possible interaction changes associated with NPQ activation. In Chapter 5, we assess whether a covalently linked PsbS dimer is still capable of contributing to NPQ. We demonstrate that PsbS dimers are capable of inducing NPQ, however, with reduced efficiency compared to WT. This stoichiometric reduction suggests that only one monomeric unit within the dimer is actively engaging in quenching interactions.
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