Proteomic analysis of acclimation in the Arabidopsis thaliana thylakoid membrane

Photosynthetic acclimation is the ability of photosynthetic organisms to respond to light irradiance by adjusting the composition of the thylakoid membrane to maintain photosynthetic efficiency. The work described in this thesis utilises mass spectrometry-based proteomics to quantify the changes in thylakoid protein abundance that occur during acclimation in Arabidopsis thaliana. A novel strategy for labelfree quantitative thylakoid proteomics was developed and combined with electron microscopy, structured illumination microscopy, and various biochemical and spectroscopic analyses to further our understanding of thylakoid proteome remodelling in response to environmental conditions. First, the thylakoid proteomes of Arabidopsis plants grown under low, moderate and high light intensity were compared. Arabidopsis grown outdoors in naturally fluctuating light conditions were then investigated to identify mechanisms particularly important for photosynthesis in the field. Finally, the phosphorylation mutants stn7 and tap38, the former previously reported as defective in long term acclimation, grown under different light irradiances were subjected to proteomic analysis, as well as the proton gradient regulation mutant pgr5. The results of this thesis revealed changes in protein abundance associated with light harvesting, electron transfer, thylakoid architecture and photoprotection. STN7 is not essential for acclimation but the effects of perturbed LHCII (de)phosphorylation on grana size and light harvesting are compensated for by alterations to photosystem stoichiometry. While phosphorylation regulates dynamic thylakoid stacking, proteomic analysis revealed changes in CURT1 and RIQ1/2 protein abundance associated with long term alterations in grana size. Low light plants maintain fast relaxation of quenching whereas plants acclimated to high light intensity increase their capacity for linear electron transfer and rapid induction of quenching. Constant light acclimated plants favour PGR5/PGRL1-mediated cyclic electron transfer while those in a natural environment focus on increasing NDH. While individual changes in thylakoid protein abundance have been studied extensively in the past, this data, which includes many regulatory proteins not previously quantified, provides a view of thylakoid proteome remodelling in unprecedented detail.