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
