In higher plants, chloroplasts are the site for the photosynthetic reactions, converting solar energy to chemical energy. Within the chloroplast the thylakoid membrane network encloses the soluble lumen compartment. Until recently the knowledge of the lumen composition and function was limited, but a more profound understanding of the thylakoid lumen content is gradually emerging. The discovery that the thylakoid lumen contains numerous enzymes, besides the already known proteins directly involved or associated with the photosynthetic reactions, have changed the view on this compartment.

The first part of the thesis the lumen proteome maps of Arabidopsis and spinach were resolved. These two proteome maps showed good correlation and the same protein groups were represented in the two proteomes. Thirty eight proteins were identified and in combination with an in silico prediction for the proteome it was estimated that at least 80 different proteins are lumen located.

The second part was to further investigate the functions of two lumen localized proteins, the cyclophilin AtCYP20-2 and peroxiredoxin Q (PrxQ). AtCYP20-2 is suggested to be responsible for the major peptidyl prolyl cis/trans isomerases (PPIase) activity in the lumen. In AtCYP20-2 knockout mutants the total PPIase activity is not altered, instead AtFKBP13 may be oxidatively activated to compensate for the loss of AtCYP20-2. With respect to the PrxQ protein we were able to show that it is a lumenal protein that seems to exist as a soluble pool in the lumen as no interaction with the thylakoid membrane could be detected.

In the last part of this thesis the dynamics of the thylakoid membrane and lumen proteome were studied during oxidative stress. Important changes to the proteome were observed in response to the stress treatment, including abundance changes of proteins related to photosynthesis, as well as proteins not previously identified in relation to stress.