The chloroplast lumen proteome of Arabidopsis thaliana

Abstract: In plants, the chloroplast organelles host the photosynthetic machinery, which catalyzes the conversion of light energy to chemical energy used for synthesis of carbohydrates. Inside the chloroplast, the lumen compartment forms an integral part of the thylakoid network that performs the light reactions of photosynthesis. Despite intensive research within the field of photosynthesis, the lumen located proteins were relatively unexplored. To get insight into the lumen proteins and their roles in photosynthesis this thesis aimed at characterising the chloroplast lumen proteome. A 2-dimensional protein map of the lumen proteome of Arabidopsis thaliana revealed a high protein content within this chloroplast compartment. Thirty-eight proteins were experimentally identified demonstrating that the chloroplast lumen contains it own specific proteome. Comparison of the Arabidopsis chloroplast lumen proteome with the spinach lumen proteome showed good correlation and demonstrated that Arabidopsis can serve as a model for characterising the lumen proteins. An in silico determination of the chloroplast lumen proteome from the Arabidopsis genome sequence data showed that the experimentally identified proteins are good representatives of the proteome. Combining the in silico proteome with the experimental proteome, the chloroplast lumen estimates to contain at least 80 different proteins. The putative ascorbate peroxidase TL29 detected in the thylakoid lumen was biochemically characterised. The protein associated to the PSII-enriched grana membrane fraction by electrostatic forces and accumulated upon high light illumination. Functional analysis showed that the TL29 protein is not a peroxidase but was able to bind ascorbate and may be involved in regulating the ascorbate levels in the chloroplast lumen. The dynamics of the lumen proteome were studied during the cold acclimation process. The lumen proteome was relatively insensitive to cold stress but important changes to the proteome were observed in the long-term developmental response to cold. These included changes in abundance of the different isoforms of the extrinsic PSII subunits, the PSII assembly factor Hcf136 and immunophilins. In comparison, the stroma proteome responded at an earlier stage in the acclimation process. Changes to the stroma proteome involved proteins related to photosynthesis, other plastid metabolism, hormone biosynthesis, and stress & signal transduction.