Proteome Map of the Chloroplast Lumen of Arabidopsis thaliana

Abstract

The thylakoid membrane of the chloroplast is the center of oxygenic photosynthesis. To better understand the function of the luminal compartment within the thylakoid network, we have carried out a systematic characterization of the luminal thylakoid proteins from the model organism Arabidopsis thaliana. Our data show that the thylakoid lumen has its own specific proteome, of which 36 proteins were identified. Besides a large group of peptidyl-prolyl cis-trans isomerases and proteases, a family of novel PsbP domain proteins was found. An analysis of the luminal signal peptides showed that 19 of 36 luminal precursors were marked by a twin-arginine motif for import via the Tat pathway. To compare the model organism Arabidopsis with another typical higher plant, we investigated the proteome from the thylakoid lumen of spinach and found that the luminal proteins from both plants corresponded well. As a complement to our experimental investigation, we made a theoretical prediction of the luminal proteins from the whole Arabidopsis genome and estimated that the thylakoid lumen of the chloroplast contains ϳ80 proteins.The ability to perform oxygenic photosynthesis belongs to the distinguishing characteristics of higher plants, algae, and cyanobacteria. In higher plants, the center of the photosynthetic process is the thylakoid membrane of the chloroplast. Here, in a synergistic series of reactions, four protein complexes, the photosystems I and II, the cytochrome b 6 f complex, and the ATP-synthase, produce NADPH and ATP that fuel the further synthesis of carbohydrates (1, 2).A key feature in the energy conversion of photosynthesis is the link between the electron transfer from photosystem II to I via the cytochrome b 6 f complex and the generation of a proton gradient over the thylakoid membrane. To balance the flow of electrical charges during the formation of the proton gradient, there is a busy traffic of chloride and calcium ions from the stroma into the lumen and of magnesium ions from the lumen into the stroma (3-6). This ion traffic plays a fundamental role for the proper function of photosynthesis. For a long time it was believed that accumulating protons and balancing the ion currents over the thylakoid membrane was the main function of the luminal compartment. The ensemble of known luminal proteins was small and consisted of the three extrinsic photosystem II proteins (PsbO, PsbP, and PsbQ) and plastocyanin. This group was later joined by some new proteins such as violaxanthin de-epoxidase (7), polyphenol oxidase (8, 9), the extrinsic photosystem I protein PsaN (10), and the carboxylterminal processing protease for the D1 protein (11).To achieve a more profound understanding of content and functions of the thylakoid lumen, we designed a method that enabled us to isolate a highly pure fraction of luminal proteins from spinach thylakoids. For the first time, we showed that the lumen of the thylakoid membrane contained at least 20 proteins and that the protein concentration of this compartment was similar to tha...

The major peptidyl‐prolyl isomerase activity in thylakoid lumen of plant chloroplasts belongs to a novel cyclophilin TLP20

“…These precursor proteins contain chloroplast targeting signal peptides and the mature homolog of TLP20 has recently been found among the proteins of the thylakoid lumen of Arabidopsis by proteomic analysis [6]. Our ¢nding of the unique three amino acid insert NPV in the amino-termini of the TLP20 proteins from spinach, rice and Arabidopsis provides a strong argument for the similarity of these particular lumenal cyclophilins.…”

“…The ChloroP algorithm predicted the signal peptide cleavage site at amino acids 56^57 and 70^71 for the precursor proteins from rice and Arabidopsis, respectively. However, the recent N-terminal sequencing of the Arabidopsis protein found in the thylakoid lumen [6] revealed the real cleavage site between amino acids 75 and 76, as indicated by the arrow in Fig. 4.…”

“…The genome-based analysis by the same authors predicted as many as 10 PPIases in the lumen [6]. The study by Peltier and colleagues [5] identi¢ed ¢ve and predicted at least four additional putative PPIases in the same compartment.…”

AtCCS is a functional homolog of the yeast copper chaperone Ccs1/Lys7

“…Arabidopsis expresses two plastocyanin genes, that are closely related in sequence [31,32]. Silencing of both copies of plastocyanin leads to a very severe growth phenotype [33] and plants with insertions in both plastocyanin genes cannot be maintained on soil [30].…”

An improved prediction of chloroplast proteins reveals diversities and commonalities in the chloroplast proteomes of Arabidopsis and rice

“…Relatively small sub-proteomes of the chloroplast have been experimentally identified (Kieselbach et al, 1998;Nakabayashi et al, 1999;Peltier et al, 2000;Ferro et al, 2002;Gomez et al, 2002;Peltier et al, 2002;Schubert et al, 2002;Balmer et al, 2003;Ferro et al, 2003;Schleiff et al, 2003), but a saturating organelle-wide proteomic screen has not yet been performed. Thus, large-scale detection of chloroplast proteins can be attempted only in silico.…”