Chloroplasts were once free-living cyanobacteria that became endosymbionts, but the genomes of contemporary plastids encode only Ϸ5-10% as many genes as those of their free-living cousins, indicating that many genes were either lost from plastids or transferred to the nucleus during the course of plant evolution. Previous estimates have suggested that between 800 and perhaps as many as 2,000 genes in the Arabidopsis genome might come from cyanobacteria, but genome-wide phylogenetic surveys that could provide direct estimates of this number are lacking. We compared 24,990 proteins encoded in the Arabidopsis genome to the proteins from three cyanobacterial genomes, 16 other prokaryotic reference genomes, and yeast. Of 9,368 Arabidopsis proteins sufficiently conserved for primary sequence comparison, 866 detected homologues only among cyanobacteria and 834 other branched with cyanobacterial homologues in phylogenetic trees. Extrapolating from these conserved proteins to the whole genome, the data suggest that Ϸ4,500 of Arabidopsis protein-coding genes (Ϸ18% of the total) were acquired from the cyanobacterial ancestor of plastids. These proteins encompass all functional classes, and the majority of them are targeted to cell compartments other than the chloroplast. Analysis of 15 sequenced chloroplast genomes revealed 117 nuclear-encoded proteins that are also still present in at least one chloroplast genome. A phylogeny of chloroplast genomes inferred from 41 proteins and 8,303 amino acids sites indicates that at least two independent secondary endosymbiotic events have occurred involving red algae and that amino acid composition bias in chloroplast proteins strongly affects plastid genome phylogeny.

Illumination changes elicit modifications of thylakoid proteins and reorganization of the photosynthetic machinery. This involves, in the short term, phosphorylation of photosystem II (PSII) and light-harvesting (LHCII) proteins. PSII phosphorylation is thought to be relevant for PSII turnover 1,2 , whereas LHCII phosphorylation is associated with the relocation of LHCII and the redistribution of excitation energy (state transitions) between photosystems 3,4 . In the long term, imbalances in energy distribution between photosystems are counteracted by adjusting photosystem stoichiometry 5,6 . In the green alga Chlamydomonas and the plant Arabidopsis, state transitions require the orthologous protein kinases STT7 and STN7, respectively 7,8 . Here we show that in Arabidopsis a second protein kinase, STN8, is required for the quantitative phosphorylation of PSII core proteins. However, PSII activity under high-intensity light is affected only slightly in stn8 mutants, and D1 turnover is indistinguishable from the wild type, implying that reversible protein phosphorylation is not essential for PSII repair. Acclimation to changes in light quality is defective in stn7 but not in stn8 mutants, indicating that short-term and long-term photosynthetic adaptations are coupled. Therefore the phosphorylation of LHCII, or of an unknown substrate of STN7, is also crucial for the control of photosynthetic gene expression.STT7 and STN7 are orthologous protein kinases required for LHCII phosphorylation and for state transitions in Chlamydomonas and Arabidopsis, respectively 7,8 . In Arabidopsis, another STT7/STN7-like protein (STN8) exists that is not required for state transitions 8 . STN8 is located in the chloroplast, as shown by in vivo subcellular localization of its amino-terminal region fused to the dsRED protein and by the import of, and transit peptide removal from, STN8 translated in vitro (Fig. 1a, b). Chloroplast subfractionation after import revealed that the protein is associated, like STT7 and STN7, with thylakoids ( Fig. 1c) (refs 7, 8).Insertion mutants for STN8 and STN7 were obtained from the Salk collection 9 , and for each gene two independent mutant alleles lacking the respective transcript were identified (Supplementary Fig. S1). The stn7 stn8 double mutant was generated by crossing stn7 and stn8 single knockouts and screening the resulting F 2 generation for homozygous double mutants. All mutants were indistinguishable from the wild type with regard to the timing of seed germination and growth rate in the greenhouse ( Supplementary Fig. S1). In stn7 and stn7 stn8 mutants, a slight decrease in the levels of neoxanthin, lutein and total chlorophyll was found (Supplementary Table S1). These subtle changes can be attributed to a minor decrease in LHCII content, not detectable by polyacrylamide-gel electrophoresis (PAGE) analysis ( Supplementary Fig. S2).Photosynthetic electron flow, measured on the basis of chlorophyll fluorescence, was not altered in the mutants (Supplementary Table S2). State transitions w...

During photosynthesis, two photoreaction centers located in the thylakoid membranes of the chloroplast, photosystems I and II (PSI and PSII), use light energy to mobilize electrons to generate ATP and NADPH. Different modes of electron flow exist, of which the linear electron flow is driven by PSI and PSII, generating ATP and NADPH, whereas the cyclic electron flow (CEF) only generates ATP and is driven by the PSI alone. Different environmental and metabolic conditions require the adjustment of ATP/NADPH ratios and a switch of electron distribution between the two photosystems. With the exception of PGR5, other components facilitating CEF are unknown. Here, we report the identification of PGRL1, a transmembrane protein present in thylakoids of Arabidopsis thaliana. Plants lacking PGRL1 show perturbation of CEF, similar to PGR5-deficient plants. We find that PGRL1 and PGR5 interact physically and associate with PSI. We therefore propose that the PGRL1-PGR5 complex facilitates CEF in eukaryotes.

Mitochondrial DNA sequences are frequently transferred to the nucleus giving rise to the so-called nuclear mitochondrial DNA (NUMT). Analysis of 13 eukaryotic species with sequenced mitochondrial and nuclear genomes reveals a large interspecific variation of NUMT number and size. Copy number ranges from none or few copies in Anopheles, Caenorhabditis, Plasmodium, Drosophila, and Fugu to more than 500 in human, rice, and Arabidopsis. The average size is between 62 (baker's yeast) and 647 bps (Neurospora), respectively. A correlation between the abundance of NUMTs and the size of the nuclear or the mitochondrial genomes, or of the nuclear gene density, is not evident. Other factors, such as the number and/or stability of mitochondria in the germline, or species-specific mechanisms controlling accumulation/loss of nuclear DNA, might be responsible for the interspecific diversity in NUMT accumulation.