Chloroplasts are the site of photosynthesis, the conversion of solar energy to chemical energy. Photosynthesis consists of two stages, the light reactions and the dark reactions, both of which involve complex molecular machineries. A substantial number of plastome-encoded genes (47 genes in angiosperms; Table 1) is dedicated to the photosynthetic apparatus. These include fifteen genes for subunits of photosystem II (PSII), the membrane protein complex catalyzing the light-driven oxidation of water. The products of another seven genes are required for photosystem I (PSI) function, the membrane protein complex that catalyzes the light-driven transmembrane electron transfer from plastocyanin (or cytochrome c6) to the ferredoxin-NADP complex. In addition to five genes for subunits of the PSI complex, the seven PSI-related genes also include ycf3 and ycf4, two genes for proteins involved in PSI assembly (Ruf et al. 1997; Boudreau et al. 1997). Six plastid genes encode subunits of the cytochrome b6f complex, the redox-coupling protein complex interconnecting the two photosystems. Another six genes encode subunits of the chloroplast ATP synthase, the enzyme that catalyzes the conversion of phosphate and adenosine diphosphate into adenosine triphosphate utilizing a proton gradient across the thylakoid membrane as energy source. Eleven genes on the plastome encode subunits of a chloroplast NAD(P)H dehydrogenase, a thy-lakoid protein complex suggested to be involved in chlororespiration and cyclic electron flow around PSI (Burrows et al. 1998; Shikanai et al. 1998; Joet et al. 2001; Munekage et al. 2004). This complex is non-essential for photosynthesis and all genes for its subunits were found to be absent from the fully sequenced plastid genomes of the gymnosperm Pinus thunbergii and the green alga Chlamy-domonas reinhardtii (Wakasugi et al. 1994; Maul et al. 2002). Finally, two plas-tid-encoded gene products are directly or indirectly involved in the dark reactions: rbcL encoding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and ycf10, a conserved open reading frame encoding a chloroplast inner envelope membrane protein reportedly involved in inorganic carbon uptake (Sasaki et al. 1993a; Rolland et al. 1997).
None of the protein complexes involved in photosynthesis is composed entirely of plastome-encoded subunits. Instead, all of them require the products of nuclear genes which are of cyanobacterial origin and, during evolution, have been transferred from the plastid to the nuclear genome. The two-subunit enzyme Rubisco provides the classical example for this intimate plastid-nuclear cooperation. In all flowering plants, the large subunit of Rubisco is encoded in the plastome whereas the small subunit is encoded in the nuclear genome, typically by a small gene family.
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