Among the three genomes of the plant cell, the plastome is the most gene-dense one with more than 100 genes in a genome of typically only 120 to 160 kb (Sugi-ura 1989, 1992; Wakasugi et al. 2001; Fig.1; Table 1). The plastid genome is the evolutionary remnant of a cyanobacterial genome. After endosymbiosis, the genome has undergone a dramatic size reduction and, thus, contemporary plastomes contain only a small proportion of the genes of their free-living cyanobacterial ancestors. Whereas the genome of the cyanobacterium Synechocystis contains more than 3000 genes (Kaneko et al. 1996; Kaneko and Tabata 1997), the plastid genomes of land plants harbor only approximately 115 genes.
Very obviously, the limited coding capacity of the plastome is by far insufficient to provide the thousands of components required to support its own gene expression system, photosynthesis and all the many other plastid-localized metabolic functions. Therefore, all cellular functions fulfilled by present-day plastids are strictly dependent upon the products of nuclear genes that are synthesized on cy-
toplasmic ribosomes and post-translationally imported into the organelle. Nuclear-encoded proteins make up the by far largest fraction of the plastid proteome (Abdallah et al. 2000; Rujan and Martin 2001; Martin et al. 2002; Hippler and Bock 2004) and it is estimated that chloroplasts import more than 95 % of their proteins from the cytosol. Consequently, the spatial and temporal expression of nuclear and organellar genes must be tightly coordinated.
Plastid-encoded genes can be roughly classified into three major groups (Shi-mada and Sugiura 1991; Kahlau et al. 2006): genetic system genes, photosynthesis-related genes and other genes. The approximately 60 genetic system genes contained in land plant plastomes encode RNA and protein components of the plastid's gene expression machinery (Fig. 1; Table 1). Approximately 50 plastid genes encode protein products involved in photosynthesis (Fig. 1; Table 1). The heterogeneous third gene group comprises all other genes and conserved open reading frames of unknown function.
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