Genetic system genes

The genetic system genes comprise the largest group of genes located on higher plant plastomes (62 genes; Table 1). To this group belong all genes whose products are involved in plastid gene expression (i.e. transcription, RNA processing, translation, protein degradation): 30 tRNA genes, four rRNA genes, 21 genes for ribosomal proteins (nine proteins of the large subunit and twelve proteins of the small subunit of the plastid 70S ribosome), four genes for subunits of the E. coli-like plastid RNA polymerase (PEP), matK suggested to encode an RNA maturase (i.e. a splicing factor involved in the removal of a subset of chloroplast group II introns; Hess et al. 1994; Liere and Link 1995; Mohr et al. 1993; Jenkins et al. 1997), clpP encoding a subunit of a chloroplast protease (Shanklin et al. 1995; Majeran et al. 2000) and infA encoding translation initiation factor IF-1 (Sijben-Muller et al. 1986).

A complete set of tRNAs for decoding all triplets in protein-coding genes is thought to comprise 32 tRNA species. Although only 30 tRNA genes are encoded in the plastome, they are nonetheless believed to be sufficient to read all codons (Jukes and Osawa 1990; Osawa et al. 1992). This is presumably achieved by an extended wobbling (referred to as 'four-way wobble') between the third codon position and the 5' nucleotide of the anticodon in the tRNA. In the case of the four alanine codons (GCU, GCC, GCA and GCG), for example, this means that the U in the first anticodon position of the single tRNA-Ala species (trnA-UGC; Table 1) can probably basepair with all four possible nucleotides in third codon position of the alanine triplets (Jukes and Osawa 1990; Osawa et al. 1992).

Remarkable differences between species exist concerning the essentiality of the plastid gene expression apparatus. Plastid translation has been demonstrated to be essential for cell survival in tobacco (Ahlert et al. 2003; Rogalski et al. 2006), but appears to be non-essential under heterotrophic culture conditions in at least some Brassicaceae species (Zubko and Day 1998, 2002) and probably also in some cereals (Hess et al. 1993, 1994).

While the RNA components of the gene expression machinery (rRNAs and tRNAs) are exclusively encoded in the plastid genome (Lung et al. 2006), many of the protein components are encoded by nuclear genes. For example, only about one third of the plastid ribosomal proteins is plastome encoded in higher plants, the other two thirds are nuclear-encoded, made in the cytosol and imported into the plastid. A similar division of labor between the nucleus and the plastid occurs in the coding of the transcriptional apparatus. The four core subunits of the E. coli-

like plastid RNA polymerase (plastid-encoded RNA polymerase, PEP) are encoded in the plastome, but the sigma factors, which are required for promoter recognition, are encoded in the nuclear genome. In addition, a second RNA-synthesizing activity in the plastid (nuclear-encoded RNA polymerase, NEP) provided by bacteriophage-type enzymes is encoded by nuclear genes (Hedtke et al. 1997; Hess and Börner 1999).

While in angiosperm plants, the set of genes encoded in the plastome is usually highly conserved between species, a small number of genetic system genes, including rpl23 and infA (Table 1), provide notable exceptions in that they have been transferred to the nucleus or replaced by nuclear genes of non-plastid origin in some lineages of evolution (Bubunenko et al. 1994; Millen et al. 2001). The presence in the plastome of pseudogenic remnants of the genes suggests that these events occurred only relatively recently in evolution. The infA gene encoding the plastid translation initiation factor 1 provides a particularly striking example. It had long been known that infA, while being a functional gene in the plastome of the liverwort Marchantia polymorpha and the higher plant rice (Ohyama et al. 1986; Hiratsuka et al. 1989), exists only as a pseudogene in the tobacco ptDNA (Shinozaki et al. 1986; Shimada and Sugiura 1991). A systematic phylogenetic analysis of infA structure in the plastomes of angiosperms revealed that the gene has repeatedly become non-functional in approximately 24 separate lineages of angiosperm evolution. Search for nuclear infA copies in four of these lineages identified expressed nuclear infA genes whose gene products are targeted to plas-tids (Millen et al. 2001).

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