A small number of genes on the plastome of land plants are not directly involved in photosynthesis or gene expression. These include the accD gene, which encodes a subunit of acetyl-CoA carboxylase, the key enzyme in fatty acid biosynthesis (Sasaki et al. 1993b, 1995). A second example is ccsA (ycf5), the protein product of which is required for heme attachment to chloroplast c-type cytochromes (Orsat et al. 1992; Xie et al. 1998; Xie and Merchant 1996).
The plastome of pland plants also harbors a few conserved open reading frames (ORFs) of unknown function (Table 1). Interspecific conservation of an ORF is usually taken as good indication that it constitutes a genuine gene. In plastids, such conserved ORFs are referred to as ycf (hypothetical chloroplast reading frame). Although during recent years, the functions of most ycfs could be determined by reverse genetics in Chlamydomonas reinhardtii and tobacco (e.g. Monod et al. 1994; Ruf et al. 1997; Hager et al. 1999; reviewed in Rochaix 1997; Bock and Hippler 2002), there are a few left whose functions have not yet been elucidated. Among them are two giant open reading frame, ycf1 and ycf2, which in tobacco, potentially encode protein products of 1901 and 2280 amino acids, respectively. Attempts to inactivate ycf1 and ycf2 in tobacco have revealed that both reading frames are essential genes (Drescher et al. 2000). This excludes a function of the gene products in photosynthesis (because photosynthesis is non-essential under in vitro culture conditions), but leaves the possibility of a function in plastid gene expression (which has been demonstrated to be essential in tobacco; Ahlert et al. 2003; Rogalski et al. 2006) or in some essential metabolic pathway.
All plastid genomes also harbor a number of non-conserved open reading frames, most of which are shorter than 150 codons. Lack of evolutionary conservation even among closely related species is usually interpreted as evidence for these ORFs fortuitously forming contiguous reading frames that have no functional significance (Kahlau et al. 2006).
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