The replicon model (Jacob et al. 1963) has been very successful and been substantiated in bacteria, animal viruses and budding yeasts such as S. cerevisiae. Problems in localising bona fide replication origins in plastids (Section 4.1, 4.2) and the nuclear genomes of multicellular organisms (Gilbert 2004) have hindered universal application of the replicon model. The apparent failure of plastid genomes to conform to the replicon model with one or two well-defined replication origins might suggest the standard model (Fig. 5a, 5b) for replication of plastid genomes (Kolodner and Tewari 1975) requires revision (Bendich 2004). The lack of progress in understanding plastid genome replication has been matched by illuminating advances in bacterial genetics, particularly by Kogoma and colleagues (Asai et al. 1994), that have identified new replication mechanisms initiated by recombination for genome maintenance. Recombination-dependent DNA replication allows stalled replication forks at double-strand DNA breaks to re-establish and enables initiation of replication in the absence of a defined origin of replication (Asai et al. 1994; Kowalczykowski 2000). The mechanism requires a linear DNA end and strand invasion to prime DNA synthesis on a circular (Fig. 5c) or linear DNA (Fig. 5d) template followed by resolution of the recombination-junction to re-establish the replication fork. Replication forks resulting from D-loops primed by strand invasion were first described in bacteriophage T4 DNA replication (Kreuzer 2000, 2005). The role of recombination in maintaining replication forks has been suggested to be the main function of recombination systems (Cox et al. 2000; Goodman 2000). Plastids are known to contain a highly active homologous recombination pathway (see Section 8 below), which is a requirement for recombination-dependent DNA replication.
The only requirement for recombination-dependent DNA replication is a free end that could be located at any position on plastid DNA. As mentioned above (Section 3.1), the linear genomes in S. cerevisiae and plant mitochondria appear to have heterogeneous ends rather than a limited number of defined ends. Recombination-dependent DNA replication has been put forward as a mechanism for replication of fungal and plant mitochondrial genomes (Oldenburg and Bendich 1998; Williamson 2002), and the minicircles present in the plastids of dinoflagellates (Nelson and Green 2005). Linear ends with 3' overhangs would allow strand invasion to prime DNA replication on other plastid DNA molecules acting as templates. Induction of double-strand breaks at specific sites in E. coli gives rise to recombination-dependent DNA replication origins that can be mapped (Asai and Kogoma 1994). Linear DNA molecules with defined ends have been found in Z. mays (Oldenburg and Bendich 2004b) and N. tabacum (Scharff and Koop 2006, 2007) plastids (Section 3.2 above). One common end in both species maps close to OriA in the large inverted repeat of N. tabacum between the 16S and 23S rRNA genes (Fig. 6b). An origin of replication has not yet been located in this position in cereal plastid genomes (Fig. 6c). These natural ends have been suggested to invade template DNA and prime DNA synthesis by recombination-dependent DNA replication (Bendich 2004; Oldenburg and Bendich 2004b). As a result they could define sites at which replication of the plastid genome is initiated. Interestingly, the locations of these ends appeared to change when OriA and OriB2 were deleted (Scharff and Koop 2007). Recombination-based-replication will lead to circular DNA molecules with tails (Fig. 5c) and linear branched structures (Fig. 5d). Linear DNA molecules are extended when their ends invade and replicate template genomes. The process leads to multimerization of linear DNA molecules and has been documented in detail during replication of bacteriophage T4 in E. coli (Kreuzer 2000). Highly branched complexes will be formed if several independent DNA molecules are connected by recombination-dependent DNA replication events. The complexity of branching increases if resolution (see resolution step shown in Fig. 5c, 5d) is not completed in some of the branches (Kreuzer 2000). Complex branched networks arising from recombination-dependent DNA replication might explain the 90-95% (by mass) of Z. mays plastid DNA found in high MW complexes (Oldenburg and Bendich 2004b; Section 3; Fig. 3c).
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