Replication slippage in plastids

Very short tandem repeats, based on mononucleotide, dinucleotide, trinucleotide, and consecutive nucleotide repeats up to the ~30-mer, are found in plastid genomes. Very short tandem repeats are considered to result from slippage of the replication fork. Replication slippage in the newly replicated daughter strand inserts a repeat whilst slippage of the template strand deletes a repeat (Fig. 12). A number of hot spots of variation in plastid genomes are associated with short tandem repeats (Newman et al. 1992; Sears et al. 1996; Stoike and Sears 1998; Ogi-hara et al. 2002). Plastome-mutator is a nuclear mutation in O. hookeri associated with a 200 to 1000-fold increase in pigment-deficient sectors and changes in plas-tid DNA (Epp 1973; Stoike and Sears 1998). The product of the plastome-mutator gene is not known but it has been suggested to be involved in plastid DNA-RRR pathways (Stoike and Sears 1998). Examination of alterations induced by plas-tome-mutator in the intergenic region between the 16S and 23S ribosomal RNA

Fig. 13. Direct repeat mediated deletion by replication slippage and recombination (Bi and Liu 1996).

genes suggested they were the result of replication slippage rather than recombination events (Stoike and Sears 1998).

Replication slippage between direct repeats and recombination (Fig. 13; Bi and Liu 1996) provides an alternative mechanism to homologous recombination (Fig. 11a) for excision of genes from plastid DNA. Replication slippage induced recombination is reduced with increasing distance between repeats and does not increase in frequency when repeat length is increased above ~100 bp in E. coli (Bi and Liu 1996). The observation that recombination between engineered repeats in plastids increases with longer repeats favours a mechanism involving homologous recombination rather than slippage (see Section 8.2 above). Replication slippage can give rise to insertions and deletions (Fig. 12) and appears to be a major force in plastid genome evolution. The 70 kb plastid genome of the non-photosynthetic parasite Epifagus virginiana is less than half the size of the 156 kb N. tabacum

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