Unique System of Replication

Linear plasmids are very common among species of Streptomyces and related actinomycetes (such as mycobacteria and rhodococci). They are often accompanied by circular plasmids in the same host. The history of the discovery of linear plasmids in Streptomyces is described in this volume by Chater and Kinashi.

Like their circular counterparts in Streptomyces, linear plasmids are generally conjugative, but rarely carry genes conferring resistance to toxic compounds or other obvious selective advantage (Hopwood and Kieser 1993; Chater and Kinashi, in this volume). Their evolutionary advantage perhaps lies mainly in their ability to promote efficient genetic exchange between their hosts and other species in the soil.

Linear plasmids of Streptomyces and related actinomycetes represent a novel class of prokaryotic linear replicons capped by "terminal proteins" (TPs) covalently bound at the 5' ends (Hirochika et al. 1985; Sakaguchi 1990; Yang et al. 2002). The same structure is shared by the linear chromosomes of Streptomyces (reviewed by Chaconas and Chen 2005) and some closely related actinomycetes, such as Actinoplanes philippinensis, Micromonospora chalcea, Nocardia asteroides, Streptoverticillium abikoense, Streptoverticil-lium cinnamoneus (Chen 2000; Redenbach et al. 2000), and Rhodococcus sp. RHA1 (McLeod et al. 2006).

Such TP-capped linear DNA molecules are also found as plasmids and viruses of both eukaryotes and other prokaryotes (Fetzner et al., in this volume; Klassen and Meinhardt, in this volume). The best-studied are bacte-riophage ^29 of Bacillus subtilis and the adenoviruses. However, beyond their TP-capped structures, the linear plasmids of actinomycetes are very different from these two model systems in structure and function. The fundamental difference concerns their replication.

^29 and adenovirus genomes replicate by an end-to-end mechanism, in which the TP serves as the primer for replication initiation. In such replication, no discontinuous synthesis is involved, and therefore there are no Okazaki fragments. The telomeres are the origin of replication. The replication of the linear plasmids and chromosomes of Streptomyces (and presumably other actinomycete linear replicons also), on the other hand, is initiated from an internal origin, and proceeds bidirectionally toward the ends. Such inside-out replication would leave single-stranded gaps at the 3' ends of the DNA molecules, creating a classical end problem that must be solved so that the DNA would not be shortened with each round of replication. In eukary-otic chromosomes, the solution is extension of the 3' ends by the action of telomerase. In Streptomyces, instead, the single-stranded gaps of the linear plasmids (and chromosomes) are filled in ("end patching") to produce termini of defined length and sequence.

End patching of the 3' overhangs during replication of Streptomyces linear replicons appears to use a previously unknown mechanism. Unlike TP-primed DNA synthesis during replication of ^29 and adenoviruses, which uses double-stranded DNA templates, the substrate for end patching in Streptomyces is a single-stranded template of 250 to 320 nucleotides (nt) (Chang and Cohen 1994; C.-H. Huang, unpublished results). The structure of this stretch of telomere DNA is much more complicated and information-rich than those of ^29 and adenoviruses. It must not only provide a proper substrate for the end patching reaction but also help to escape attack by cellular nucleases.

In this chapter, I summarize progress in studying replication of the linear plasmids of Streptomyces during growth and conjugal transfer with particular emphasis on the events at the telomeres and the roles of two of the major players: the telomere DNA and the TP. Postreplicational processes, such as segregation and partitioning, and some remarkable functions of the TPs will also be discussed.

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