Linear protein-primed replicating plasmids frequently occur in two kingdoms of eukarya, i.e., in planta and fungi. The S plasmids from Zea mays were the first discovered linear double-stranded DNA (dsDNA) elements (Pring et al. 1977); soon after, similar genetic traits were detected in the yeast Kluyveromyces lactis and in the filamentous ascomycete Ascobolus immersus (Gunge et al. 1981; Francou 1981). Though linear plasmids were initially considered to represent rare exceptions from the commonly accepted rule defining plasmids as extrachromosomal covalently closed circular replicons, a great and still growing number of linear elements have since been discovered. To date, they are recognized as rather frequently occurring, extrachromosomal genetic elements with growing evidence for a viral evolutionary origin. Here, we focus on protein-primed replicating linear plasmids in eukaryotic microorganisms, i.e., filamentous fungi and yeasts. Reviews addressing linear plasmids from filamentous fungi and yeasts separately have been published over the years (Meinhardt et al. 1990; Stark et al. 1990; Griffiths 1995; Gunge 1995; Meinhardt and Schaffrath 2001; Gunge and Tokunaga 2004; Jeske et al. 2006a). However, recently established techniques, such as allelic replacement, gene shuffling, site-specific mutagenesis, and—more importantly—the extended molecular characterization of a number of linear plasmids to the sequence level, have greatly increased our knowledge at the molecular genetic level.

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