Evolution of Linear Plasmids in Eukaryotes

Eukaryotic linear plasmids, either mitochondrial or cytoplasmic, in principle replicate like genomes of adenoviruses and phi29-like bacteriophages (see above), which has led to the conclusion that they share a common ancestor (Meinhardt et al. 1986, 1990; Kuzmin et al. 1988; Oeser and Tudzynski 1989; Rohe et al. 1992; Kempken et al. 1992). For reconstruction of the phylogeny, both DNA and RNA polymerases have been employed, since the respective genes were found in almost every linear plasmid system. Figure 4 shows an updated phylogenetic tree based on the viral B-type DNA polymerase sequences with basic features agreeing with previous calculations (Rohe et al.

Pichia kluyveri pPK2

Enterobacteria phage PR4 Enterobacteria phage PRD1

Bacillus subtilis phage B103 Bacillus subtilis phage phi29 Bacillus thuringiansis phage Bam35c

i atchallsii pPEAB Pichia acaciae pPac1-1 Saccharomyces kluyveri pSKL Kluyveromyces lactis pGKL2

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1992; Kempken et al. 1992). Mitochondrial and cytoplasmic linear plasmids are clearly separated, which is indicative of early phylogenetic divergence and adaptation to different cellular compartments. Moreover, cytoplasmic DNA polymerases are more closely related to enzymes from adenoviruses than to those of mitochondrial plasmids. Along with the plant linear plasmids, which also reside in mitochondria, the latter form a separate branch. Adenoviruses as well as the bacteriophage PRD1 (which infects Gram-negative bacteria and employs a phi29-like replication mechanism) were recently shown to display clear similarities concerning virion structure (Benap and Steven 2000; Benson et al. 1999, 2000; San Martin and Burnett 2003). Such findings agree with the assumption that adenoviruses and (PRD1/phi29-like) bacteriophages have a common ancestor which predates the occurrence of eukaryotes (Davison et al. 2003).

The calculated relatedness of cytoplasmic linear plasmids and aden-oviruses points to separation from their ancestor prior to the emergence of

A Fig. 4 Phylogenetic tree for protein-primed replicating genetic elements based on B-type DNA polymerases. Besides bacteriophages, present day manifestations in eukaryotes exist in mitochondria, in the cytoplasm, and in the nucleus (adenoviruses). Since mitochon-drial elements are clearly separated from the cytoplasmic and nuclear plasmids, they must have diverged early during evolution; divergence of the nuclear and cytoplasmic elements dates back to a later point. Yet later, autonomous and nonautonomous elements split. The bar denotes 10% divergence. GenBank accession numbers of individual sequences: CAC08221.2: Pichia etchellsii pPE1A; CAA38621.1: Saccharomyces kluyveri pSKL; CAA25568.1: Kluyveromyces lactis pGKL1; CAA30603.1: K. lactis pGKL2; CAA09497.1: Debaryomyces hansenii pDHL1; CAD91889.1: Pichia inositovora pPin1-3; CAA72340.1: Pichia kluyveri pPK2; BAB13496.1: Flammulina velutipes pFV1; CAA36327.1: Neurospora intermedia kalilo; NP_053000.1: Pleurotus ostreatus pMLP1; CAA43117.2: Podospora anse-rina pAL2-1; NP_862206.1: Blumeria graminis f. sp. hordei pBgh; AAB41447.1: Gelasi-nospora sp. G114 Gel-kal; JQ0301: Claviceps purpurea pClK1; S26947: Podospora anse-rina pAL2-1; S05362: Ascobolus immersus pAI2; S26985: Neurospora crassa maranhar; CAA45364.2: Morchella conica pMC3-2; BAC16364.1: Brassica napus linear plasmid; P10582: Zea mays S-1; NP_659515.1: Ovine adenovirus D; AP_000236.1: Porcine adenovirus 5; YP_094032.1: Bovine adenovirus A; AAN84890.1: Tree shrew adenovirus 1; AP_000478.1: Turkey adenovirus 3; AP_000613.1: Canine adenovirus type 2; YP_213966.1: Simian adenovirus 1; AAA42478.1: Human adenovirus type 12; NP_040853.1: Human adenovirus F; P03680: phage phi29; AAP83475.1: phage Bam35c; NP_690635.1: phage B103; AAX45903.1: phage PRD1; AAX45594.1: phage PR4

eukaryotes. In contrast, the distinct separation of mitochondrial elements from both cytoplasmic linear plasmids and adenoviruses suggests that mi-tochondrial elements diverged later, possibly in the postendosymbiont era. Consistently, plasmid pPK2 of Pichia kluyveri, one of the few known mitochondrial linear yeast elements (Blaisonneau et al. 1999), is more closely related to mitochondrial linear plasmids from filamentous fungi and plants than to the cytoplasmic linear plasmids from other Pichia species. In general, the relatedness of mitochondrial linear elements reflects the phylogenetic relations of their hosts (Rohe et al. 1992), suggesting them to originate from a single mitochondrial ancestor which may have been acquired as an endosymbiotic (bacteriophage-like) genetic element. In contrast to bacte-riophages and adenoviruses, linear plasmids lost almost all viral attributes (such as a capsid or an infectious cycle), presumably as an adaptation to the propagation mode of their hosts, since extranuclear inheritance, either as cytoplasmic or mitochondrial element, does not necessarily include an infectious virion for efficient propagation.

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