DNA polymerases synthesize DNA from deoxyribonucleotides in a semiconservative manner and serve as the core of DNA replication and repair machinery. In eukaryotic cells, there are 2 genome-containing organelles, mitochondria, and plastids, which were derived from an alphaproteobacterium and a cyanobacterium, respectively. Except for rare cases of genome-lacking mitochondria and plastids, both organelles must be served by nucleus-encoded DNA polymerases that localize and work in them to maintain their genomes. The evolution of organellar DNA polymerases has yet to be fully understood because of 2 unsettled issues. First, the diversity of organellar DNA polymerases has not been elucidated in the full spectrum of eukaryotes. Second, it is unclear when the DNA polymerases that were used originally in the endosymbiotic bacteria giving rise to mitochondria and plastids were discarded, as the organellar DNA polymerases known to date show no phylogenetic affinity to those of the extant alphaproteobacteria or cyanobacteria. In this study, we identified from diverse eukaryotes 134 family A DNA polymerase sequences, which were classified into 10 novel types, and explored their evolutionary origins. The subcellular localizations of selected DNA polymerases were further examined experimentally. The results presented here suggest that the diversity of organellar DNA polymerases has been shaped by multiple transfers of the PolI gene from phylogenetically broad bacteria, and their occurrence in eukaryotes was additionally impacted by secondary plastid endosymbioses. Finally, we propose that the last eukaryotic common ancestor may have possessed 2 mitochondrial DNA polymerases, POP, and a candidate of the direct descendant of the proto-mitochondrial DNA polymerase I, rdxPolA, identified in this study.

Center for Computational Sciences University of Tsukuba Tsukuba Japan

Deep Sea Biodiversity Research Group Research Institute for Global Change Yokosuka Japan

Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czech Republic

Division of EcoScience Ewha Womans University Seoul South Korea

Division of Invertebrate Zoology American Museum of Natural History New York NY USA

Faculty of Life and Environmental Sciences University of Tsukuba Tsukuba Japan

Graduate School of Agriculture Kyoto University Kyoto Japan

Graduate School of Life and Environmental Sciences University of Tsukuba Tsukuba Japan

Interdisciplinary Theoretical and Mathematical Sciences program RIKEN Wako Saitama Japan

Research Center for Advanced Analysis National Agriculture and Food Research Organization Tsukuba Japan

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A cryptic plastid and a novel mitochondrial plasmid in Leucomyxa plasmidifera gen. and sp. nov. (Ochrophyta) push the frontiers of organellar biology