Supplementary data for: Encyclopaedia of family A DNA polymerases localized in organelles: Evolutionary contribution of bacteria including the proto-mitochondrion

DNA polymerases (DNAPs) synthesize DNA from deoxyribonucleotides in a
semi-conservative manner and serve as the core of DNA replication and
repair machinery. In eukaryotic cells, there are two genome-containing
organelles, mitochondria and plastids, that were derived from an
α-proteobacterium and a cyanobacterium, respectively. Except for rare
cases of genome-lacking mitochondria and plastids, both organelles must be
served by nucleus-encoded DNAPs that localize and work in them to maintain
their genomes. The evolution of organellar DNAPs has yet to be fully
understood because of two unsettled issues. First, the diversity of
organellar DNAPs has not been elucidated in the full spectrum of
eukaryotes. Second, it is unclear when the DNAPs that were used originally
in the endosymbiotic bacteria giving rise to mitochondria and plastids
were discarded, as the organellar DNAPs known to date show no phylogenetic
affinity to those of the extant α-proteobacteria or cyanobacteria. In this
study, we identified from diverse eukaryotes 134 family A DNAP sequences,
which were classified into 10 novel types, and explored their evolutionary
origins. The subcellular localizations of selected DNAPs were further
examined experimentally. The results presented here suggest that the
diversity of organellar DNAPs 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 two mitochondrial DNAPs, POP and a candidate of the direct
descendant of the proto-mitochondrial DNAP, rdxPolA, identified in this
study.