by Maria Prostova | Evgeniy Shilkin | Alexandra A. Kulikova | Alena Makarova | Sergei Ryazansky |
Andrey Kulbachinskiy | Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”,
Moscow 123182, Russia | Institute of Molecular Genetics, National Research Centre “Kurchatov
Institute”, Moscow 123182, Russia | Institute of Molecular Genetics, National Research Centre
“Kurchatov Institute”, Moscow 123182, Russia | Institute of Molecular Genetics, National Research
Centre “Kurchatov Institute”, Moscow 123182, Russia | Institute of Molecular Genetics, National
Research Centre “Kurchatov Institute”, Moscow 123182, Russia
DNA polymerases of the X family (PolX) play essential functions in eukaryotic DNA repair.
PolX polymerases are also found in prokaryotes but their diversity and functions remain
largely unstudied. We have performed a comprehensive bioinformatic analysis of
prokaryotic PolXs and found that they are widespread in bacteria and are also present in
several archaeal lineages. Most polymerases share a common architecture, with the central
polymerase part consisting of the thumb, palm and fingers domains, preceded by an Nterminal dRP-lyase domain and followed by a C-terminal exonuclease PHP domain.
Unexpectedly, we have revealed a previously unrecognized group of noncanonical PolXs
that seem to be lacking DNA polymerase activity. They contain substitutions of key catalytic
residues and deletions in their polymerase and dNTP binding sites in the palm and fingers
domains, but contain a functional exonuclease domain. Biochemical experiments with
representative noncanonical PolXs from the Deinococcus genus confirmed that they are
indeed inactive as DNA polymerases but are highly efficient 3’-5’ exonucleases. The
biological function of altered polymerases is possibly connected with double-strand break
DNA repair, since both canonical and altered PolXs are often encoded together with the
components of the non-homologous end joining pathway, suggesting an evolutionary
conservation of this PolX function. This is a remarkable example of polymerases that have
lost their main polymerase activity, but may be involved in the nuclease processing of DNA
repair intermediates.