Human Mitochondrial DNA Polymerase Metal Dependent UV Lesion Bypassing Ability

Joon Park; Noe Baruch-Torres; Shigenori Iwai; Geoffrey K Herrmann; Luis G Brieba; Y Whitney Yin

doi:10.3389/fmolb.2022.808036

Human Mitochondrial DNA Polymerase Metal Dependent UV Lesion Bypassing Ability

Front Mol Biosci. 2022 Mar 9:9:808036. doi: 10.3389/fmolb.2022.808036. eCollection 2022.

Authors

Joon Park^{1

2}, Noe Baruch-Torres³, Shigenori Iwai⁴, Geoffrey K Herrmann^{1

2}, Luis G Brieba³, Y Whitney Yin^{1

2}

Affiliations

¹ Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States.
² Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States.
³ Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico.
⁴ Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Japan.

Abstract

Human mitochondrial DNA contains more UV-induced lesions than the nuclear DNA due to lack of mechanism to remove bulky photoproducts. Human DNA polymerase gamma (Pol γ) is the sole DNA replicase in mitochondria, which contains a polymerase (pol) and an exonuclease (exo) active site. Previous studies showed that Pol γ only displays UV lesion bypassing when its exonuclease activity is obliterated. To investigate the reaction environment on Pol γ translesion activity, we tested Pol γ DNA activity in the presence of different metal ions. While Pol γ is unable to replicate through UV lesions on DNA templates in the presence of Mg²⁺, it exhibits robust translesion DNA synthesis (TLS) on cyclobutane pyrimidine dimer (CPD)-containing template when Mg²⁺ was mixed with or completely replaced by Mn²⁺. Under these conditions, the efficiency of Pol γ's TLS opposite CPD is near to that on a non-damaged template and is 800-fold higher than that of exonuclease-deficient Pol γ. Interestingly, Pol γ exhibits higher exonuclease activity in the presence of Mn²⁺ than with Mg²⁺, suggesting Mn²⁺-stimulated Pol γ TLS is not via suppressing its exonuclease activity. We suggest that Mn²⁺ ion expands Pol γ's pol active site relative to Mg²⁺ so that a UV lesion can be accommodated and blocks the communication between pol and exo active sites to execute translesion DNA synthesis.

Keywords: DNA polymerase gamma; TLS; UV lesion; metal-dependence; mitochondrial DNA.