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Identification of a novel bifunctional uracil DNA glycosylase from Thermococcus barophilus Ch5

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Abstract

Genomes of hyperthermophiles are facing a severe challenge due to increased deamination rates of cytosine induced by high temperature, which could be counteracted by base excision repair mediated by uracil DNA glycosylase (UDG) or other repair pathways. Our previous work has shown that the two UDGs (Tba UDG247 and Tba UDG194) encoded by the genome of the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 can remove uracil from DNA at high temperature. Herein, we provide evidence that Tba UDG247 is a novel bifunctional glycosylase which can excise uracil from DNA and further cleave the phosphodiester bo nd of the generated apurinic/apyrimidinic (AP) site, which has never been described to date. In addition to cleaving uracil-containing DNA, Tba UDG247 can also cleave AP-containing ssDNA although at lower efficiency, thereby suggesting that the enzyme might be involved in repair of AP site in DNA. Kinetic analyses showed that Tba UDG247 displays a faster rate for uracil excision than for AP cleavage, thus suggesting that cleaving AP site by the enzyme is a rate-limiting step for its bifunctionality. Phylogenetic analysis showed that Tba UDG247 is clustered on a separate branch distant from all the reported UDGs. Overall, we designated Tba UDG247 as the prototype of a novel family of bifunctional UDGs.

Key points

  • We first reported a novel DNA glycosylase with bifunctionality.

  • Tba UDG247 possesses an AP lyase activity.

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Funding

This work was supported by the Natural Science Foundation of Jiangsu Province (No. BK20191219), High Level Talent Support Program of Yangzhou University, and the Academic Leader of Middle and Young People of Yangzhou University Grant.

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Authors and Affiliations

  1. College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China

    Likui Zhang, Donghao Jiang, Qi Gan, Haoqiang Shi & Li Miao

  2. Guangling College, Yangzhou University, Yangzhou, China

    Likui Zhang

  3. Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Guangzhou, China

    Yong Gong

  4. Univ Lyon, INSA de Lyon, CNRS UMR 5240, Villeurbanne, France

    Philippe Oger

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  1. Likui Zhang
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  2. Donghao Jiang
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  5. Li Miao
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  6. Yong Gong
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Contributions

LZ, YG, and PO designed experiments; DJ, QG, HS, and LM performed experiments; LZ, YG, DJ, and QG analyzed data; LZ, YG, and PO wrote and revised the paper.

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Correspondence to Likui Zhang, Yong Gong or Philippe Oger.

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Zhang, L., Jiang, D., Gan, Q. et al. Identification of a novel bifunctional uracil DNA glycosylase from Thermococcus barophilus Ch5. Appl Microbiol Biotechnol 105, 5449–5460 (2021). https://doi.org/10.1007/s00253-021-11422-8

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  • DOI: https://doi.org/10.1007/s00253-021-11422-8

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