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DNA repair new insight under SUSTech research

DATE:2019-09-01

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DNA damage from various sources can adversely affect genome stability and cell viability. The most common DNA lesions, abasic sties, are generated by spontaneous base loss or base damage caused by ionizing radiation (IR), UV radiation (UV) and alkylating agents such as methyl methanesulfonate (MMS). Whilst these sites in double-stranded DNA are primarily repaired by a cellular mechanism known as the base excision repair (BER) pathway, their repair mechanism in single-stranded DNA is only just being uncovered. 

Late last month, a research group led by Associate Professor Huang Hongda from the Department of Biology at Southern University of Science and Technology, had a paper published in the internationally renowned journal ‘Nucleic Acids Research’, entitled "Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK". The paper sought to unveil the molecular basis of abasic sites sensing in ssDNA by yedK.

The abasic site is the most common type of DNA damage. It is estimated that each cell of the human body can produce 5,000 to 10,000 abasic sites per day. Abasic sites that are not repaired in time can hinder RNA polymerase transcription and DNA polymerase replication, which may lead to further mutations, genomic instability, and even cancer.

Previous studies have focused on damage repair of abasic sites on double-stranded DNA. Recently, the HMCES protein and its homologous protein yedK have been found to protect abasic sites on single-stranded DNA, thereby mediating high fidelity repair of abasic sites. However, the mechanism of action of HMCES and yedK proteins and how they mediate downstream repair pathways are unclear.

This study analyzed a series of high-resolution complex structures of yedK protein and single-stranded DNA, including the structure of yedK binding non-specific substrates (natural single-stranded DNA), the structure of binding specific substrates (tetrahydrofuran mimic of abasic site), and the structure of binding post-reaction products.

It is further revealed that yedK can specifically recognize the abasic site through the electrostatic repulsion between glutamic acid 105 and the phosphate group of single-stranded DNA; yedK nucleophilic attacks on the 1'-carbon atom of the abasic site in the single-stranded DNA through the thiol and a-amino groups of the cysteine residue in its active center;Finally, a thiazolidine ring is formed, which covalently crosslinks yedK protein and single-stranded DNA. The mechanism of yedK was further elucidated by in vitro biochemical and enzymatic assays.

The Department of Biology of Southern University of Science and Technology is the only correspondent unit of the article. Among them, the post-doctoral researchers Wang Na and Bao Hongyu are the co-first authors of the paper. Associate Professor Huang Hongda and post-doctoral researcher Wu Baixing are the correspondence authors of the paper.

All structural data of the study were collected at the beamlines BL19U/18U/17U of Shanghai Synchrotron

Radiation Facility. The research team obtained funding from the National Key R&D Program of China, Shenzhen Government ‘Peacock Plan,’ and Chinese National Natural Science Foundation.

Original article - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz744/5555671

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Source: Department of Biology

Translated and Adapted: Chris Edwards