Recently, the international academic journalNucleic Acids Research published a paper entitled "Base excision repair system targeting DNA adducts of trioxacarcin/LL-D49194 antibiotics for self-resistance" online. This new research result was achieved under the joint efforts ofTang Gongli's research group from the School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study (HIAS), UCAS/Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences and Brandt F. Eichman's research group from Vanderbilt University, the USA.In this research, a unique family of DNA glycosylases is found. Enzymes of this type can eliminate DNA damage caused by Trioxacarcins (TXN) and LL-D49194 (LLD), two alkylating agent-like natural products, and make microorganisms self-resistant to these highly active antibiotics.

(“https://doi.org/10.1093/nar/gkac085”)

Base excision repair (BER) is a common damage repair pathway used to eliminate alkylated DNA in cells. DNA glycosylases, key proteins thatidentify and remove damaged bases, are the first step of the BER pathway. In recent years, based on studies on the self-resistance mechanisms of DNA-alkylating natural products, AlkD/YtkR2 and AlkZ/YcaQ are two families of DNA glycosylases in the antibiotic-producing strains that can recognize and repair DNA damage formed by DNA alkylates azinomycin B and yatakemycin, DNA alkylating compounds.

Trioxacarcins (TXN) and LL-D49194 (LLD) are polycyclic aromatic polyketide natural products with highly complex structures, which contain multiple glycosylation groups allowing embedment into the DNA backbones and a highly active polycyclic-spiro epoxy three-membered ring structure. The two can be embedded into the major and minor DNA grooves and alkylated with guanine on the DNA chains to form stable DNA damage, realizing anti-malarial, anti-bacterial and anti-tumor activities. Tang Gongli's research grcup has long been committed to researching the biosynthesis and resistance mechanism of TXNs, and successively clarified TXNs' initial elements and subsequent modification steps. Recently, they conducted an in-depth analysis of unknown functional genes in the gene clusters, from which they found four encoded DNA glycosylases (TxnU2, TxnU4, LldU1 and LldU5) conducting the alkylation damage repair of TXN A and LLD. These enzymes will provide self-resistance for TXN A and LLD producing strains.

The amino acid sequence-based analysis of a protein's structure (using AlphaFold) shows that TxnU, LldU, and DNA glycosylase AlkZ/YcaQ are homologous; the in-vitro enzyme activity experiments prove that TxnU and LldU are single-functional DNA glycosylases acting on alkylguanine adducts at the N7 position. However, compared with homologous proteins and other DNA glycosylases that act on alkylpurine adducts, TxnU and LldU differ from each other regarding the substrate specificity and enzyme catalytic mechanism. TxnU/LldU can process the specific elimination of TXN A/LLD-DNA damage and is inactive against substrates of AlkD/YtkR2 and AlkZ/YcaQ, less stable alkylguanine adducts. Similarly, the TXN A/LLD-DNA adducts cannot be excised by any other alkylpurine DNA glycosylase. The results of docking modeling and point mutation experiments show that TxnU4 and LldU1 have unique catalytically active sequence motifs, from which their unique substrate specificities and catalytic mechanisms are explained.

Chen Xiaorong, a postdoctoral researcher at HIAS, UCAS, Noah P. Bradley, a postdoctoral researcher at Vanderbilt University, and Lu Wei, a postgraduate at the Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, are the co-first authors of the paper;Research Fellow Tang Gongli and Professor Brandt F. Eichman are co-corresponding authors. The work received a large sum of funding from theNational Natural Science Foundation of China and the Chinese Academy of Sciences.

Source | School of Chemistry and Materials Science

Typesetter | Chen Xingyu

Executive Editor | Jiang Xuchen

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