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Project 1: Mechanistic studies of Rpn antiphage defense system.
Research into bacterial immunity has led to the discovery of critical tools for molecular biology, including restriction enzymes and CRISPR systems. Recombination-promoting nuclease (Rpn) proteins are widely distributed. What makes the Rpn antiphage defense system unique is the coding of two proteins by a single gene and the presence of variable four amino acid repeats in both the RpnL toxin and the RpnS antitoxin. We will employ cutting-edge genetic and biochemical techniques to investigate the regulation of the Rpn system and the evolution of its four amino acid repeats. The goal of this project is to provide detailed mechanistic insights into the Rpn antiphage defense system that could be harnessed, as has been the case with restriction enzymes and CRISPR systems.
Project 2: Discovery of novel small antiphage defense molecules.
The majority of newly discovered antiphage defense systems contain proteins or protein–nucleic acid complexes. Recent studies indicate that small molecules such as ddhCTP, doxorubicin, and apramycin also play roles in antiphage defense. We plan to discover additional novel antiphage defense molecules through two complementary strategies.
Project 3: Biosynthetic studies of key metabolites in the human microbiome.
In collaboration with Dr. Xiaofang Jiang, a tenure-track investigator at the National Library of Medicine, we identified bilirubin reductase (Nat. Microbiol. 2024), the enzyme responsible for the yellow coloration of urine. More recently, we discovered a novel family of gut bacteria–encoded reductases capable of biotransforming steroid hormones (Nat. Commun. 2025). Building on these findings, we will continue to elucidate the biosynthetic pathways of key metabolites in the human microbiome through integrative metagenomic analyses and biochemical validation.
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