Author: Dr Ken Yokoyama, Ph.D.

We contributed two reviews to the latest edition of the Comprehensive Natural Products III.  The first review entitled “Biosynthesis and Mode of Action of Antifungal Pepetidyl Nucleoside Natural Products” was written with Mathew as the first author and comprehensively summarized the current state of our understanding in the mode of action and biosynthesis of antifungal peptidyl nucleosides (PNs).  PNs are represented by nikkomycins and polyoxins that have been used as agricultural fungicides or investigated as novel antifungals against invasive fungal infections. In the past ~15 years, there have been a significant advancement in our understanding of their biosynthesis, which could facilitate the future development of these compounds into clinically useful drugs.

The second review entitled “Radical-Mediated Carbon Skeleton Formation in Natural Products and Cofactor Biosynthesis” summarizes an emerging group of radical SAM enzymes that catalyze carbon skeleton formations in natural products and cofactor biosynthesis with particular focus on the mechanism of radical quenching. These enzymes play key roles in their biosynthetic pathways, and thus their functional and mechanistic characterizations are critical for the understanding of the pathways. The review highlights the as yet poorly understood mechanisms of radical quenching that provide diversity in their reactivities.

Haoran and Edward’s work on the catalytic mechanism of MoaA was published in JACS. MoaA catalyzes the first step in the molybdenum cofactor biosynthesis; a unique radical cyclization of guanosine 5’-triphosphate. In this work, Edward initially found an accumulation of a unique radical species, 5′-deoxyadenos-4′-yl radical, and Haoran kinetically characterized it and came up with the mechanistic model, which revealed the rate constants of the radical cyclization step for the first time. Moreover, Haoran initiated a collaboration with Pan Zhang in the Weitao Yang lab in the Chemistry Department to demonstrate that MoaA accelerates the radical C-C bond formation by 6-9 orders of magnitudes by constraining the radical conformation and stabilizing the transition state by the Arg17 residue. Together, the study revealed the first evidence that a radical SAM enzyme accelerates radical chemistry using its unique active site environment. The study also revealed the function of Arg17 whose mutation is known to cause Moco deficiency disease in humans. Congratulations to everyone.

Abhi successfully defended his PhD dissertation.  He studied the mechanism of 1,3-beta-D-glucan synthase by developing a novel SEC assay for glucan length determination and chain length terminators. A part of his work has been published in Biochemistry. Congratulations, Dr. Abhi!

Dr. Ogasawara visited Duke to give a seminar about his studies on peptide natural product biosynthesis. We had a group meeting with him and had a very insightful discussion. It was great to have you here, and we look forward to more interactions in the future! Dr. Ogasawara is an assistant professor at Hokkaido University and the 2018 recipient of the award for young researchers from Japan Society for Bioscience, Biotechnology, and Agrochemistry.

This paper describes the mechanistic characterization of a yeast beta-1,3-D-glucan synthase (GS). GS is a proven target of FDA-approved antifungal drugs, but its catalytic mechanism is poorly understood. Using a newly developed size exclusion chromatography (SEC) assay, we were able to monitor the chain elongation for the first time and found that GS catalyzes the formation of a long glucan (~2,000 – 7,000 mer) at an amazing efficiency (~50-60 Glc unit polymerized per sec). The use of substrate analogs also revealed that the enzyme catalyzes the polymerization at the nonreducing end. The study also discusses the first comprehensive model of the GS catalytic cycle.

Hai and Matthew won the poster award in the Biochemistry Department retreat. Hai presented his work on mitomycin biosynthesis, where he successfully demonstrated that the early steps of mitomycin biosynthesis proceed with intermediates linked to an acyl carrier protein (ACP). The work was published earlier this year. Matthew presented his progress in the study of nikkomycin/polyoxin biosynthesis. He received this award two years in a row! Congratulations to both of you.

 

Abhi gave a poster presentation of his work on the mechanism of (1,3)-beta-D-glucan synthase in the 2019 Enzymes Coenzymes and Pathway GRC, and won a poster award.  Congratulations!!

Hai’s work on the characterization of MitE and MitB enzymes in mitomycin biosynthesis was published in ACS Biochemistry. In this paper, we provide experimental evidence that the early steps of mitomycin biosynthesis proceeds with the biosynthetic intermediates linked to an acyl carrier protein (ACP). This is one of the first examples of ACP-dependent non-PKS/NRPS pathways, and the first step towards understanding the complex mechanism of mitomycin biosynthesis.

Kenichi Yokoyama, Ph.D. has been selected as the 2019 recipient of the Pfizer Award in Enzyme Chemistry administered by the American Chemical Society (ACS). The Pfizer Award was established in 1945 and aims to stimulate fundamental research in enzyme chemistry by scientists, not over forty years of age. Dr. Yokoyama is the second recipient of this award in this department. The first awardee was Dr. Paul Modrich in 1983.  

 

Matthew received the poster award in the Biochemistry annual retreat. He presented his thesis work on the biosynthesis studies of antifungal peptidyl nucleoside natural products. Congratulations!! This is the fifth poster award for the lab since the establishment in 2011.