We are a chemical biology group that focuses on the study of natural products. Natural products are highly evolved and functionally privileged compounds that often display complex chemical structures. These molecules have inspired generations of synthetic organic chemists, unveiled numerous fundamental biological processes as chemical probes, and served as the most significant source of chemical matter for drug discovery.
As the field of genomics has expanded, it has revealed a vast untapped wealth of natural products encoded in the DNA of sequenced organisms, particularly bacteria. Our lab has developed new tools to expedite the discovery of natural products from genomic information, including molecules from bacteria that cannot be cultivated in a lab. In particular, our lab focuses on Ribosomally synthesized and Post-translationally modified Peptides (RiPPs) which have genetically encoded substrates and an incredible diversity of post-translational modifications. Using a genes-to-molecule approach, we have uncovered numerous structurally unique RiPP molecules and revealed the unprecedented mechanistic enzymology through which they form. We can then leverage this knowledge to produce new-to-nature compounds with improved properties or novel activity with the long-term goal of unleashing the full synthetic potential of Nature to reshape the diagnosis and treatment of human disease.
Congrats to Sangeetha, who has successfully defended her Ph.D. Thesis!
Sangeetha, along with collaborators in Dipti Nayak's lab at UC Berkeley have published a paper in PNAS where they use cryoEM to resolve the role of McrD in methyl-coenzyme M reductase assembly.
Congrats to Kyle for successfully defending his Ph.D. Thesis!
Congratulations to Tim for his recent paper being selected as the 2023 ACS Editors Choice for March 1st!
Tim, Sangeetha, Shravan and Lonnie, along with former member Bryce, have published a paper in ACS Bio & Med Chem Au. They investigate the relationships between RiPP rSAMs and proffer a new method to identical novel sactisynthases.
Congratulations to Dinh, who won a Biological Chemistry Research award and will be speaking at the upcoming ACS conference about a RiPP BGC that uses three distinct Fe-dependent enzymes.
Shravan and collaborators from the Zhao and Sarlah labs published a paper in Nature Communications discovering the new “daptide” RiPP class. Using the RiPP Recognition Element (RRE) as a genomic handle, Shravan and co-workers built a class-independent genome mining workflow to identify biosynthetic gene clusters (BGCs) in new classes. After heterologous expression and chemical characterization of two predicted BGCs, it was found that the daptides’ C-terminus had been replaced by an amine and that daptides can disrupt cell membranes. A combination of pathway refactoring, substrate scope analysis, and protein structure prediction also determined the role for each enzyme in the biosynthetic gene cluster. This work showcases the utility of genome mining and synthetic biology in discovering new PTMs and RiPP classes.
Tim, Sangeetha, Shravan and Lonnie, along with former member Bryce, have published a paper in ACS Bio & Med Chem Au. They investigate the relationships between RiPP rSAMs and proffer a new method to identical novel sactisynthases. By using the RRE as a bioinformatic handle, they report a set of ~15,000 rSAM enzymes likely to modify RiPP substrates. A set of paraphyletic sactisynthases in this dataset is unified by a comparative analysis of residues in proximity to the catalytic site in these proteins. Using insights gleaned from the above analysis, they predict several groups of sactisynthases that were unidentifiable by full-length sequence analysis. One of these predicted sactisynthases, from S. sparsogenes, is validated experimentally.
Ashley, Mayuresh, Susanna and several former lab members published a paper in Biochemistry exploring the interaction between RiPP RREs and the leader peptidase. By leveraging thousands of predicted biosynthetic pathways, they were able to predict the structure of the leader peptidase and show its interaction with the RRE using evolutionary covariance and NMR. These interactions showed the full activity of the leader peptidase requires the RRE engaged with a leader peptidase containing the RRE-recognition sequence. Together, these data shows a dual role of the RRE in substrate delivery and activity of the leader peptidase by completing the S2 proteolytic pocket, defining a new mechanism of protease regulation.
Andrew and collaborators in the Nair, Bowers, and Pogorelov labs published a paper in J. Am. Chem. Soc. investigating the thus far elusive mechanism by which pyridine synthases such as TbtD catalyze macrocycle formation in thiopeptide biosynthesis. Through a combination of targeted mutagenesis, kinetic assays, substrate analogs, enzyme–substrate cross-linking, and chemical rescue experiments, we delineate the role of a conserved tyrosine in heterocycle aromatization. We anticipate this information to be of use in future engineering efforts with these enzymes.
A collaboration between our lab, the Zhao lab, and the van der Donk lab developed a robotic system for RiPP biosynthetic gene cluster refactoring, which was used along with RODEO and heterologous expression in E. coli to isolate 30 novel modified peptides. These peptides represent six different classes of RiPPs, and three of them exhibited antibacterial activity against members of the ESKAPE pathogens.