IGB team discovers new natural products at an unprecedented speed and scale

iBioFAB accelerates the biological engineering process by integrating artificial intelligence/machine learning with automation.

By Shelby Lawson

Many of the drugs utilized in modern medicine are naturally produced by microbes. One of the most notable is penicillin, an antibiotic that was derived from certain molds and became one of the most important advances in medicine and human health.

As DNA sequencing has become cheaper and faster, scientists now have access to hundreds of thousands of microbial genomes and the natural products they produce. However, chemistry Professor Doug Mitchell said that massive number still pales in comparison to the number of compounds these organisms have the capacity to make using the genetic pathways they possess.

“This is just the tip of the iceberg,” said Mitchell, the John and Margaret Witt Professor of Chemistry at the University of Illinois Urbana Champaign. “There’s a disparity in what we know today in terms of known molecules versus what nature has the capacity to produce. Like 100 to one at least.”

One group of natural products that has become a popular source of antibiotics are called ribosomally synthesized and post-translationally modified peptides, or simply, “RiPPs.” Traditional methods for accessing RiPPs are slow and involve taking genes one by one and putting them into a model organism, like E. coli, to see what compound it produces.

In a massive collaborative effort on the UIUC campus, a team of researchers in the Department of Chemistry and in Chemical and Biomolecular Engineering were able to discover and characterize new RiPPs with unprecedented speed and at an unprecedented scale by using the Illinois Biological Foundry for Advanced Biomanufacturing at the Carl R. Woese Institute for Genomic Biology. Their findings were recently published in Nature Communications. 

Side by side head shots of the three primary investigators on this project.
From left, Doug Mitchell, Wilfred van der Donk and Huimin Zhao.

iBioFAB is a laboratory automation system which can evaluate and assemble multiple synthetic gene pathways from hundreds of genes at once, something that would traditionally take many researchers and much more time to accomplish. The collaboration included researchers from Mitchell’s lab as well as researchers in the lab of Huimin Zhao, the Steven L. Miller Chair of chemical and biomolecular engineering, and the lab of Wilfred van der Donk, Richard E. Heckert Endowed Chair in Chemistry and Howard Hughes Medical Institute Investigator.

The paper's three co-first authors are Alex Battiste, a fourth-year PhD student in the Mitchell lab, Chengyou Shi, a fifth-year PhD candidate in the Zhao lab, and Richard Ayikpoe, a postdoctoral researcher in the van der Donk lab. Battiste, Shi, and Ayikpoe explained how they each led a part of the project in their respective labs.

Shi’s team ordered synthetic genes and then assembled them into candidate pathways, or gene clusters, using iBioFAB integrated with a genome mining program called RODEO. Then, different classes of the gene clusters were given to Battiste and Ayikpoe’s teams to test which pathways were functional and likely to produce new RiPPs in E. coli. Any structures of RiPPs that showed antibiotic activities were characterized in detail by Ayikpoe’s team. The high-throughput technology allowed for 96 pathways comprised of about 400 genes to be tested at once, with the production of 30 new compounds.

Out of the new compounds discovered, three were found to have antibacterial properties. When tested against Klebsiella pneumoniae, which are highly virulent antibiotic-resistant bacteria, the newly discovered antibacterial RiPPs were found to be effective at killing the dangerous bacteria. The researchers say this could be a new avenue for discovering compounds that are effective against bacteria that are resistant to current antibiotic drugs.

“We found three RiPPs that have antimicrobial properties against pathogens that are known to be involved in hospital acquired infections, including Klebsiella,” said Ayikpoe. “This research shows that by using this platform to extend the number of biosynthetic gene clusters that we can screen at once, we are more likely to discover anti-microbial compounds that could have therapeutic properties.”

The team says the goal of the paper is two-fold: to demonstrate the ability of the high-throughput technology to quickly construct and test gene clusters for new RiPPs, but also to emphasize the kind of large-scale collaborative projects that are made possible within the IGB.

Side by side portraits of the three student researchers
From left, Shengyou Chi, Alex Battiste, and Richard Ayikpoe.

“There's no way that any one of our labs could have done all of this on their own. The IGB has provided the crucible for this kind of interdisciplinary research,” Mitchell said.

Battiste described how the IGB naturally inspires collaborative projects like this one, which is a project within the institute's Mining Microbial Genomes (MMG) research theme, which brings together a team of microbiologists, chemists, and engineers to search, or mine, microbial genomes for the ability to produce new metabolites. The mission is learning how primary metabolites are produced in microorganisms and understanding the enzymatic transformations responsible for their synthesis.

“The IGB makes it very easy to just talk to people when you see them all the time in your theme, which lowers the barrier for starting projects with them,” Battiste said. “Everyone in the MMG theme works on similar stuff even if we’re from different labs. So, we all have different types of expertise, but they mesh well together, and you get to learn about the types of techniques they’re using. It's been one of my favorite parts of working here, the sense of camaraderie amongst all of the people on the team.”

Watch a video about this research project and the spirit of collaboration that made it possible.

All three co-first authors said their education, research, and job prospects have benefitted from collaborative projects like this one, and the combination of people and technology make IGB a great place to conduct research.

“The collaborative atmosphere that the IGB offers in diversity and growth, both in terms of science and social life, is really remarkable.” Ayikpoe said.

This research was supported by funding from the National Institutes of Health. The paper is available via Nature Communicationsdoi.org/10.1038/s41467-022-33890-w.

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