Living things produce a wide range of organic compounds that are useful in contemporary therapeutics and medicine. The majority of natural products now come from bacteria and other microbes, including the expanding family of ribosomally synthesized and post-translationally modified peptides, or RiPPs. The chemistry laboratories of Huimin Zhao (CABBI/BSD/GSE/MMG), Steven L. and Margaret Witt Professor of Computer Science, and Douglas Mitchell (MMG), John and Margaret Witt Professor of Chemistry, are located in the same building. Miller Chair of Chemical and Biomolecular Engineering at the University of Illinois at Urbana-Champaign have been collaborating to find and assess fresh RIPs that might make promising candidates for drug discovery and therapeutics.
RiPPs are still understudied in comparison to other classes of natural products like alkaloids, terpenes, and polyketides, in part because their biosynthetic gene clusters are relatively small and were previously frequently disregarded, according to Zhao. “So, we made the decision to create new technologies to find novel RiPPs with biological activity.”.
“Now that we’re in the genomics age, we’re understanding exactly how prevalent these sets of natural chemicals are, particularly in bacteria,”
Shravan Dommaraju, a Ph.D. candidate in Mitchell’s lab.
“We’re realizing just how widespread these groups of natural products are now that we’re in the genomics era, especially in bacteria,” said Shravan Dommaraju, a Ph.D. candidate in Mitchell’s laboratory. The goal is to find as many as we can because we don’t yet know what all of them do, but we do know that they’re out there, and we’re basically in this exploration phase.”.
In a recent paper, the Zhao and Mitchell labs reported the discovery of a distinct, novel class of RiPPs, which they have named “daptides,” with co-first authors Dommaraju and Hengqian Ren, a postdoctoral researcher in Zhao’s lab. Daphtides have two positively charged termini as opposed to the typical peptide’s one positively and one negatively charged terminus.
We discovered a ribosomal peptide that has two amino termini, contrary to what is stated in textbooks, which state that peptides have an amino terminus and a carboxy terminus. “Daptides have some intriguing bioactivities because they have positive charges at both ends.”.
The scientists explained that although this change in termini may appear insignificant, the positive charges on both termini allow daptides to interact with negatively charged materials, such as cell membranes. The team put the daptides in a dish with red blood cells to test this. They discovered that the daptides displayed hemolytic activity, which meant that they tore apart the cell membranes and caused the cells to burst. Zhao stated that hemolytic activity is very uncommon in the RiPPs the team works with and that antimicrobial or antifungal activity is much more typical.
Dommaraju said, “We were thinking about the structure and what is the evolutionary drive to cause a peptide to lose the negatively charged C terminus and replace it with a positively charged amino group.”. “From an engineering standpoint, you would add a lot of positive charges to a peptide to make it capable of interacting with a membrane. And in fact, that’s what motivated us to test this for hemolytic activity in the first place because we were aware that it had a modification that should make that possible.
It’s difficult to find new RiPPs. Initially, the researchers compared gene clusters using bioinformatics in an effort to find potential RiPPs. The targeted cluster is then cloned and put into an organism to be expressed, after which they can examine any natural products that were produced. Even after obtaining the products, there is still the question of what the products do and how they are made, which can be tested with bioassays, gene knockouts, and a variety of other tests. Dommaraju, however, claims that when the labs work together to streamline the process, they each draw on their areas of strength.
Therefore, Dommaraju explained, “on a project like this, the Mitchell lab does the bioinformatics and finds cool gene clusters, and the Zhao lab gets the synthetic biology system up and running to express these peptides and make them. In order to complete the project, we can use our combined experience and overlapped tasks.”.
The next steps, according to the researchers, are to comprehend how the daptide enzymes work and to use bioinformatics analysis to determine whether there are other gene combinations that are involved in the production of daptides. Future research should focus on the therapeutic potential of daptides as well as the ecological significance of the daptide-producing bacteria. Although there are still additional classes of RiPPs to be discovered, Ren and Dommaraju both concurred that they are interested in conducting more RiPP experiments in the future than just those involving daptides.
We’re interested in studying as many different natural product classes as we can using our bioinformatics tool, said Ren. The frontier of unexplored RiPP classes is so vast at the moment, and it’s exciting to be on the cutting edge and uncover new opportunities. There’s always a chance that the next item you discover could represent a significant advancement in treatment!”.
The research article appears in Nature Communications.
More information: Hengqian Ren et al, Genome mining unveils a class of ribosomal peptides with two amino termini, Nature Communications (2023). DOI: 10.1038/s41467-023-37287-1
