Methylotrophs: underexplored bacteria for discovering novel natural products and biochemistry

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PROJECT SUMMARY Natural products (NPs) and their derivatives are one of our main sources of therapeutics, due to the millennia these compounds have had to evolve interactions with their biological targets. However, the discovery of novel NPs from traditional sources has waned in recent decades, while at the same time we are facing mounting threats to human health such as increased antibiotic resistance. We therefore need new sources of NPs. One underexplored source of NPs is methylotrophs; bacteria that grow on reduced carbon compounds lacking carbon-carbon bonds such as methane gas. These organisms were overlooked during past NP discovery efforts due to their growth requirements, but genomic analysis demonstrates that they have significant potential to make novel NP scaffolds. I have been working with methylotrophs for close to a decade during my postdoctoral and independent research, and during that time I have developed genetic and metabolomic tools for these organisms. We are now ready to apply these tools to discover new methylotroph NPs with therapeutic value, as well as new enzymatic transformations that are involved in NP biosynthesis. Our research program is divided into two main directions. First, we will use our collection of ~100 unique bacterial strains isolated from methane enrichments to discover new therapeutically relevant leads. We are constructing a fraction library from this strain collection for use in bioactivity-based screens for antibiotic and anticancer compounds. Based on our findings, we will prioritize hits and perform advanced testing on these compounds with the help of our collaborators and supporting core centers. Because these strains almost all have sequenced genomes, we are also using similarity networking approaches and our genetic tools to identify and activate biosynthetic gene clusters that are likely to produce novel NPs. In our second research direction, we are capitalizing on our lab’s recently reported inverse stable isotopic labeling approach to identify methylotroph NPs that incorporate a known precursor. With this approach we will discover new NP scaffolds and associated novel biochemical transformations, and characterize these transformations both in vitro as well as in vivo in the native NP producing organisms. For both research directions, we have significant preliminary results that serve as examples of the types of projects that are developing within our research program. This work will identify new therapeutic leads with antibiotic and anticancer potential, and will also vet methods for prioritizing and activating the production of NPs from these underexplored bacteria. It will also address knowledge gaps in the biosynthesis of important NP classes (ribosomally synthesized and post-translationally modified peptides as well as enediynes), and characterize new enzymatic transformations that can be used as biocatalysts in medicinal chemistry efforts.