Gates, D. R. | Search bioRxiv

bioRxiv2026

Bacterial-derived cyclic lipopeptides suppress dauer arrest in C. elegans

Secondary bacterial metabolites can regulate animal physiology, but the specific bacterial genes and molecules responsible for regulating, synthesizing, and transporting these molecules and the mechanisms by which they impact animal physiology often remain unclear. Here, we used Caenorhabditis elegans dauer formation as a gross morphological readout to identify bacterial mechanisms that promote development when animal TGF-{beta} or insulin signaling is impaired. We found that the native C. elegans microbiome constituent, Pseudomonas lurida, suppresses dauer arrest and that this activity requires the two-component system, GacS/GacA, and the downstream massABC[KD2.1][KN2.2][XW2.3] nonribosomal peptide synthetase cluster. Using sequential chromatography followed by mass spectrometry and NMR, we identified Massetolide F, a bacterial cyclic lipopeptide biosurfactant, as a massABC-dependent product. In addition, we found that purified Massetolide F was sufficient to restore dauer suppression to P. lurida {triangleup}massBC. We also found that surfactin[AT3.1][KN3.2][XW3.3] C, a cyclic lipopeptide from B. subtilis, similarly suppressed dauer formation whereas the cyclic lipopeptide antibiotic daptomycin did not, indicating that dauer suppression is shared by a subset of cyclic lipopeptides rather than being a general property of the class. Lastly, we found that massABC-dependent Massetolide F production induces the expression of the acid sphingomyelinase asm-3 in C. elegans, that asm-3 is required for Massetolide F induced dauer suppression, and that loss of Massetolide F production also leads to reduced bacterial clearance in host animals. Together, these findings identify Massetolide F as a microbiome-derived molecule that promotes animal development and reveal an unexpected function for bacterial biosurfactants in regulating animal physiology.

microbiology↗

bioRxiv2024

A high-throughput screening platform for discovering bacterial species and small molecules that modify animal physiology

Canonical polyamines such as agmatine, putrescine, and spermidine are evolutionarily conserved metabolites found in nearly all forms of life ranging from bacteria to humans. Recently, interactions between polyamines produced by gut bacteria and human intestinal cells have been proposed to contribute to both Irritable Bowel Syndrome with Diarrhea (IBS-D) and inflammatory bowel diseases. However, the molecular mechanisms that underlie these effects are often unclear due in part to limitations in the methods used to manipulate and study polyamine functions in vivo. Here, we developed a Caenorhabditis elegans based screening platform and a modified LC-MS approach for profiling polyamine metabolites. We combined these methods to make the unexpected discovery that dysfunctional polyamine metabolism in both Gram-negative (E. coli) and Gram-positive (B. subtilis) bacteria can result in the accumulation of a noncanonical polyamine intermediate, N1-Aminopropylagmatine (N1-APA). We further find that N1-APA is produced via spermidine synthase (SpeE) and that it is bioactive when encountered by animals. Specifically, we find that when N1-APA is produced by bacteria in animal intestines it can be transported into intestinal cells via the polyamine transporter CATP-5 where it antagonizes both animal development and mitochondrial function across diverse animal species. Lastly, we find that N1-APA functions analogously to the deoxyhypusine synthase inhibitor GC7. For example, like GC7, N1-APA antagonizes eIF5A hypusination and inhibits the alternative activation of mammalian macrophages. To our knowledge, these findings are the first to demonstrate that N1-APA is a bioactive metabolite and that bacteria can produce a small molecule that functions similarly to existing deoxyhypusine synthase inhibitors. Furthermore, these results suggest an exciting new mechanistic hypothesis for why the loss of speB in gut microbes, including E. coli, has been both linked to inflammatory bowel disease (IBD) in humans and found to drive IBD in germ free mice.

genetics↗