Biology subjects

Nauta, K. M.

Publications and source records attributed to Nauta, K. M..

6 recordsLinked to original sources

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↗

bioRxiv2026

Bacterial pyruvate metabolism regulates host insulin sensitivity in C. elegans

Two different individuals can consume an identical diet but experience different physiological outcomes. While there are many potential mechanistic reasons for this, one increasingly recognized reason is that differences in an animals microbiome can lead to differences in the processing of dietary nutrients. Thus, though a diet might start out the same, how it is experienced by a host is dependent on their microbiome. While exciting, mechanistic studies of diet-microbiome-host effects are often limited by the lack of high throughput laboratory techniques to identify and define interactions between dietary metabolites, microbial metabolism, and host biology. We hypothesized that the model organism Caenorhabditis elegans is an advantageous animal model for rapidly identifying and genetically dissecting interactions between dietary nutrients, microbial metabolism, and host physiology. Here, we used an established model of the effects of dietary glucose on insulin resistant mutant animals (daf-2/IR mutants) to study how differences in bacterial metabolism influence the consequences of dietary sugars on animal physiology. We found that the effect of dietary sugars on daf-2 mutant physiology is dependent on how the microbiome metabolizes dietary sugars. We found dietary sugar suppresses multiple daf-2 mutant phenotypes in the presence of some bacteria but has no effect in the presence of others. To determine how bacteria mediate the effects of dietary sugars on host physiology we screened 5,000 transposon mutations in the canonical C. elegans dietary bacteria, E. coli OP50 for effects on animal insulin signaling. From this, we found that the effects of exogenous sugars on the phenotype of daf-2 mutant animals is dependent on the function of pyruvate dehydrogenase in bacteria and that the loss of bacterial pyruvate dehydrogenase genes (ex. aceE) is sufficient to mimic the effects of dietary sugars on dauer formation, longevity, and gene expression in insulin signaling deficient animals. Collectively, our findings further support the growing body of evidence that the effects of dietary nutrients on animal physiology can be influenced by the gut microbiome. In addition, these studies demonstrate the advantages of the C. elegans model system for studying 3-way diet-microbiome-host interactions that are difficult to dissect in other model systems.

microbiology↗

bioRxiv2025

Oocyte mitochondria link maternal environment to offspring phenotype

During oogenesis and maturation oocytes undergo a recently discovered mitochondrial electron transport chain (ETC) remodeling in flies1, frogs1, and humans2. This conserved oocyte ETC remodeling is regulated by maternal insulin signaling, but its role in biology remains unclear. In the model animal Caenorhabditis elegans, we previously found that insulin signaling to oocytes regulates offsprings ability to adapt to future osmotic stress by altering offspring metabolism. However, the molecular mechanisms that function in oocytes to mediate this intergenerational stress response are similarly unknown. Here, we developed a low-input oocyte proteomics workflow and combined it with our C. elegans intergenerational stress response model to find that both a mothers environment and maternal insulin signaling regulate the abundance of ETC proteins in oocytes - particularly the abundance of proteins involved in the transfer of electrons from QH2 to cytochrome C by ETC Complex III. Using genetic perturbations of ETC function we further found that promoting ETC Complex III function in oocytes was both necessary and sufficient to link a mothers environment to adaptive changes in offspring metabolism. Lastly, we found that the effects of Complex III dysfunction in oocytes on offspring were mediated via an AMP-kinase (AAK-2) dependent mechanism and that AAK-2 functions in offspring to promote ATP preservation and glycerol metabolism in response to stress. Collectively, our data suggest that the role of oocyte ETC remodeling in biology includes linking maternal environments to changes in offspring metabolism that promote offspring survival in the environment experienced by their mother.

genetics↗

bioRxiv2024

kinact/KI Value Determination for Penicillin-Binding Proteins in Live Cells

Penicillin-binding proteins (PBPs) are an essential family of bacterial enzymes that are inhibited by the {beta}-lactam class of antibiotics. PBP inhibition disrupts cell wall biosynthesis, which results in deficient growth and proliferation, and ultimately leads to lysis. IC50 values are often employed as descriptors of enzyme inhibition and inhibitor selectivity but can be misleading in the study of time-dependent, irreversible inhibitors. Due to this disconnect, the second order rate constant kinact/KI is a more appropriate metric of covalent inhibitor potency. Despite being the gold standard measurement of potency, kinact/KI values are typically obtained from in vitro assays, which limits assay throughput if investigating an enzyme family with multiple homologs (such as the PBPs). Therefore, we developed a whole-cell kinact/KI assay to define inhibitor potency for the PBPs in Streptococcus pneumoniae using the fluorescent activity-based probe Bocillin-FL. Our results align with in vitro kinact/KI data and show a comparable relationship to previously established IC50 values. These results support the validity of our in vivo kinact/KI method as a means of obtaining a full picture of {beta}-lactam potency for a suite of PBPs. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/592586v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@e265ecorg.highwire.dtl.DTLVardef@1917decorg.highwire.dtl.DTLVardef@e2253forg.highwire.dtl.DTLVardef@fb6c60_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

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↗

bioRxiv2019

Activation of the Extracytoplasmic Function σ factor σP by β-lactams in Bacillus thuringiensis requires the site-2 protease RasP

Bacteria can utilize alternative {sigma} factors to regulate sets of genes in response to changes in the environment. The largest and most diverse group of alternative {sigma} factors are the Extracytoplasmic Function (ECF) {sigma} factors. {sigma}P is an ECF {sigma} factor found in Bacillus anthracis, B. cereus, and B. thuringiensis. Previous work showed {sigma}P is induced by ampicillin, a {beta}-lactam antibiotic, and required for resistance to ampicillin. However, it was not known how activation of {sigma}P is controlled or what other antibiotics may activate {sigma}P. Here we report that activation of {sigma}P is specific to a subset of {beta}-lactams and {sigma}P is required for resistance to these {beta}-lactams. We demonstrate that activation of {sigma}P is controlled by the proteolytic destruction of the anti-{sigma} factor, RsiP, and that degradation of RsiP requires multiple proteases. Upon exposure to {beta}-lactams, the extracellular domain of RsiP is cleaved by an unknown protease, which we predict cleaves at site-1. Following cleavage by the unknown protease, the N-terminus of RsiP is further degraded by the site-2 intramembrane protease, RasP. Our data indicate that RasP cleavage of RsiP is not the rate-limiting step in {sigma}P activation. This proteolytic cascade leads to activation of {sigma}P which induces resistance to {beta}-lactams likely via increased expression of {beta}-lactamases.\n\nImportanceThe discovery of antibiotics to treat bacterial infections has had a dramatic and positive impact on human health. However, shortly after the introduction of a new antibiotic bacteria often develop resistance. The bacterial cell envelope is essential for cell viability and is the target of many of the most commonly used antibiotics including {beta}-lactam antibiotics. Resistance to {beta}-lactams is often dependent upon {beta}-lactamases. In B. cereus, B. thuringiensis and some B. anthracis strains the expression of some {beta}-lactamases is inducible. This inducible {beta}-lactamase expression is controlled by activation of an alternative {sigma} factor called {sigma}P. Here we show that {beta}-lactam antibiotics induce {sigma}P activation by degradation of the anti-{sigma} factor RsiP.

microbiology↗