Biology subjects

Clardy, J.

Publications and source records attributed to Clardy, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Microbial-associated acylated putrescines as immunomodulatory molecules in inflammatory bowel diseases

The gut microbiota regulates intestinal immunity through metabolite production, yet most disease-associated metabolites remain functionally uncharacterized. In inflammatory bowel diseases (IBD), where the microbial metabolome is profoundly altered, we identify N-acyl putrescines as microbiome-associated metabolites enriched across two independent cohorts. N-oleoylputrescine (NOP) emerges as the primary immunomodulatory candidate, inducing robust transcriptional responses in dendritic cells and colonic organoids. Enterocloster species harboring nonribosomal peptide synthetase gene clusters synthesize NOP, confirmed by isotope-tracing in vitro and germ-free mouse colonization in vivo. NOP suppresses core IBD inflammatory pathways in mouse dendritic cells and human monocytes, reducing signatures of histologic inflammation and therapy non-response. NOP dampens inflammation in four colitis models, decreases myeloid cell NF-{kappa}B activation, and suppresses type 1 immune responses through a T cell-intrinsic mechanism. That NOP accumulates in IBD despite its anti-inflammatory properties reveals a holobiont defense strategy: the gut microbiota deploys immunomodulatory metabolites as a compensatory response to restore homeostasis.

immunology↗

bioRxiv2026

An ancient receptor family illuminates the evolution of animal sensation

Animals use nervous systems to sense and respond to their environment. Yet single-celled organisms can also detect cues to execute diverse behaviors, suggesting that core components for animal sensation predate multicellularity and nervous systems. Here, we report that choanoflagellates, the closest living animal relatives, use an ancient sensory receptor family to detect bacterial prey. These receptors are related to transient receptor potential ion channels but are distinguished by WD40 domains, defining TRPW. TRPW1 detects specific bacterial lipids to modulate flagellar beating, providing a mechanism for attraction towards prey. TRPW emerged in early eukaryotes and reveals ancestral architectural and ligand-binding features that predate animal somatosensory receptors. In multicellular choanoflagellates, TRPW1 elicits collective responses, linking bacterial ecology to the evolution of receptors, sensory organelles, and multicellular life.

evolutionary biology↗

bioRxiv2026

Blautia wexlerae Transforms Dietary Fatty Acids to Activate Enteroendocrine Signaling and Improve Metabolic Health in Mice and Humans

Metabolites produced by the gut microbiome influence host metabolic health, but how this occurs remains incompletely defined. Here, we report that a common human gut commensal, Blautia wexlerae, converts dietary fats into bioactive metabolites that induce gut hormone production to affect glucose metabolism and suppress appetite. We found that colonization with Blautia wexlerae correlated with healthier eating behaviors in humans. Blautia wexlerae encodes a unique acyl transferase and is capable of producing acyl amines from nutrient substrates. These Blautia acyl amines stimulated human enteroendocrine cells to secrete GLP-1 and other gut peptide hormones more potently than endogenously produced acyl amines. When fed to mice, acyl amines improved glycemic control and decreased appetite. In humans, higher stool levels of Blautia DNA encoding acyl amine synthesis genes correlated with leanness and decreased dietary fat intake. These results define a mechanism of action for how Blautia wexlerae affects host metabolic control.

microbiology↗

bioRxiv2026

Aerocavin is an antibiotic with potent and specific anti-Neisserial activity

Gonorrhea, caused by N. gonorrhoeae, is a widespread sexually transmitted disease that is becoming resistant to all currently used antibiotics. Therefore, new therapeutics against gonorrhea are desperately needed. Here, we show that a natural product - aerocavin, is highly potent and specific against Neisseria. Aerocavin accumulates in N. gonorrhoeae at high levels and inhibits bacterial RNA polymerase (RNAP) by binding the switch region. Aerocavin resistance mutations evolve in N. gonorrhoeae at a low rate and are absent in clinical isolates. Previously overlooked narrow-spectrum antimicrobials like aerocavin may enable microbiome-sparing treatments of gonorrhea.

microbiology↗

bioRxiv2026

4,5-dihydroxyhexanoic acid is a robust circulating and urine marker of mitochondrial disease and its severity

Management of patients with mitochondrial respiratory chain diseases is challenging, in part because of our incomplete understanding of pathogenesis and a lack of biomarkers. Unknown metabolites account for >90% of detected features in modern metabolomics experiments and hold immense untapped promise for new basic and biomedical research. We recently used mass spectrometry-based metabolomics to identify and validate 19 circulating blood-based biomarkers for patients with the mitochondrial DNA (mtDNA) m.3243A>G pathogenic variant, which is the most frequent cause of the mitochondrial disorder MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes). However, the most significantly changing biomarker corresponded to an "unknown" metabolite. Here, we combine cheminformatics with analytical chemistry and identify that feature as 4,5-dihydroxyhexanoic acid (4,5-DHHA), a metabolite previously associated with inherited defects of gamma-aminobutyric acid (GABA) catabolism, but with no prior links to mitochondrial respiratory chain disorders. We validate this finding in an independent MELAS cohort and further show that 4,5-DHHA levels correlate with disease severity and are elevated in patients with other forms of mitochondrial disease and sepsis. Furthermore, brain 4,5-DHHA levels were elevated in two genetic mouse models of mitochondrial disease. In vitro and tissue culture experiments indicate that 4,5-DHHA is generated when the GABA catabolite succinic semialdehyde reacts with an intermediate of the pyruvate dehydrogenase reaction and is sensitive to mitochondrial complex I function. Our work identifies 4,5-DHHA as a robust plasma and urine marker of mitochondrial dysfunction in humans and reveals new connections between the respiratory chain and GABA metabolism. Significance StatementInborn errors of the mitochondrial respiratory chain cause severe, progressive diseases, yet effective treatments and biomarkers remain limited. Modern metabolomics detects thousands of molecules in biofluids, but the vast majority are unidentified. In this study, we investigate the most significantly altered blood metabolite in patients with the most common mitochondrial disease - MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) - and identify it as an 4,5-dihydroxyhexanoic acid (4,5-DHHA). We show that 4,5-DHHA is reproducibly elevated and correlates with severity. Levels are increased across multiple mitochondrial disorders as well as in sepsis and rise when respiratory chain function is impaired. These findings establish 4,5-DHHA as a promising biomarker of mitochondrial dysfunction and reveal a link to dysregulated GABA metabolism.

biochemistry↗

bioRxiv2026

Ecological Interactions Drive Metabolomic Diversification in Amazonian Pseudonocardia Symbionts

Fungus-growing ants engage in a multipartite symbiosis, including Pseudonocardia bacteria that produce antifungal metabolites to protect their fungal cultivar from the specialized pathogen Escovopsis. While different bioactive metabolites have been reported from ant-associated Pseudonocardia, most studies have focused on a limited number of strains, leaving the extent of chemical diversity across broader ecological contexts less resolved. Here, we investigated the antagonistic potential and metabolomic repertoires of 36 Pseudonocardia strains isolated from Amazonian Paratrachymyrmex ants. Pairwise bioactivity assays against two Escovopsis isolates revealed striking variability, with inhibition generally stronger and more diverse against the pathogenic fungus originating from the same ant genus. Untargeted LC-MS/MS metabolomics coupled with 16S rRNA-based phylogenetic analyses showed that closely related strains harbored highly divergent chemical profiles, underscoring a decoupling between taxonomy and metabolite output. Detailed analyses of selected isolates revealed the production of structurally diverse metabolites, including dentigerumycin analogs, provipeptide A, {beta}-carbolines, and tetracycline-related compounds. Co-culture analysis uncovered metabolites absent in monocultures, including lichenysins, pepstatins, and hallobacillins, as well as conserved attinimicin, whose production was enhanced under pathogen challenge. These results highlight that both strain-specific metabolic repertoires and interaction-induced chemistry contribute to the defensive arsenal of Pseudonocardia. Together, our findings likely demonstrate that ecological pressures and local adaptation, rather than phylogeny alone, drive metabolomic diversification in this defensive symbiosis. Beyond their potential for novel bioactive compound discovery, these results provide insights into the chemical basis of multipartite symbioses, the dynamics of defensive mutualisms, and the ecological forces shaping microbial diversity in underexplored environments such as the Amazon. IMPORTANCEMicrobial symbionts are central to host defense and natural product discovery, yet the factors driving their chemical diversification remain unclear. The fungus-growing ant-Pseudonocardia-Escovopsis system offers a powerful model to study how ecological context shapes microbial metabolism. By systematically characterizing multiple Amazonian Pseudonocardia strains, we show that antagonistic capacity and metabolomic repertoires vary widely, even among strains with highly similar 16S rRNA gene sequences, revealing a pronounced discordance between 16S-based phylogenetic relatedness and specialized metabolite production. These findings highlight the likely importance of ecological pressures and local adaptation in shaping metabolomic output, emphasizing symbiotic actinobacteria as both key ecological players and promising sources of antifungal natural products.

microbiology↗

bioRxiv2025

Acetoacetate suppresses colon cancer via an MR1-MAIT axis

Colorectal cancer (CRC) is a leading cause of cancer mortality and additional preventative, and therapeutic strategies are urgently needed. Ketogenic diets have mixed effects on tumorigenesis and compliance is challenging. Exogenous ketones, {beta}-hydroxybutyrate ({beta}HB) or acetoacetate (AcAc), offer an alternative approach. While {beta}HB has been investigated, the anti-cancer effects of AcAc are poorly defined. Here, we show that orally administering ethyl AcAc (EAA) suppresses tumor growth in several pre-clinical CRC models. Single-cell RNA sequencing, flow cytometry, and genetic and antibody-mediated depletion studies reveal that EAA selectively expands and activates cytotoxic mucosal-associated invariant T (MAIT) cells in an MHC class I-related protein 1 (MR1)-dependent manner. EAA increases MR1 expression by tumor monocytes, which is recapitulated in human cell cultures, where AcAc and 5-amino-6-D-ribitylaminouracil (5-A-RU) induce MAIT cell expansion and tumor killing. Mechanistically, AcAc converts to methylglyoxal, combining with microbially-derived 5-A-RU to generate 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil (5-OP-RU), a potent MR1 ligand. These findings identify an AcAc-MR1-MAIT cell axis as a potential immunotherapy approach for CRC therapy.

immunology↗

bioRxiv2025

The gut microbiome of the Passalid beetle has high cellulolytic potential and constitutes an unrecognized system for production of greenhouse gasses in neotropical forests

Herbivores, and their associated microbiomes, play a major role in the global carbon cycle. Recalcitrant cellulose molecules are broken down by microorganisms that colonize the herbivore gut, releasing greenhouse gasses in the process. Passalid beetles are tropical herbivores that feed only on decaying wood and present subsocial behavior that may lead to the acquisition and sharing of microbial symbionts for efficient biomass and energy production. We collected five groups of Veturius sp. Passalid beetles from different logs in the Costa Rican rainforest and analyzed the microbial communities of larval and adult guts, as well as the substrate material in which they resided (partially chewed wood material mixed with feces that covers their tunnels). Adults, larvae, and substrate harbor different microbial communities, with substrate showing the highest diversity and richness, and larvae gut comprising a high abundance of methanogenic archaea. Reconstructed metagenome assembled genomes (MAGs) revealed that larvae and adults are enriched in genomes encoding a myriad of glycosyl hydrolases. Methanogenic taxa were enriched within the larval MAGs and bins, suggesting that larval microbiota participate in the final steps of cellulose decomposition in the system. Finally, we assessed methane production rates by Passalid beetles and compared them with termites. Our results show that Passalid larvae and adults produce methane at rates comparable to termites. Passalid and other beetle larvae are potentially underappreciated contributors to the carbon cycle and the biotic production of the greenhouse gas methane.

microbiology↗

bioRxiv2025

Environmental microbiomes drive chemotactile sensation in octopus

Microbial communities coat nearly every surface in the environment and have co-existed with animals throughout evolution. Whether animals exploit omnipresent microbial cues to navigate their surroundings is not well understood. Octopuses use "taste by touch" chemotactile receptors (CRs) to explore the seafloor, but how they distinguish meaningful surfaces from the rocks and crevices they encounter is unknown. Here, we report that secreted signals from microbiomes of ecologically relevant surfaces activate CRs to guide octopus behavior. Distinct molecules isolated from specific bacterial strains located on prey or eggs bind single CRs in subtly different structural conformations to elicit distinct mechanisms of receptor activation, ion permeation and signal transduction, and maternal care and predation behavior. Thus, microbiomes on ecological surfaces act at the level of primary sensory receptors to inform behavior. Our study demonstrates that uncovering interkingdom interactions is essential to understanding how animal sensory systems evolved in a microbe rich world. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/641191v1_ufig1.gif" ALT="Figure 1"> View larger version (140K): org.highwire.dtl.DTLVardef@15f365eorg.highwire.dtl.DTLVardef@1ea5606org.highwire.dtl.DTLVardef@1b5ad1aorg.highwire.dtl.DTLVardef@779e6e_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIChemotactile receptors (CRs) detect microbiomes of prey and progeny C_LIO_LIDiverse microbial signals bind single CRs with distinct structural conformations C_LIO_LIDistinct microbial signals activate single CRs to permeate different ions C_LIO_LIEnvironmental microbes elicit octopus predatory and maternal behaviors C_LI

physiology↗

bioRxiv2024

Vaginal lactobacilli produce anti-inflammatory beta-carboline compounds.

The vaginal microbiome is a lactobacilli-dominant, human-adapted community consistently found in people around the world. Presence of lactobacilli-dominant vaginal microbial communities, apart from Lactobacillus iners, is associated with reduced vaginal inflammation and reduced levels of pro-inflammatory cytokines. Loss of lactobacilli-dominance is associated with inflammatory conditions such as bacterial vaginosis. It remains unclear if health-associated lactobacilli actively promote the anti-inflammatory immune homeostasis of the vaginal mucosa and if so, by which mechanisms. We have identified that Lactobacillus crispatus, a key vaginal bacterial species, secretes a family of {beta}-carboline compounds with anti-inflammatory activity. These compounds suppress NF{kappa}B and interferon signaling downstream of multiple pattern recognition receptors in human macrophages and significantly dampen type I interferon receptor activation. Topical vaginal application of an anti-inflammatory {beta}-carboline compound, perlolyrine, was sufficient to significantly reduce vaginal inflammation in a mouse model of genital herpes infection. Together, we identify a key family of compounds by which vaginal lactobacilli mediate host immune homeostasis and could highlight a new therapeutic avenue for vaginal inflammation.

microbiology↗

bioRxiv2021

Neuronal control of maternal provisioning in response to social cues

Mothers contribute cytoplasmic components to their progeny in a process called maternal provisioning. Provisioning is influenced by the parental environment, but the molecular pathways that transmit environmental cues from mother to progeny are not well understood. Here we show that in C. elegans, social cues modulate maternal provisioning to regulate gene silencing in offspring. Intergenerational signal transmission depends on a pheromone-sensing neuron and neuronal FMRF (Phe-Met-Arg-Phe)-like peptides. Parental FMRF signaling promotes the deposition of mRNAs for translational components in progeny, which in turn reduces gene silencing. Previous studies had implicated FMRF signaling in short-term responses such as modulated feeding behavior in response to the metabolic state1,2, but our data reveal a broader role, to coordinate energetically expensive processes such as translation and maternal provisioning. This study identifies a new pathway for intergenerational communication, distinct from previously discovered pathways involving small RNAs and chromatin, that links sensory perception to maternal provisioning.

genetics↗

bioRxiv2021

Burkholderia from fungus gardens of fungus-growing ants produce antifungals that inhibit the specialized parasite Escovopsis

Within animal associated microbiomes, the functional roles of specific microbial taxa are often uncharacterized. Here, we use the fungus-growing ant system, a model for microbial symbiosis, to determine the potential defensive roles of key bacterial taxa present in the ants fungus gardens. Fungus gardens serve as an external digestive system for the ants, with mutualistic fungi in the genus Leucoagaricus spp. converting plant substrate into energy for the ants. The fungus garden is host to specialized parasitic fungi in the genus Escovopsis. Here, we examine the potential role of Burkholderia spp. that occur within ant fungus gardens in inhibiting Escovopsis. We isolated members of the bacterial genera Burkholderia spp. and Paraburkholderia spp. from 50% of the 52 colonies sampled, indicating that the family Burkholderiaceae are common fungus garden inhabitants of a diverse range of fungus-growing ant genera. Using antimicrobial inhibition bioassays, we found that 28 out of 32 isolates inhibited at least one Escovopsis strain with a zone of inhibition greater than 1 cm. Genomic assessment of Burkholderiaceae isolates indicated that isolates with strong inhibition all belonged to the genus Burkholderia and contained biosynthetic gene clusters that encoded the production of two antifungals: burkholdine1213 and pyrrolnitrin. Organic extracts of cultured isolates confirmed these compounds as responsible for antifungal activity that inhibit Escovopsis but, at low concentrations, not Leucoagaricus spp. Overall, these new findings, combined with previous evidence, suggest that members of the fungus garden microbiome play an important role in maintaining the health and function of the fungus-farming ant colony. IMPORTANCEMany organisms partner with microbes to defend themselves against parasites and pathogens. Fungus-growing ants must protect Leucoagaricus spp., the fungal mutualist that provides sustenance for the ants, from a specialized fungal parasite, Escovopsis spp. The ants take multiple approaches, including weeding their fungus gardens to remove Escovopsis spores, as well as harboring Pseudonocardia that produce antifungals that inhibit Escovopsis. In addition, a genus of bacteria commonly found in fungus gardens, Burkholderia spp., is known to produce secondary metabolites that inhibit Escovopsis spp. In this study, we isolated Burkholderia spp. from fungus-growing ants, assessed the isolates ability to inhibit Escovopsis spp., and identified two compounds responsible for inhibition. Our findings suggest that Burkholderia spp. are often found in fungus gardens, adding another possible mechanism within the fungus-growing ant system to suppress the growth of the specialized parasite Escovopsis.

microbiology↗

bioRxiv2020

Bacterially produced small molecules stimulate diatom growth

Diatoms are photosynthetic microalgae that fix a significant fraction of the worlds carbon. Because of their photosynthetic efficiency and high-lipid content, diatoms are priority candidates for biofuel production. Here, we report that sporulating Bacillus thuringiensis when in co-culture with a marine diatom Phaeodactylum tricornutum significantly increases the diatom cell count. Bioassay-guided purification led to the identification of two diketopiperazines (DKPs) that both stimulate P. tricornutum growth and increase its lipid content. RNA-seq analysis revealed upregulation of a small set of P. tricornutum genes involved in iron starvation response and nutrient recycling when DKP was added to the diatom culture. This work demonstrates that two DKPs produced by a bacterium could positively impact P. tricornutum growth and lipid content, offering new approaches to enhance P. tricornutum-based biofuel production. As increasing numbers of DKPs are isolated from marine microbes, the work gives potential clues to bacterially produced growth factors for marine microalgae. One sentence summaryTwo diketopiperazines (DKPs) produced by sporulating bacterium Bacillus thuringiensis stimulate diatom P. tricornutum growth and increase diatom lipid content.

plant biology↗

bioRxiv2020

Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways

The intestinal epithelium senses nutritional and microbial stimuli using epithelial sensory enteroendocrine cells (EECs). EECs can communicate nutritional information to the nervous system, but similar mechanisms for microbial information are unknown. Using in vivo real-time measurements of EEC and nervous system activity in zebrafish, we discovered that the bacteria Edwardsiella tarda specifically activates EECs through the receptor transient receptor potential ankyrin A1 (Trpa1) and increases intestinal motility in an EEC-dependent manner. Microbial, pharmacological, or optogenetic activation of Trpa1+EECs directly stimulates vagal sensory ganglia and activates cholinergic enteric neurons through 5-HT. We identified a subset of indole derivatives of tryptophan catabolism produced by E. tarda and other gut microbes that potently activates zebrafish EEC Trpa1 signaling and also directly stimulates human and mouse Trpa1 and intestinal 5-HT secretion. These results establish a molecular pathway by which EECs regulate enteric and vagal neuronal pathways in response to specific microbial signals.

physiology↗

bioRxiv2019

Biogeography and Microscale Diversity Shape the Biosynthetic Potential of Fungus-growing Ant-associated Pseudonocardia

The geographic and phylogenetic scale of ecologically relevant microbial diversity is still poorly understood. Using a model mutualism, fungus-growing ants and their defensive bacterial associate Pseudonocardia, we analyzed genetic diversity and biosynthetic potential in 46 strains isolated from ant colonies in a 20km transect near Barro Colorado Island in Panama. Despite an average pairwise core genome similarity of greater than 99%, population genomic analysis revealed several distinct bacterial populations matching ant host geographic distribution. We identified both genetic diversity signatures and divergent genes distinct to each lineage. We also identify natural product biosynthesis clusters specific to isolation locations. These geographic patterns were observable despite the populations living in close proximity to each other and provides evidence of ongoing genetic exchange. Our results add to the growing body of literature suggesting that variation in traits of interest can be found at extremely fine phylogenetic scales.

microbiology↗

bioRxiv2019

Cycloheximide-Producing Streptomyces Associated with Xyleborinus saxesenii and Xyleborus affinis Fungus-Farming Ambrosia Beetles

Symbiotic microbes help a myriad of insects acquire nutrients. Recent work suggests that insects also frequently associate with actinobacterial symbionts that produce molecules to help defend against parasites and predators. Here we explore a potential association between Actinobacteria and two species of fungus-farming ambrosia beetles, Xyleborinus saxesenii and Xyleborus affinis. We isolated and identified actinobacterial and fungal symbionts from laboratory reared nests, and characterized small molecules produced by the putative actinobacterial symbionts. One 16S rRNA phylotype of Streptomyces (XylebKG-1) was abundantly and consistently isolated from the nests and adults of X. saxesenii and X. affinis nests. In addition to Raffaelea sulphurea, the symbiont that X. saxesenii cultivates, we also repeatedly isolated a strain of Nectria sp. that is an antagonist of this mutualism. Inhibition bioassays between S. griseus XylebKG-1 and the fungal symbionts from X. saxesenii revealed strong inhibitory activity of the actinobacterium towards the fungal antagonist Nectria sp. but not the fungal mutualist R. sulphurea. Bioassay guided HPLC fractionation of S. griseus XylebKG-1 culture extracts, followed by NMR and mass spectrometry identified cycloheximide as the compound responsible for the observed growth inhibition. A biosynthetic gene cluster putatively encoding cycloheximide was also identified in S. griseus XylebKG-1. The consistent isolation of a single 16S phylotype of Streptomyces from two species of ambrosia beetles, and our finding that a representative isolate of this phylotype produces cycloheximide, which inhibits a parasite of the system but not the cultivated fungus, suggests that these actinobacteria may play defensive roles within these systems.

microbiology↗

bioRxiv2018

Amycomicin: a potent and specific antibiotic discovered with a targeted interaction screen

The rapid emergence of antibiotic-resistant pathogenic bacteria has accelerated the search for new antibiotics. Many clinically used antibacterials were discovered through culturing a single microbial species under nutrient-rich conditions, but in the environment, bacteria constantly encounter poor nutrient conditions and interact with neighboring microbial species. In an effort to recapitulate this environment we generated a nine-strain Actinomycete community and used 16S rDNA sequencing to deconvolute the stochastic production of antimicrobial activity that was not observed from any of the axenic cultures. We subsequently simplified the community to just two strains and identified Amycolatopsis sp. AA4 as the producing strain and Streptomyces coelicolor M145 as an inducing strain. Bioassay-guided isolation identified amycomicin, a highly modified fatty acid containing an epoxide isonitrile warhead as a potent and specific inhibitor of Staphylococcus aureus. Amycomicin targets an essential enzyme in fatty acid biosynthesis (FabH) and reduces S. aureus infection in a mouse skin infection model. The discovery of amycomicin demonstrates the utility of screening complex communities against specific targets to discover small-molecule antibiotics.\n\nSignificanceBacteria, especially actinomycetes, produce the majority of our clinically useful small-molecule antibiotics. Genomic analyses of antibiotic-producing strains indicate that earlier discovery efforts found only a fraction of the likely antibiotic candidates. In an effort to uncover these previously missed candidates we developed an approach that utilizes the ability of microbial communities to produce antibiotics that are not produced by any single member in isolation. Successful communities were established and deconvoluted to identify both producers and inducers of antibiotic activity. One inducer-producer pair made amycomicin, a potent and specific antibiotic against Staphylococcus aureus, an important human pathogen. Amycomicin targets fatty acid biosynthesis and exhibits in vivo efficacy against skin infections in a mouse model.

microbiology↗

bioRxiv2018

Mammalian Cells Engineered to Produce Novel Steroids

Steroids can be difficult to modify via traditional organic synthesis methods, but many enzymes regio- and stereo-selectively process a wide variety of steroid substrates. We tested whether steroid-modifying enzymes could make novel steroids from non-native substrates. Numerous genes encoding steroid-modifying enzymes, including some bacterial enzymes, were expressed in mammalian cells by transient transfection and found to be active. We made three unusual steroids by expression in HEK293 cells of the 7-hydroxylase CYP7B1, which was selected because of high native product yield. These cells made 7,17-dihydroxypregnenolone and 7{beta},17-dihydroxypregnenolone from 17-hydroxypregnenolone, and produced 11,16-dihydroxyprogesterone from 16-hydroxyprogesterone. The latter two products resulted from previously unobserved CYP7B1 hydroxylation sites. A Rosetta docking model of CYP7B1 suggested that these substrates D-ring hydroxylations may prevent them from binding in the same way as the native substrate, bringing different carbons near the active ferryl oxygen. This new approach could use other enzymes and substrates to produce many novel steroids for drug candidate testing.

synthetic biology↗