Biology subjects

Schroeder, F. C.

Publications and source records attributed to Schroeder, F. C..

At least 19 recordsLinked to original sources

bioRxiv2026

Omics-scale capture of electrophilic metabolites

The majority of metabolic pathways rely on the production of activated electrophilic intermediates, e.g., coenzyme-A esters, and their chemical structures and abundances are central to understanding enzyme function and biochemical mechanisms. However, most electrophilic metabolites are lost in traditional metabolomic analysis and thus remain poorly characterized. Here we introduce a biochemical probe, O-(trimethylammoniobutyl)-hydroxylamine (TAMOHA), that enables comprehensive profiling of electrophilic species such as coenzyme-A esters, ketones, and aldehydes. TAMOHA incorporates a highly nucleophilic hydroxyl amine that reacts quickly with electrophilic species upon tissue lysis, trapping them as stable derivatives that feature a tetraalkylammonium moiety whose constitutive charge and characteristic MS2 fragmentation fingerprint enable their highly sensitive detection. Using TAMOHA to survey the electrophilomes of E. coli, C. elegans, and mouse revealed several thousand electrophilic metabolites, most of which have not been characterized. We then demonstrate trapping of electrophilic metabolites with TAMOHA in the context of specific biochemical pathways, confirming previously proposed functions of two fatty acid metabolism enzymes, detecting formaldehyde production in mice, and providing new insights into the biosynthesis of ascaroside pheromones in C. elegans. We anticipate that use of TAMOHA for the profiling of electrophilic species will help clarify enzyme function and uncover previously elusive biochemical mechanisms in a wide range of biological systems. Table of Contents artwork O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/743530v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@79a416org.highwire.dtl.DTLVardef@3b937org.highwire.dtl.DTLVardef@74cae9org.highwire.dtl.DTLVardef@1b5a915_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Charting the small-molecule universe from mass spectra with neuro-symbolic AI

Mass spectrometry (MS) has revealed millions of small organic molecules across organisms, yet most remain uncharacterized, limiting progress in biology and medicine. Despite computational advances, MS workflows rely heavily on expert input and reference libraries that cover only a fraction of known chemical space. Here, we introduce AIMe (AI Molecule Explorer), a multi-agent neuro-symbolic AI framework that transforms the interpretation of unknown spectra into an omics-scale exploration across the known structural space, providing chemically interpretable annotations. At its core, AIMe combines chemical reasoning with structure- informed learning to predict MS2 spectra by modeling fragmentation as a sequence of actions, outperforming existing methods. AIMe dynamically constructs fragmentation pathways by assigning likelihoods to individual fragmentation actions, linking spectral peaks to explicit fragment molecular formulas and structures. At scale, AIMe predicted MS2 spectra for over 100 million small organic molecules in PubChem and organized them into MS2KOSMOS, a substructure-informed community resource comprising over 800 million predicted spectra that expands the searchable small-molecule universe by roughly three orders of magnitude relative to experimental libraries. Analogous to sequence homology-based searches in genomics and proteomics, AIMe maps unknown spectra to molecular neighborhoods in MS2KOSMOS. Exact- formula indexing enables ranked retrieval of candidates and related structures, with peak-level structural and fragmentation-pathway annotations. Applied to mouse microbiota-dependent metabolites, AIMe enabled putative annotation of knowns and guided structure elucidation of unknowns, revealing previously unreported types of microbiota-dependent polyamines that also occur in humans. At repository scale, AIMe enabled putative annotation of roughly a third of 7 million spectral clusters representing most of the unknowns in the GNPS database. By extending MS2 annotation beyond curated-library matching to interpretable search across the known small-molecule universe, AIMe accelerates discovery and large-scale exploration of small molecules across biomedicine, agriculture, and ecology.

biochemistry↗

bioRxiv2026

Interactomics-driven discovery of alkaloid biosynthetic pathways in kratom

Plant monoterpene indole alkaloids (MIAs) exhibit important pharmacological activities, yet understanding of their biosyntheses remains incomplete. Since protein-protein interactions (PPIs) represent a conserved regulatory mechanism in MIA-producing plants, we developed a large-scale, yeast-based screening pipeline to profile PPIs of a key enzyme, strictosidine {beta}-D-glucosidase (SGD) from Mitragyna speciosa (kratom). This screen identified six novel medium-chain dehydrogenases/reductases (MDRs) as high-confidence interaction partners of SGD. Biochemical characterization revealed that all six MsMDRs produce an MIA we named charlamine by acting directly on the reactive strictosidine aglycone intermediate, preventing its spontaneous rearrangement and establishing a functional rationale for SGD-MDR interaction. One MsMDR additionally catalyzed the reduction of vallesiachotamine, derived from the spontaneous rearrangement of strictosidine aglycone, to another previously unreported MIA, vallesiachotaminol. Parallel transcriptomics and genomics analyses uncovered a biosynthetic gene cluster containing a dihydrocorynantheine aldehyde esterase, functioning downstream of MsMDRs. Collectively, these findings demonstrate the utility of interactomics-driven plant pathway discovery. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/722234v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1ccc22dorg.highwire.dtl.DTLVardef@1e03f3borg.highwire.dtl.DTLVardef@15773deorg.highwire.dtl.DTLVardef@782ae0_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Nuclear receptor-neurotransmitter coupling links behavior to metabolic state

Animals must flexibly respond to environmental stimuli to survive, and optimal responses critically depend on the organisms current needs. Many organisms have evolved both cell-intrinsic and intertissue signaling pathways that integrate metabolic status. However, how this information is encoded in molecular signals is currently not well understood. Here we show that the nematode C. elegans employs lipidated neurohormones that combine the neurotransmitter octopamine and fat metabolism-derived building blocks to relay information about lipid metabolic status and drive inhibition of aversive olfactory responses during food removal. Using targeted metabolomics, we show that lipidated neurohormone synthesis requires the carboxylesterase CEST-2.1, which links octopamine-glucosides with endogenous methyl-branched or diet-derived cyclopropane fatty acids that act as agonists of the nuclear receptor and master regulator of fat metabolism, NHR-49/PPAR. Loss of cest-2.1, loss of bacterial cyclopropane fatty acid production, or loss of endogenous biosynthesis of the methyl-branched fatty acid substrates of CEST-2.1 mimics the behavioral responses of animals lacking octopamine, indicating that regulation of neurotransmitter-dependent behavior is linked to the coordination of fat metabolism via NHR-49/PPAR. Biosynthesis and subsequent neuromodulation via lipidated neurohormone relies on an intertissue trafficking pathway in which octopamine is shuttled first into the intestine where it is chemically modified, which is likely followed by neuronal import and intracellular hydrolysis to finally release free octopamine. We propose that esterase-dependent synthesis and subsequent hydrolysis of lipidated neurohormones represents a chemical encoding mechanism by which animals integrate information from neurotransmitter signaling and lipid homeostasis to direct appropriate behaviors.

neuroscience↗

bioRxiv2025

Lactate promotes longevity through redox-driven lipid remodeling in Caenorhabditis elegans.

Lactate has emerged as a key metabolite involved in multiple physiological processes, including memory formation, immune response regulation, and muscle biogenesis. However, its role in aging and cellular protection remains unclear. Here, we show that lactate promotes longevity in C. elegans through a mechanism that requires early-life intervention, indicating a hormetic priming effect. This pro-longevity action depends on its metabolic conversion via LDH-1 and NADH, which drives redox-dependent metabolic reprogramming. Multi-omics approaches revealed that lactate induces early-stage metabolic adaptations, with a strong modulation of lipid metabolism, followed by late-life transcriptional remodeling. These shifts are characterized by enhanced stress response pathways and suppression of energy- associated metabolic processes. Our genetic screening identified sir-2.1/SIRT1 and rict- 1/RICTOR as essential for lactate-mediated lifespan extension. Our findings establish lactate as a pro-longevity metabolite that couples redox signaling with lipid remodeling and nutrient- sensing pathways. This work advances our understanding of lactates dual role as a metabolic intermediary and geroprotector signaling molecule, offering insights into therapeutic strategies for age-related metabolic disorders.

physiology↗

bioRxiv2025

Cyclohexyl acetate functions like a volatile sex pheromone mimic in Caenorhabditis nematodes

Nematodes communicate via diverse sex pheromones, including long-range volatile signals, short-range chemical cues, and contact-dependent molecules. While the ascaroside family of small molecules that mediate short-range attraction is well characterized, the identities and roles of volatile sex pheromones (VSPs) that act over longer ranges remain unknown. Using GC-MS analysis of crude VSP extracts, we identified cyclohexyl acetate (CA) as a candidate mimic, sharing retention time and mass spectral features with natural VSPs. Behavioral assays demonstrated that CA acts as a concentration-dependent, male-specific attractant in Caenorhabditis. Pre-exposure to VSPs induced cross-adaptation to CA, suggesting shared sensory processing. Surprisingly, genetic and calcium imaging analyses revealed that CA perception is mediated primarily by AWCon (str-2-expressing) neurons and involves VSPs chemoreceptor srd-1-independent pathways, which are distinct from the neural pathways involved in natural VSPs perception. These findings establish that CA is not a major component of VSPs but a structural and functional mimic of nematode VSPs, operating through a parallel sensory circuit. Although the endogenous source of CA remains unknown, its structural and behavioral mimicry provides new insights into the complexity of chemosensory signaling and the potential for interspecies chemical eavesdropping in nematode ecology.

biochemistry↗

bioRxiv2025

A male-derived volatile sex pheromone in nematodes identified through its mimicry by a predator

Recent studies demonstrated that the predacious fungi Arthrobotrys oligospora emits a mixture of volatile chemical cues that function to attract nematode prey. The strong attraction elicited by one of the mixture components, methyl 3-methyl-2-butenoate (MMB), was highly female- and hermaphrodite-specific within several Caenorhabditis species, including C. remanei and C. elegans, suggesting that MMB might function as a mimic of an endogenous, male-produced, volatile sex pheromone (VSP) within these species. Here, we report evidence that MMB is produced by C. remanei males at levels that are attractive to C. remanei females and C. elegans hermaphrodites. Notably, MMB production was not detected for C. elegans males; a finding which correlates with behavioral assays for which worm-conditioned media (WCM) prepared from C. remanei, but not from C. elegans adult males is strongly attractive to both C. remanei females and C. elegans hermaphrodites. Our findings establish MMB as the first chemically identified VSP in nematodes and show that A. oligospora exploits a dual strategy of chemical deception--mimicry and eavesdropping--to enhance prey capture.

animal behavior and cognition↗

bioRxiv2025

O-Acyltransferase Genes Involved in the Production of Volatile Sex Pheromones in Caenorhabditis elegans

Gene family expansions are critical for functional diversification, yet paralog contributions to metabolic pathways are often unclear. In Caenorhabditis, the expanded O-acyltransferase (OAC) family--enzymes that transfer acyl groups to hydroxylated substrates--remains poorly characterized despite having been implicated in lipid metabolism. Using CRISPR-Cas9 mutagenesis, behavioral assays, gas chromatographic-mass spectral (GC-MS) analyses, and metabolomics, we systematically analyzed 59 OAC-family protein-coding genes to define their roles in regulating signaling molecules. We found that four adjacent paralogs (oac-13, oac-16, oac-25, and oac-28) on chromosome I are required for synthesizing volatile sex pheromones (VSPs)--airborne signals critical for male mate-searching. Specifically, oac-13 and oac-16 are necessary for producing both major pheromone components, while the identical tandem paralogs oac-25 and oac-28 regulate the production of the later-eluting component in gas chromatography. Disruption of these genes reduced production of key pheromone components and impaired male attraction. Metabolomics revealed that oac-16 and other OACs also modulate synthesis and secretion of non-volatile ascaroside pheromones, indicating dual roles in chemical signaling. This work uncovers functional specialization within an expanded gene family, illustrating how redundancy and divergence enable adaptive evolution of communication systems.

biochemistry↗

bioRxiv2025

Whole-brain chemosensory responses of both C. elegans sexes

Sexually-dimorphic neural circuits play a critical role in shaping sex-specific animal behaviors. Maps of the structural dimorphisms in these circuits have been explored by analyzing "synaptic connectomes", electron micrograph reconstructions of synaptic connectivity. Nevertheless, recent studies in the model organism C. elegans have shown little to no correlation between the synaptic connectome and dynamic neural activity. Therefore, the extent of sexual dimorphism in functional neural activity remains unknown. To determine the extent of functional sexual-dimorphisms in C. elegans we compared activity, neuron-by-neuron, across all neurons in the heads of both sexes. To sample a broad view of responses to different sensory modalities, we tested a diverse panel of ethologically-relevant olfactory, gustatory, and chemical stimuli, representing both attractive and aversive cues. We found that nearly every sensory neuron responded dimorphically to at least one cue and monomorphically to other cues, indicating that sexually-dimorphic circuits are pervasive and stimulus dependent. This dimorphic and monomorphic activity was present to a lesser extent in downstream interneurons and even less so in motoneurons, implicating sensory neurons as the primary source and location of sexually-dimorphic activity. Comparing the functional activity we measured to the published synaptic connectomes of both sexes revealed that sexual dimorphism in functional connectivity was distinct from and complementary to sexual dimorphism in synaptic connectivity. Our results provide a first-of-its-kind comparison of whole-brain dynamics between sexes at the level of single neurons, serving as an extensive resource for further investigations of functional sex differences.

neuroscience↗

bioRxiv2025

Serotonergic signaling governs C. elegans sensory response to conflicting olfactory stimuli

Neural circuits that consolidate sensory cues are essential for neurological functioning. Neural circuits that perform sensory integration can vary greatly because the sensory processing regions of the brain employ various neural motifs. Here, we investigate a neural circuit that mediates the response to conflicting olfactory stimuli in C. elegans. We concurrently expose animals to an aversive dispersal pheromone, osas#9, and an attractive bacterial extract. While worms usually avoid osas#9 alone, they suppress this avoidance behavior in the presence of a bacterial extract. Loss-of-function mutants and cell-specific rescues reveal that serotonergic signaling from the ADF neuron is essential for bacterial extract-induced osas#9 avoidance attenuation. The inhibitory serotonin receptor, MOD-1, which is widely expressed on interneurons and motor neurons, is required for this sensory integration, suggesting that serotonin acts in an inhibitory manner. By performing calcium imaging on the ADF neurons in synaptic signaling (unc-13) and peptidergic (unc-31) signaling mutant backgrounds, we show that the ADF neurons require input from other neurons, likely the ASK neurons, to respond to food extracts. We reveal a cue integration neural circuit in which serotonergic signaling at the sensory neuron level silences an aversive neural signal. SignificanceAnimals use sensory cues to make behavioral choices and sometimes, these cues convey opposite information. The nervous system consolidates competing sensory cues to create a coherent response to external stimuli. The neural circuits that govern this process are important, and still largely unknown. We use C. elegans, a soil-dwelling nematode, to uncover a neural circuit governing the consolidation of competing cues by concurrently exposing worms to positive and negative stimuli . We find that the neurotransmitter serotonin can suppress aversive neural signals created by negative stimuli. These results show the important neurological role that serotonin plays in modulating neural signals.

neuroscience↗

bioRxiv2024

Naturally occurring variation in a cytochrome P450 modifies thiabendazole responses independent of beta-tubulin

Widespread anthelmintic resistance has complicated the management of parasitic nematodes. Resistance to the benzimidazole (BZ) drug class is nearly ubiquitous in many species and is associated with mutations in beta-tubulin genes. However, mutations in beta-tubulin alone do not fully explain all BZ resistance. We performed a genome-wide association study using a genetically diverse panel of Caenorhabditis elegans strains to identify loci that contribute to resistance to the BZ drug thiabendazole (TBZ). We identified a quantitative trait locus (QTL) on chromosome V independent of all beta-tubulin genes and overlapping with two promising candidate genes, the cytochrome P450 gene cyp-35d1 and the nuclear hormone receptor nhr-176, identified by another mapping technique. Both genes were previously demonstrated to play a role in TBZ metabolism. NHR-176 binds TBZ and induces the expression of CYP-35D1, which metabolizes TBZ. We generated single gene deletions of nhr-176 and cyp-35d1 and found that both genes play a role in TBZ response. A predicted high-impact lysine-to-glutamate substitution at position 267 (K267E) in CYP-35D1 was identified in a sensitive parental strain, and reciprocal allele replacement strains in both genetic backgrounds were used to show that the lysine allele conferred increased TBZ resistance. Using competitive fitness assays, we found that neither allele is deleterious, but the lysine allele is selected in the presence of TBZ. Additionally, we found that the lysine allele significantly increased the rate of TBZ metabolism compared to the glutamate allele. Moreover, yeast expression assays showed that the lysine version of CYP-35D1 had twice the enzymatic activity of the glutamate allele. To connect our results to parasitic nematodes, we analyzed four Haemonchus contortus cytochrome P450 orthologs but did not find variation at the 267 position in fenbendazole-resistant populations. Overall, we confirmed that variation in this cytochrome P450 gene is the first locus independent of beta-tubulin to play a role in BZ resistance. Author SummaryBenzimidazoles (BZs) are the most common drug class used to control parasitic nematodes, but because of overuse, resistance is widespread. The known genetic causes of BZ resistance are associated with mutations in beta-tubulin and are the most well understood of any anthelmintic class. However, BZ response varies significantly and differential levels of resistance likely require mutations in genes independent of beta-tubulin. We used the free-living model nematode Caenorhabditis elegans to identify and characterize a novel cytochrome P450 gene, cyp-35d1, associated with natural resistance to the BZ drug thiabendazole (TBZ). We demonstrated that a lysine at position 267 confers TBZ resistance and is selected over multiple generations after TBZ treatment. This allele significantly increased the rate of TBZ metabolism in both C. elegans and yeast. In conclusion, we have characterized the role of variation in a cytochrome P450 that contributes to TBZ resistance, independent of mutations in beta-tubulin.

genetics↗

bioRxiv2024

Mining for microbial metabolites associated with disease progression in an age-dependent model of experimental autoimmune encephalomyelitis

Age is a risk factor for the neurological decline and physical disability that characterize progressive multiple sclerosis (MS). The intestinal microbiota and the bioactive compounds it produces can influence aging, immunity, and the central nervous system (CNS). Here, we use an experimental autoimmune encephalomyelitis (EAE) model that mimics features of progressive MS in aged, but not young, mice to address the intersection of age and the microbiota on EAE outcomes. Although the microbiota of SJL/J mice aged under controlled laboratory conditions does not promote an aged non-remitting EAE phenotype, young mice harboring heterochronic human fecal microbiota transplants (hFMT) developed a range of EAE phenotypes. Metabolomic profiling of mice colonized with an aged hFMT that promoted non-remitting EAE indicated a severe reduction in circulating levels of the microbiota-derived tryptophan metabolite indole 3-propionic acid (IPA). IPA-supplementation enforced remission in mice colonized with the non-remitting hFMT, demonstrating the utility of this in vivo pipeline for discovering metabolites associated with progressive MS-like disease. SummaryThe microbiota is a critical determinant of disease susceptibility in mouse models of MS. Here, Pu & Fettig et al. demonstrate that disease outcomes (remitting or non-remitting) are microbiota-responsive, and describe an in vivo pipeline that can be mined for microbial metabolites with therapeutic potential for progressive MS.

immunology↗

bioRxiv2024

Sensory integration of food availability and population density during the diapause exit decision involves insulin-like signaling in Caenorhabditis elegans

Decisions made over long time scales, such as life cycle decisions, require coordinated interplay between sensory perception and sustained gene expression. The Caenorhabditis elegans dauer (or diapause) exit developmental decision requires sensory integration of population density and food availability to induce an all-or-nothing organismal-wide response, but the mechanism by which this occurs remains unknown. Here, we demonstrate how the ASJ chemosensory neurons, known to be critical for dauer exit, perform sensory integration at both the levels of gene expression and calcium activity. In response to favorable conditions, dauers rapidly produce and secrete the dauer exit-promoting insulin-like peptide INS-6. Expression of ins-6 in the ASJ neurons integrate population density and food level and can reflect decision commitment since dauers committed to exiting have higher ins-6 expression levels than those of non-committed dauers. Calcium imaging in dauers reveals that the ASJ neurons are activated by food, and this activity is suppressed by pheromone, indicating that sensory integration also occurs at the level of calcium transients. We find that ins-6 expression in the ASJ neurons depends on neuronal activity in the ASJs, cGMP signaling, a CaM-kinase pathway, and the pheromone components ascr#8 and ascr#2. We propose a model in which decision commitment to exit the dauer state involves an autoregulatory feedback loop in the ASJ neurons that promotes high INS-6 production and secretion. These results collectively demonstrate how insulin-like peptide signaling helps animals compute long-term decisions by bridging sensory perception to decision execution. Summary/Significance StatementAnimals must respond appropriately to multiple sensory stimuli to make informed decisions. It remains unclear how the nervous system is able to integrate different sensory cues and propagate that information towards making decisions over longer timescales. We use the nematode Caenorhabditis elegans to investigate how sensory integration occurs during the decision to exit diapause, a stress-resistant developmentally arrested state triggered by multiple sensory inputs including food availability and population density. We show how expression of an insulin-like peptide critical to dauer exit reflects the sensory integration process and decision commitment, and we dissect the regulation of this insulin-like peptides expression. Our study explicitly analyzes the relationship between neuronal activity and neuropeptide expression during a complex decision with diverse sensory inputs.

neuroscience↗

bioRxiv2024

Mapping protein-metabolite interactions in E. coli by integrating chromatographic techniques and co-fractionation mass spectrometry.

In our pursuit of understanding the protein-metabolite interactome, we introduced PROMIS, a co-fractionation mass spectrometry (CF-MS) technique focusing on biosynthetic and regulatory processes. However, the challenge lies in distinguishing true interactors from coincidental co-elution when a metabolite co-fractionates with numerous proteins. To address this, we integrated two chromatographic techniques-- size exclusion and ion exchange--to enhance the mapping of protein-metabolite interactions (PMIs) in Escherichia coli. This integration aims to refine the PMI network by considering size and charge characteristics, resulting in 994 interactions involving 51 metabolites and 465 proteins. The PMI network is enriched for known and predicted interactions validating our approachs efficacy. Furthermore, the analysis of protein targets for different metabolites revealed novel functional insights, such as the connection between proteinogenic dipeptides and fatty acid biosynthesis. Notably, we uncovered an inhibitory interaction between the riboflavin degradation product lumichrome and orotate phosphoribosyltransferase (PyrE), a key enzyme in de novo pyrimidine synthesis. Lumichrome supplementation mimicked the biofilm formation inhibition observed in a{Delta} pyrE mutant strain, suggesting lumichrome role in integrating pyrimidine and riboflavin metabolism with quorum sensing and biofilm formation. In summary, our integrated chromatographic approach significantly advances PMI mapping, offering novel insights into functional associations and potential regulatory mechanisms in E. coli.

biochemistry↗

bioRxiv2023

ATP-release pannexin channels are gated by lysophospholipids

In addition to its role as cellular energy currency, adenosine triphosphate (ATP) serves as an extracellular messenger that mediates diverse cell-to-cell communication. Compelling evidence supports that ATP is released from cells through pannexins, a family of membrane proteins that form heptameric large-pore channels. However, the activation mechanisms that trigger ATP release by pannexins remain poorly understood. Here, we discover lysophospholipids as endogenous pannexin activators, using activity-guided fractionation of mouse tissue extracts combined with untargeted metabolomics and electrophysiology. We show that lysophospholipids directly and reversibly activate pannexins in the absence of other proteins. Secretomics experiments reveal that lysophospholipid-activated pannexin 1 leads to the release of not only ATP but also other signaling metabolites, such as 5-methylthioadenosine, which is important for immunomodulation. We also demonstrate that lysophospholipids activate endogenous pannexin 1 in human monocytes, leading to the release of IL-1{beta} through inflammasome activation. Our results provide a connection between lipid metabolism and purinergic signaling, both of which play major roles in immune responses.

biophysics↗

bioRxiv2022

Natural genetic variation in the pheromone production of C. elegans

From bacterial quorum sensing to human language, communication is essential for social interactions. Nematodes produce and sense pheromones to communicate among individuals and respond to environmental changes. These signals are encoded by different types and mixtures of ascarosides, whose modular structures further enhance the diversity of this nematode pheromone language. Interspecific and intraspecific differences in this ascaroside pheromone language have been described previously, but the genetic basis and molecular mechanisms underlying the variation remain largely unknown. Here, we analyzed natural variation in the production of 44 ascarosides across 95 wild Caenorhabditis elegans strains using high-performance liquid chromatography coupled to high-resolution mass spectrometry (HPLC-HRMS). By cross-analyzing genomes and exo-metabolomes of wild strains, we discovered quantitative trait loci (QTL) that underlie the natural differences in pheromone bouquet composition. Fine mapping of the QTL further uncovered associations between mitochondrial metabolism and pheromone production. Our findings demonstrate how natural genetic variation in core metabolic pathways can affect the production of social signals.

evolutionary biology↗

bioRxiv2022

In silico, biochemical, and in vitro analysis of silvestrol binding to the DEAD box RNA helicase eIF4A reveals broad anti-pathogen potential of rocaglates across the eukaryotic tree of life

Selective inhibition of eukaryotic initiation factor 4A (eIF4A), an RNA helicase, has been proposed as a strategy to fight pathogens. Plant-derived rocaglates exhibit some of the highest specificities among eIF4A inhibitors. Sensitivity to rocaglates is determined by key amino acid (aa) residues mediating reversible clamping of the eIF4A:RNA complex. To date, no comprehensive assessment of eIF4A sensitivity to rocaglates across the eukaryotic tree of life has been performed to determine their anti-pathogenic potential. We performed an in silico analysis of the substitution patterns of six aa residues in eIF4A1 critical to rocaglate binding (human positions 158, 159, 163, 192, 195, 199), uncovering 35 pattern variants among 365 eIF4As sequenced to date. In silico molecular docking analysis of the eIF4A:RNA:rocaglate complexes of the 35 variants, modeled in a human eIF4A environment, and in vitro thermal shift assays with recombinantly expressed human eIF4A mutants, representing select natural and artificial variants, revealed that sensitivity to a natural or one of two synthetic rocaglates--silvestrol, CR-1-31-B, or zotatifin--was associated with lower inferred binding energies and higher melting temperature shifts. Helicase activities were comparable across variants and independent of sensitivity to rocaglates. In vitro testing with silvestrol validated predicted resistance based on position 163 substitutions in Caenorhabditis elegans and Leishmania amazonensis and predicted sensitivity in Aedes sp., Schistosoma mansoni, Trypanosoma brucei, Plasmodium falciparum, and Toxoplasma gondii. Our analysis shows resistance to rocaglates emerging in disparate eukaryotic clades pointing to resistance being a selective neutral trait except in rocaglate-producing Aglaia plants and their fungal parasite Ophiocordyceps. The analysis further revealed the possibility of targeting important insect, plant, animal, and human pathogens including Galleria mellonella, Ustilago maydis, Babesia ovata, and Cryptosporidium sp., with rocaglates. Finally, combined docking and thermal shift analyses might help design novel synthetic rocaglate derivatives or alternative eIF4A inhibitors to fight pathogens. Author SummaryIn the ongoing search for novel ways to fight non-viral and non-bacterial pathogens, targeting translation--the universal process of protein synthesis--to inhibit growth and cell proliferation has emerged as an attractive strategy. Here, we focused on the potential of rocaglates, a group of plant-derived compounds, to inhibit an early step in translation mediated by a RNA helicase called eIF4A. We performed a comprehensive analysis of eIF4A sequence variants to determine their potential sensitivities to rocaglates, especially in pathogens of prokaryotic, fungal, or animal origin. We complemented this in silico analysis with enzyme-based in vitro and whole pathogen in vivo experiments to confirm the sensitivity or resistance to rocaglates of specific variants of eIF4A. Our analysis provides the first comprehensive picture of rocaglate sensitivity among pathogens and establishes targeting important insect, plant, animal, and human pathogens such as wax moth larvae, a major parasite of honey bees, corn smut, a widely distributed fungal disease, Babesia, a livestock parasite that causes anemia and babesiois, and Cryptosporidium, the causative organism of cryptosporidiosis in humans, with rocaglates as a viable anti-pathogen strategy.

molecular biology↗

bioRxiv2022

Vitamin B12 produced by gut bacteria modulates excitatory neurotransmission

A growing body of evidence indicates that gut microbiota influence brain function and behavior. However, the molecular basis of how gut bacteria modulate host nervous system function is largely unknown. Here we show that vitamin B12-producing bacteria that colonize the intestine can modulate excitatory synaptic transmission and behavior in the host Caenorhabditis elegans. We find that vitamin B12 reduces cholinergic signaling in the nervous system through rewiring of the methionine (Met)/S-Adenosylmethionine (SAM) cycle in the intestine. We identify a conserved metabolic crosstalk between the Met/SAM cycle and the choline oxidation pathway. We show that metabolic rewiring of these pathways by vitamin B12 reduces cholinergic transmission by limiting the availability of free choline required by neurons to synthesize acetylcholine. Our study reveals a gut-brain communication pathway by which enteric bacteria modulate host behavior and may affect mental health.

neuroscience↗