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At least 19 recordsLinked to original sources
PubMed2025

Uridine 5'-monophosphate (UMP) synthesis connects nucleotide metabolism to programmed cell death in C. elegans.

Nucleotide metabolism is essential for fundamental cellular functions such as growth, repair and proliferation. Emerging evidence suggests that metabolic pathways also influence programmed cell death (PCD), though the underlying mechanisms remain poorly understood. One model organism that has provided key insights into the regulation of PCD is Caenorhabditis elegans (C. elegans). In this nematode, apoptosis is often initiated through asymmetric cell division (ACD), a process that unequally distributes fate determinants between daughter cells to produce a larger surviving cell and a smaller cell destined for apoptosis. Here, we demonstrate that the simultaneous disruption of PCD and ACD leads to aberrant cell survival and the formation of extra hypodermal cells. Through a genetic screen in the grp-1 ACD mutant background, we identified pyr-1 as a regulator of PCD. pyr-1 encodes the C. elegans carbamoyl-phosphate synthetase/aspartate transcarbamoylase/dihydroorotase (CAD) enzyme which catalyzes the rate-limiting step of de novo pyrimidine biosynthesis, producing uridine 5'-monophosphate (UMP). UMP is a critical metabolite for the synthesis of nucleotides, lipids and carbohydrates. Genetic analysis of UMP metabolic pathways, combined with exogenous nucleoside supplementation, confirms that UMP availability is essential for PYR-1-mediated PCD. Loss of grp-1 induces cellular stress by disrupting fate determinant partitioning during ACD, whereas pyr-1 mutations cause metabolic stress through UMP depletion. While both mutations independently activate autophagy, they function redundantly to upregulate the mitochondrial chaperone hsp-6. Knockdown of autophagy-related genes and hsp-6 reveals that these pathways serve as compensatory mechanisms to protect against cell death in the pyr-1; grp-1 double mutants. Collectively, our findings establish a direct link between metabolism and cell death, demonstrating how UMP availability and proper ACD coordinate apoptotic regulation and developmental outcomes. This study highlights the intricate interplay between metabolic homeostasis and PCD, providing new insights into the metabolic control of cell fate decisions.

Caenorhabditis elegans↗
PubMed2004

WormBase as an integrated platform for the C. elegans ORFeome.

The ORFeome project has validated and corrected a large number of predicted gene models in the nematode C. elegans, and has provided an enormous resource for proteome-scale studies. To make the resource useful to the research and teaching community, it needs to be integrated with other large-scale data sets, including the C. elegans genome, cell lineage, neurological wiring diagram, transcriptome, and gene expression map. This integration is also critical because the ORFeome data sets, like other 'omics' data sets, have significant false-positive and false-negative rates, and comparison to related data is necessary to make confidence judgments in any given data point. WormBase, the central data repository for information about C. elegans and related nematodes, provides such a platform for integration. In this report, we will describe how C. elegans ORFeome data are deposited in the database, how they are used to correct gene models, how they are integrated and displayed in the context of other data sets at the WormBase Web site, and how WormBase establishes connection with the reagent-based resources at the ORFeome project Web site.

Animals↗
PubMed2025

4D Microscopy and Tracking of Chromosomes and the Spindle in C. elegans Early Embryos.

Maintaining genomic integrity throughout successive cell divisions is essential for the proper development and functioning of organisms. Chromosome alignment and segregation occur on a microtubule-based spindle originating from centrosomes. The molecular and cellular mechanisms involved in accurate chromosome segregation during early embryonic divisions are highly conserved between worms and humans. Therefore, C. elegans serves as a robust model for investigating mitotic cell divisions within a metazoan system. Throughout early embryonic development, filming and tracking successive cell divisions becomes progressively more challenging as the number of cells increases and cell size decreases. To address this challenge, we describe a method for preparing live samples, performing 4D time-lapse imaging, and semi-automated tracking of chromosomes and spindle poles during early mitotic divisions in C. elegans embryos.

Caenorhabditis elegans↗
PubMed2025

Fluorescent protein tagging of C. elegans core apoptosis pathway components reveals mitochondrial localization of CED-9 Bcl-2, CED-4 Apaf1 and CED-3 Caspase in non-apoptotic and apoptotic cells.

We used CRISPR-Cas-mediated modification of the genomic loci for C. elegans genes ced-9 Bcl-2, ced-4 Apaf1 and ced-3 Caspase to add the coding sequence for the mNeonGreen (mNG) fluorescent protein to the endogenous open reading frames. In each case, the addition of mNG caused little or no apparent alteration of gene function. We found that tagged versions of CED-9, CED-4 and CED-3 proteins colocalize with mitochondria in all cells of live mid-late stage embryos and are distributed along the entire length of mitochondria. However, CED-4 also exhibits localized puncta of ~4-fold enrichment, and these are preferentially oriented toward the nucleus. We do not observe any shift in the localization pattern of tagged CED-4 in cells that are committing to apoptosis during normal development. However, when egl-1 BH3-only is overexpressed or ced-9 removed by mutation, CED-4::mNG is no longer distributed along the entire length of mitochondria and instead becomes enriched in the bright puncta. Finally, localization of CED-3::mNG to mitochondria is independent of both CED-9 and CED-4. This study represents the first analysis of the distribution and sub-cellular localization of endogenous CED-9 Bcl-2, CED-4 Apaf1 and CED-3 Caspase proteins in live embryos. Our results impact the current model of apoptosis commitment in C. elegans.

Animals↗
PubMed2026

The pseudokinase domain PK1 of UNC-89/obscurin is required for mitochondrial morphology and function in C. elegans.

UNC-89 is a giant modular protein located at the sarcomeric M-line of C. elegans striated muscle and is required for sarcomere organization and function. UNC-89 contains two protein kinase domains, PK1 and PK2, separated by 850 residues, that includes a 645-residue long intrinsically disordered sequence that acts like an elastic spring. Bioinformatic analysis suggests that PK2 is an active kinase whereas PK1 is a pseudokinase. We recently reported that a genome-edited worm, unc-89(sf22), that expresses UNC-89 carrying a kinase-inactivating point mutation in PK2 has an unusual phenotype with normally organized sarcomeres and SR, normal muscle function and yet fragmented mitochondria, increased ATP levels, increased glycolysis and alterations in electron transport chain complexes and respiration. Here, we show that a genome-edited worm unc-89(sf23), that expresses UNC-89 with an in-frame deletion of the C-lobe of PK1 has approximately the same phenotype as the PK2 catalytically dead mutant. The fact that mutations in two different regions of UNC-89 result in a mitochondrial phenotype is further evidence of communication between the sarcomere and mitochondria. We further demonstrate that in vitro PK2 interacts with full length PK1 and the C-lobe of PK1. The protein kinase domains of giant sarcomeric proteins are autoinhibited by parts of their own sequence, and this is also likely for PK2, but the mechanism by which PK2 would be activated is unknown. Our data is compatible with a model in which PK1 interacts with PK2 and thereby stimulates PK2 kinase activity.

Animals↗
PubMed2026

The Small but Versatile Cyclin-Dependent Kinase Subunit CKS: C. elegans CKS-1 Regulates Anaphase Onset and Is Required for Anaphase B During Oocyte Meiosis.

The cyclin-dependent kinase subunit (CKS) remains the least well-understood component of the tripartite cyclin-dependent kinase (CDK) complexes that specify the proper sequence of events required to duplicate and segregate genomes during eukaryotic cell division. Our recent investigation of CKS requirements during Caenorhabditis elegans oocyte meiosis I and II documents an essential role for CKS in the execution of anaphase B and expands the known range of CKS influence on cell cycle regulation to a third class of E3 ligases. Our findings also further document how C. elegans oocytes use very different mechanisms to progress through these two sequential cell divisions that ultimately produce a haploid oocyte. In this Think Again article, we discuss our findings as they relate to previous studies of CKS in different model systems.

Animals↗
PubMed2025

Oligomerization and positive feedback on membrane recruitment encode dynamically stable PAR-3 asymmetries in the C. elegans zygote.

Studies of PAR polarity have emphasized a paradigm in which mutually antagonistic PAR proteins form complementary polar domains in response to transient cues. A growing body of work suggests that the oligomeric scaffold PAR-3 can form unipolar asymmetries without mutual antagonism, but how it does so is largely unknown. Here we combine single molecule analysis and modeling to show how the interplay of two positive feedback loops promotes dynamically stable unipolar PAR-3 asymmetries in early C. elegans embryos. First, the intrinsic dynamics of PAR-3 membrane binding and oligomerization encode negative feedback on PAR-3 dissociation. Second, membrane-bound PAR-3 promotes its own recruitment through a mechanism that requires the anterior polarity proteins PAR-6 and PKC-3. Using a kinetic model tightly constrained by our experimental measurements, we show that these two feedback loops are individually required and jointly sufficient to encode dynamically stable and locally inducible unipolar PAR-3 asymmetries in the absence of posterior inhibition. Given the central role of PAR-3, and the conservation of PAR-3 membrane-binding, oligomerization, and core interactions with PAR-6/PKC-3, these results have widespread implications for PAR-mediated polarity in metazoa.

Journal Article↗
PubMed2026

Genetic and physical interactions reveal overlapping and distinct contributions to meiotic double-strand break formation in C. elegans.

Double-strand breaks (DSBs) are the most deleterious lesions experienced by our genome. Yet, DSBs are intentionally induced during gamete formation to promote the exchange of genetic material between homologous chromosomes. While the conserved topoisomerase-like enzyme Spo11 catalyzes DSBs, additional regulatory proteins-referred to as 'Spo11 accessory factors'-regulate the number, timing, and placement of DSBs during meiotic prophase, ensuring that SPO-11 does not wreak havoc on the genome. Despite the importance of the accessory factors, they are poorly conserved at the sequence level, suggesting that these factors may adopt unique functions in different species. In this work, we present a detailed analysis of the genetic and physical interactions between the DSB factors in the nematode Caenorhabditis elegans, providing new insights into conserved and novel functions of these proteins. This work shows that HIM-5 is the determinant of X-chromosome-specific crossovers and that its retention in the nucleus is dependent on DSB-1, the sole accessory factor that interacts with SPO-11. We further provide evidence that HIM-5 mediates interactions with the different accessory factors subgroups, providing insights into how components on the DNA loops may interact with the chromosome axis.

Animals↗
PubMed2026

Initiation of Hybrid Polyketide-Nonribosomal Peptide Biosynthesis via Two Distinct Pathways in C. elegans.

Nemamide A and B are hybrid polyketide-nonribosomal peptides that are produced by the PKS-1-NRPS-1 enzymatic assembly line in the canal-associated neurons (CANs) of the nematode Caenorhabditis elegans. These signaling molecules promote survival during and recovery from starvation-induced larval arrest. Here, using genome editing and targeted metabolomics, we probed the roles of the different domains of PKS-1 in the initiation of nemamide biosynthesis. We showed that the first four domains of PKS-1 are not required for the biosynthesis of the triene-containing nemamide A, but are required for the biosynthesis of the tetraene-containing nemamide B. By targeting genes that are highly expressed in the CANs, we identified two additional enzymes that participate in the biosynthetic pathway: the peroxisomal carnitine O-octanoyl transferase CROT-1, which is required for the biosynthesis of nemamide A, and the enoyl-CoA hydratase ECH-7, which is required for the biosynthesis of nemamide B. We heterologously expressed CROT-1 and showed that it prefers hexanoyl-CoA and octanoyl-CoA as substrates, converting them to the corresponding carnitine esters. According to our model, ECH-7 is needed to supply the starter unit for nemamide B biosynthesis, which is loaded onto the first carrier protein of PKS-1 and extended by the first module, thereby installing the double bond that is unique to nemamide B. Meanwhile, CROT-1 is needed to supply the starter unit for nemamide A biosynthesis, which is loaded onto the second carrier protein of PKS-1. Our data suggest that the biosynthetic pathways of nemamide A and B are under the control of two different initiation mechanisms and, thus, that the production of these two secondary metabolites may be independently regulated.

Animals↗
PubMed2026

In Vivo Screen of Parkinson's Disease GWAS Risk Genes Identifies ARIH2 as a Novel Regulator of α-Synuclein Toxicity in Dopaminergic Neurons.

Parkinson's disease (PD) is a late-onset neurodegenerative disease characterized by preferential degeneration of midbrain dopaminergic neurons and α-synuclein-containing Lewy bodies that are found in both familial and sporadic forms. Genome-wide association studies (GWAS) have identified many loci associated with risk of sporadic PD, but their role in PD pathogenesis remains largely unknown. We screened a subset of GWAS genes in Caenorhabditis elegans (C. elegans) as potential modulators of α-synuclein-mediated degeneration of dopaminergic neurons. Loss of ari-2 (human ARIH2), an E3 ubiquitin ligase, was identified as the strongest suppressor of dopaminergic neurodegeneration in C. elegans. Unbiased proteomics analysis in human-induced pluripotent stem cell-derived dopaminergic neurons revealed novel substrates of ARIH2 including TPPP3, a regulator of microtubule dynamics. Importantly, TPPP3 was required for ARIH2's effects on α-synuclein-induced dopaminergic neurodegeneration. Our studies reveal an unexpected genetic interaction between two PD-linked genes, α-synuclein and ARIH2, and suggest that inhibition of ARIH2's enzymatic activity may serve as a potential therapeutic approach in PD.

Animals↗
PubMed2026

A lipid-sensitive food choice behavior influences aging outcomes from a longevity-promoting diet.

Organisms utilize sophisticated neurocircuitry to select optimal food sources. Methylobacterium is a lifespan-promoting diet for C. elegans that drives faster development and longevity; however, after ingestion, C. elegans consistently choose any other food option available. A screen for genetic regulators of this avoidance behavior toward Methylobacterium identified the AWB/AWC sensory neurons and the odr-1 guanylate cyclase expressed in those four ciliated neurons as mediators of the aversive response. Metabolic profiling of the Methylobacterium diet reveals enrichment for saturated fats, and here, we show that C. elegans sense and integrate signals related to these ingested lipids that subsequently cue food-related behaviors. Moreover, disruption of endogenous lipid metabolism modifies the intensity of the avoidance from Methylobacterium, suggesting the current state of lipid homeostasis influences food preference. Taken together, our work reveals that C. elegans modify food choice contemporaneously based in part on the chemosensory capacity to detect and utilize dietary lipids, which has longevity-promoting consequences.

AWB↗
PubMed1979

Bacterial and fungal oxidation of dibenzofuran.

Cunninghamella elegans and a mutant strain (B8/36) of Beijerinckia both oxidized dibenzofuran to 2,3-dihydroxy-2,3-dihydrodibenzofuran. The bacterial metabolite was extremely unstable and, in the presence of acid, was rapidly converted into a mixture of 2- and 3-hydroxydibenzofuran. In contrast, the 2,3-dihydroxy-2,3-dihydrodibenzofuran formed by C. elegans was stable and only yielded 2- and 3-hydroxydibenzofuran when heated under acidic conditions. The results suggest that Beijerinckia B8/36 and C. elegans form the respective cis- and trans-isomers of 2,3-dihydroxy-2,3-dihydrodibenzofuran. C. elegans also oxidized dibenzofuran to 2- and 3-hydroxydibenzofuran under conditions that would not lead to the dehydration of the trans-dihydrodiol. These observations implicate the initial formation of dibenzofuran- 2,3-epoxide in the fungal oxidation of dibenzofuran. Beijerinckia B8/36 also produced a second unstable dihydrodiol that was tentatively identified as cis-1,2-dihydroxy-1,2-dihydrodibenzofuran. This compound gave 2-hydroxydibenzofuran as the major dehydration product and the cis relative stereochemistry was suggested by the isolation and characterization of an isopropylidine derivative. A preparation of cis-naphthalene dihydrodiol dehydrogenase and cell extracts of the parent strain of Beijerinckia oxidized both bacterial dihydrodiols to catechols. Cell extracts prepared from C. elegans catalysed an analogous oxidation of trans-2,3-dihydroxy-2,3-dihydrodibenzofuran to 2,3-dihydroxydibenzofuran. The latter product was also isolated and identified from culture filtrates. The results suggest that bacteria and fungi utilize different mechanisms to initiate the oxidation of dibenzofuran.

Bacteria↗
PubMed2024

Identifying transgene insertions in Caenorhabditis elegans genomes with Oxford Nanopore sequencing.

Genetically modified organisms are commonly used in disease research and agriculture but the precise genomic alterations underlying transgenic mutations are often unknown. The position and characteristics of transgenes, including the number of independent insertions, influences the expression of both transgenic and wild-type sequences. We used long-read, Oxford Nanopore Technologies (ONT) to sequence and assemble two transgenic strains of Caenorhabditis elegans commonly used in the research of neurodegenerative diseases: BY250 (pPdat-1::GFP) and UA44 (GFP and human α-synuclein), a model for Parkinson's research. After scaffolding to the reference, the final assembled sequences were ∼102 Mb with N50s of 17.9 Mb and 18.0 Mb, respectively, and L90s of six contiguous sequences, representing chromosome-level assemblies. Each of the assembled sequences contained more than 99.2% of the Nematoda BUSCO genes found in the C. elegans reference and 99.5% of the annotated C. elegans reference protein-coding genes. We identified the locations of the transgene insertions and confirmed that all transgene sequences were inserted in intergenic regions, leaving the organismal gene content intact. The transgenic C. elegans genomes presented here will be a valuable resource for Parkinson's research as well as other neurodegenerative diseases. Our work demonstrates that long-read sequencing is a fast, cost-effective way to assemble genome sequences and characterize mutant lines and strains.

Caenorhabditis elegans↗
PubMed2026

A conserved antioxidant defense at the endoplasmic reticulum membrane.

Oxidative protein folding in the endoplasmic reticulum (ER) is essential for eukaryotic cells yet generates hydrogen peroxide (H2O2), a reactive oxygen species. The ER-transmembrane protein that supports ER proteostasis and guards the cytosol for antioxidant defense remains unidentified. Here, we combine AlphaFold2 and functional screens in C. elegans to discover a previously uncharacterized and evolutionarily conserved protein ERGU-1 that fulfills these roles. Deleting ERGU-1 upregulates H2O2 and NRF2/SKN-1-dependent gene expression. ERGU-1 deficiency also impairs organismal reproduction and behavioral responses to H2O2. Both C. elegans ERGU-1 and human homolog TMEM161B localize to ER membranes, forming reticular networks. Human and Drosophila homologs of ERGU-1 rescue C. elegans mutant phenotypes, demonstrating ancient and conserved functions. In addition, purified ERGU-1 and TMEM161B exhibit redox-modulated oligomeric states. Together, our results reveal an ER-membrane-specific machinery, suggesting a conserved mechanism for maintaining ER redox homeostasis and proteostasis in animal cells.

Animals↗
PubMed1979

Fungal metabolism of biphenyl.

Cunninghamella elegans grown on Sabouraud dextrose broth transformed biphenyl to produce 2-, 3- and 4-hydroxybiphenyl, as well as 4,4'-dihydroxybiphenyl as free phenols. A compound tentatively identified as 2,4'-dihydroxybiphenyl was also produced. When 4-hydroxybiphenyl or 2-hydroxybiphenyl replaced biphenyl as the substrate, C. elegans produced 4,4'-dihydroxybiphenyl and 2,5-dihydroxybiphenyl respectively. The compound identified as 2,4'-dihydroxybiphenyl was produced from both substrates. A survey of 11 species of fungi known to degrade hydrocarbons revealed two species that were comparable to C. elegans in their ability to convert biphenyl into free phenols. In addition to free phenolic metabolites, deconjugation experiments indicated that 44% of the known metabolites present in the culture filtrate were present in the form of conjugates. These results suggest that the transformation of biphenyl by C. elegans is similar to that found in mammalian systems.

Biphenyl Compounds↗
PubMed2022

SAIBR: a simple, platform-independent method for spectral autofluorescence correction.

Biological systems are increasingly viewed through a quantitative lens that demands accurate measures of gene expression and local protein concentrations. CRISPR/Cas9 gene tagging has enabled increased use of fluorescence to monitor proteins at or near endogenous levels under native regulatory control. However, owing to typically lower expression levels, experiments using endogenously tagged genes run into limits imposed by autofluorescence (AF). AF is often a particular challenge in wavelengths occupied by commonly used fluorescent proteins (GFP, mNeonGreen). Stimulated by our work in C. elegans, we describe and validate Spectral Autofluorescence Image Correction By Regression (SAIBR), a simple platform-independent protocol and FIJI plug-in to correct for autofluorescence using standard filter sets and illumination conditions. Validated for use in C. elegans embryos, starfish oocytes and fission yeast, SAIBR is ideal for samples with a single dominant AF source; it achieves accurate quantitation of fluorophore signal, and enables reliable detection and quantification of even weakly expressed proteins. Thus, SAIBR provides a highly accessible low-barrier way to incorporate AF correction as standard for researchers working on a broad variety of cell and developmental systems.

Animals↗
PubMed1978

Nutritional factors and conditions for the axenic culture of free-living nematodes.

1. Soy-peptone has been fractionated to yield a series of increasingly purified components which sharply increase the populations of Caenorhabditis briggsae and Caenorhabditis elegans when added to the basal medium. The nutritionally active material appears to be a small polypeptide. 2. C. briggsae and C. elegans routinely reach populations of 150,000/ml or greater in 9 days in still culture, starting from an inoculum of only 500 organisms per ml. C. elegans is particularly sensitive to the depth of the medium. However, large populations can be achieved in deep cultures if continuous shaking is carried out. 3. Panagrellus silusiae shows improved populations if the basal medium is supplemented with the nutritional factor from soy-peptone. However, 0.5% acetic acid or 1% ethanol added to the medium serves equally well. There is no additive effect of ethanol and the factor.

Animals↗