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1.
Proc Natl Acad Sci U S A ; 121(25): e2322588121, 2024 Jun 18.
Article En | MEDLINE | ID: mdl-38861598

The nematode intestine is the primary site for nutrient uptake and storage as well as the synthesis of biomolecules; lysosome-related organelles known as gut granules are important for many of these functions. Aspects of intestine biology are not well understood, including the export of the nutrients it imports and the molecules it synthesizes, as well as the complete functions and protein content of the gut granules. Here, we report a mass spectrometry (MS)-based proteomic analysis of the intestine of the Caenorhabditis elegans and of its gut granules. Overall, we identified approximately 5,000 proteins each in the intestine and the gonad and showed that most of these proteins can be detected in samples extracted from a single worm, suggesting the feasibility of individual-level genetic analysis using proteomes. Comparing proteomes and published transcriptomes of the intestine and the gonad, we identified proteins that appear to be synthesized in the intestine and then transferred to the gonad. To identify gut granule proteins, we compared the proteome of individual intestines deficient in gut granules to the wild type. The identified gut granule proteome includes proteins known to be exclusively localized to the granules and additional putative gut granule proteins. We selected two of these putative gut granule proteins for validation via immunohistochemistry, and our successful confirmation of both suggests that our strategy was effective in identifying the gut granule proteome. Our results demonstrate the practicability of single-tissue MS-based proteomic analysis in small organisms and in its future utility.


Caenorhabditis elegans Proteins , Caenorhabditis elegans , Lysosomes , Proteomics , Animals , Caenorhabditis elegans/metabolism , Caenorhabditis elegans/genetics , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans Proteins/genetics , Proteomics/methods , Lysosomes/metabolism , Proteome/metabolism , Intestines , Intestinal Mucosa/metabolism , Gonads/metabolism , Mass Spectrometry/methods , Organelles/metabolism
2.
Nat Commun ; 15(1): 4904, 2024 Jun 08.
Article En | MEDLINE | ID: mdl-38851828

Age-related depletion of stem cells causes tissue degeneration and failure to tissue regeneration, driving aging at the organismal level. Previously we reported a cell-non-autonomous DAF-16/FOXO activity in antagonizing the age-related loss of germline stem/progenitor cells (GSPCs) in C. elegans, indicating that regulation of stem cell aging occurs at the organ system level. Here we discover the molecular effector that links the cell-non-autonomous DAF-16/FOXO activity to GSPC maintenance over time by performing a tissue-specific DAF-16/FOXO transcriptome analysis. Our data show that dos-3, which encodes a non-canonical Notch ligand, is a direct transcriptional target of DAF-16/FOXO and mediates the effect of the cell-non-autonomous DAF-16/FOXO activity on GSPC maintenance through activating Notch signaling in the germ line. Importantly, expression of a human homologous protein can functionally substitute for DOS-3 in this scenario. As Notch signaling controls the specification of many tissue stem cells, similar mechanisms may exist in other aging stem cell systems.


Caenorhabditis elegans Proteins , Caenorhabditis elegans , Forkhead Transcription Factors , Germ Cells , Receptors, Notch , Signal Transduction , Stem Cells , Animals , Caenorhabditis elegans/metabolism , Caenorhabditis elegans/genetics , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans Proteins/genetics , Forkhead Transcription Factors/metabolism , Forkhead Transcription Factors/genetics , Germ Cells/metabolism , Receptors, Notch/metabolism , Receptors, Notch/genetics , Stem Cells/metabolism , Stem Cells/cytology , Aging/metabolism , Aging/genetics , Humans
3.
Proc Natl Acad Sci U S A ; 121(25): e2321228121, 2024 Jun 18.
Article En | MEDLINE | ID: mdl-38857399

Ciliary defects are linked to ciliopathies, but impairments in the sensory cilia of Caenorhabditis elegans neurons extend lifespan, a phenomenon with previously unclear mechanisms. Our study reveals that neuronal cilia defects trigger the unfolded protein response of the endoplasmic reticulum (UPRER) within intestinal cells, a process dependent on the insulin/insulin-like growth factor 1 (IGF-1) signaling transcription factor and the release of neuronal signaling molecules. While inhibiting UPRER doesn't alter the lifespan of wild-type worms, it normalizes the extended lifespan of ciliary mutants. Notably, deactivating the cyclic nucleotide-gated (CNG) channel TAX-4 on the ciliary membrane promotes lifespan extension through a UPRER-dependent mechanism. Conversely, constitutive activation of TAX-4 attenuates intestinal UPRER in ciliary mutants. Administering a CNG channel blocker to worm larvae activates intestinal UPRER and increases adult longevity. These findings suggest that ciliary dysfunction in sensory neurons triggers intestinal UPRER, contributing to lifespan extension and implying that transiently inhibiting ciliary channel activity may effectively prolong lifespan.


Caenorhabditis elegans Proteins , Caenorhabditis elegans , Cilia , Longevity , Unfolded Protein Response , Animals , Caenorhabditis elegans/metabolism , Cilia/metabolism , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans Proteins/genetics , Cyclic Nucleotide-Gated Cation Channels/metabolism , Cyclic Nucleotide-Gated Cation Channels/genetics , Intestines/cytology , Signal Transduction , Neurons/metabolism , Endoplasmic Reticulum/metabolism , Insulin-Like Growth Factor I/metabolism , Intestinal Mucosa/metabolism
4.
Sci Rep ; 14(1): 12936, 2024 06 05.
Article En | MEDLINE | ID: mdl-38839826

Circadian rhythms are endogenous oscillations in nearly all organisms, from prokaryotes to humans, allowing them to adapt to cyclical environments for close to 24 h. Circadian rhythms are regulated by a central clock, based on a transcription-translation feedback loop. One important protein in the central loop in metazoan clocks is PERIOD, which is regulated in part by Casein kinase 1ε/δ (CK1ε/δ) phosphorylation. In the nematode Caenorhabditis elegans, period and casein kinase 1ε/δ are conserved as lin-42 and kin-20, respectively. Here, we studied the involvement of lin-42 and kin-20 in the circadian rhythms of the adult nematode using a bioluminescence-based circadian transcriptional reporter. We show that mutations of lin-42 and kin-20 generate a significantly longer endogenous period, suggesting a role for both genes in the nematode circadian clock, as in other organisms. These phenotypes can be partially rescued by overexpression of either gene under their native promoter. Both proteins are expressed in neurons and epidermal seam cells, as well as in other cells. Depletion of LIN-42 and KIN-20, specifically in neuronal cells after development, was sufficient to lengthen the period of oscillating sur-5 expression. Therefore, we conclude that LIN-42 and KIN-20 are critical regulators of the adult nematode circadian clock through neuronal cells.


Caenorhabditis elegans Proteins , Caenorhabditis elegans , Circadian Rhythm , Animals , Caenorhabditis elegans/genetics , Caenorhabditis elegans/physiology , Caenorhabditis elegans/metabolism , Caenorhabditis elegans Proteins/genetics , Caenorhabditis elegans Proteins/metabolism , Circadian Clocks/genetics , Circadian Rhythm/genetics , CLOCK Proteins/genetics , CLOCK Proteins/metabolism , Gene Expression Regulation , Mutation , Neurons/metabolism , Transcription Factors
5.
Commun Biol ; 7(1): 694, 2024 Jun 06.
Article En | MEDLINE | ID: mdl-38844830

Wounding initiates intricate responses crucial for tissue repair and regeneration. Yet, the gene regulatory networks governing wound healing remain poorly understood. Here, employing single-worm RNA sequencing (swRNA-seq) across 12 time-points, we delineated a three-stage wound repair process in C. elegans: response, repair, and remodeling. Integrating diverse datasets, we constructed a dynamic regulatory network comprising 241 transcription regulators and their inferred targets. We identified potentially seven autoregulatory TFs and five cross-autoregulatory loops involving pqm-1 and jun-1. We revealed that TFs might interact with chromatin factors and form TF-TF combinatory modules via intrinsically disordered regions to enhance response robustness. We experimentally validated six regulators functioning in transcriptional and translocation-dependent manners. Notably, nhr-76, daf-16, nhr-84, and oef-1 are potentially required for efficient repair, while elt-2 may act as an inhibitor. These findings elucidate transcriptional responses and hierarchical regulatory networks during C. elegans wound repair, shedding light on mechanisms underlying tissue repair and regeneration.


Caenorhabditis elegans Proteins , Caenorhabditis elegans , Gene Regulatory Networks , Wound Healing , Animals , Caenorhabditis elegans/genetics , Wound Healing/genetics , Caenorhabditis elegans Proteins/genetics , Caenorhabditis elegans Proteins/metabolism , Transcription Factors/metabolism , Transcription Factors/genetics , Sequence Analysis, RNA , Gene Expression Regulation
6.
Sci Adv ; 10(24): eadk9481, 2024 Jun 14.
Article En | MEDLINE | ID: mdl-38865452

The molecular mechanisms underlying diversity in animal behavior are not well understood. A major experimental challenge is determining the contribution of genetic variants that affect neuronal gene expression to differences in behavioral traits. In Caenorhabditis elegans, the neuroendocrine transforming growth factor-ß ligand, DAF-7, regulates diverse behavioral responses to bacterial food and pathogens. The dynamic neuron-specific expression of daf-7 is modulated by environmental and endogenous bacteria-derived cues. Here, we investigated natural variation in the expression of daf-7 from the ASJ pair of chemosensory neurons. We identified common genetic variants in gap-2, encoding a Ras guanosine triphosphatase (GTPase)-activating protein homologous to mammalian synaptic Ras GTPase-activating protein, which modify daf-7 expression cell nonautonomously and promote exploratory foraging behavior in a partially DAF-7-dependent manner. Our data connect natural variation in neuron-specific gene expression to differences in behavior and suggest that genetic variation in neuroendocrine signaling pathways mediating host-microbe interactions may give rise to diversity in animal behavior.


Caenorhabditis elegans Proteins , Caenorhabditis elegans , Genetic Variation , Animals , Caenorhabditis elegans/genetics , Caenorhabditis elegans/physiology , Caenorhabditis elegans Proteins/genetics , Caenorhabditis elegans Proteins/metabolism , Gene Expression Regulation , Neurosecretory Systems/metabolism , Feeding Behavior , Behavior, Animal/physiology , Neurons/metabolism , Signal Transduction , Transforming Growth Factor beta
7.
Nat Commun ; 15(1): 4935, 2024 Jun 10.
Article En | MEDLINE | ID: mdl-38858388

Cell polarity mechanisms allow the formation of specialized membrane domains with unique protein compositions, signalling properties, and functional characteristics. By analyzing the localization of potassium channels and proteins belonging to the dystrophin-associated protein complex, we reveal the existence of distinct planar-polarized membrane compartments at the surface of C. elegans muscle cells. We find that muscle polarity is controlled by a non-canonical Wnt signalling cascade involving the ligand EGL-20/Wnt, the receptor CAM-1/Ror, and the intracellular effector DSH-1/Dishevelled. Interestingly, classical planar cell polarity proteins are not required for this process. Using time-resolved protein degradation, we demonstrate that -while it is essentially in place by the end of embryogenesis- muscle polarity is a dynamic state, requiring continued presence of DSH-1 throughout post-embryonic life. Our results reveal the unsuspected complexity of the C. elegans muscle membrane and establish a genetically tractable model system to study cellular polarity and membrane compartmentalization in vivo.


Caenorhabditis elegans Proteins , Caenorhabditis elegans , Cell Polarity , Dystrophin , Muscles , Wnt Signaling Pathway , Animals , Caenorhabditis elegans/metabolism , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans Proteins/genetics , Dystrophin/metabolism , Dystrophin/genetics , Muscles/metabolism , Dishevelled Proteins/metabolism , Dishevelled Proteins/genetics , Receptor Tyrosine Kinase-like Orphan Receptors/metabolism , Receptor Tyrosine Kinase-like Orphan Receptors/genetics , Cell Membrane/metabolism , Dystrophin-Associated Protein Complex/metabolism , Dystrophin-Associated Protein Complex/genetics , Wnt Proteins/metabolism , Signal Transduction
8.
J Hazard Mater ; 472: 134598, 2024 Jul 05.
Article En | MEDLINE | ID: mdl-38743975

N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine quinone (6-PPDQ) is an emerging pollutant transformed from 6-PPD. However, the effect of 6-PPDQ exposure on mitochondrion and underlying mechanism remains largely unclear. Using Caenorhabditis elegans as animal model, exposed to 6-PPDQ at 0.1-10 µg/L was performed form L1 larvae to adult day-1. Exposure to 6-PPDQ (1 and 10 µg/L) could increase oxygen consumption rate and decease adenosine 5'-triphosphate (ATP) content, suggesting induction of mitochondrial dysfunction. Activities of NADH dehydrogenase (complex I) and succinate dehydrogenase (complex II) were inhibited, accompanied by a decrease in expressions of gas-1, nuo-1, and mev-1. RNAi of gas-1 and mev-1 enhanced mitochondrial dysfunction and reduced lifespan of 6-PPDQ exposed nematodes. GAS-1 and MEV-1 functioned in parallel to regulate 6-PPDQ toxicity to reduce the lifespan. Insulin peptides and the insulin signaling pathway acted downstream of GAS-1 and MEV-1 to control the 6-PPDQ toxicity on longevity. Moreover, RNAi of sod-2 and sod-3, targeted genes of daf-16, caused susceptibility to 6-PPDQ toxicity in reducing lifespan and in causing reactive oxygen species (ROS) production. Therefore, 6-PPDQ at environmentally relevant concentrations (ERCs) potentially caused mitochondrial dysfunction by affecting mitochondrial complexes I and II, which was associated with lifespan reduction by affecting insulin signaling in organisms.


Caenorhabditis elegans Proteins , Caenorhabditis elegans , Electron Transport Complex I , Longevity , Mitochondria , Animals , Caenorhabditis elegans/drug effects , Longevity/drug effects , Caenorhabditis elegans Proteins/genetics , Caenorhabditis elegans Proteins/metabolism , Mitochondria/drug effects , Mitochondria/metabolism , Electron Transport Complex I/metabolism , Electron Transport Complex I/genetics , Electron Transport Complex II/metabolism , Electron Transport Complex II/genetics , Insulin/metabolism , Adenosine Triphosphate/metabolism , Reactive Oxygen Species/metabolism , NADH Dehydrogenase , Cytochromes b
9.
J Inorg Biochem ; 257: 112593, 2024 Aug.
Article En | MEDLINE | ID: mdl-38754275

Four Ru(II) complexes (A2-A5) were synthesized from the reaction of coumarin Schiff base ligands (7da2-tsc, 7da3-mtsc, 7da4-etsc and 7da5-ptsc) with [RuHCl(CO)(PPh3)3]. The compounds were characterized by FT-IR, UV-Vis, 1H, 13C and 31P NMR, mass spectrometry and crystallographic analysis. Calf Thymus DNA (CT-DNA) binding studies revealed the intercalative mode of binding of the complexes with DNA. The results of Bovine serum albumin (BSA) binding studies established the interaction between BSA followed static quenching mechanism. The cytotoxic effects of the complexes and the ligands were evaluated against breast (MCF-7 and MDA-MB-231) and lung carcinoma cell lines (A549 and NCI-H460) using MTT assay. Complex A4 demonstrated potent cytotoxic effects on both breast and lung cancer cells. Furthermore, morphological observations and FACS analysis showed the decrease in cell density by complex A4 by induced morphological changes and apoptotic body formation and cell death in both breast and lung cancer cells. Moreover, the invertebrate model Caenorhabditis elegans was employed to assess the in vivo anticancer activity of compound A4. The findings indicated that the treatment with A4 reduced tumor development and significantly extended organismal lifespan by 64 % in the tumoral strain JK1466 without adversely affecting essential physiological functions of the worm. Additionally, A4 demonstrated an upregulation of two crucial antioxidant defense genes. Overall, these results suggested that the compound A4 can be a potential candidate with novel chemotherapeutic applications.


Antineoplastic Agents , Caenorhabditis elegans , Coordination Complexes , Ruthenium , Animals , Humans , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemistry , Antineoplastic Agents/chemical synthesis , Ruthenium/chemistry , Caenorhabditis elegans/drug effects , Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism , Coordination Complexes/pharmacology , Coordination Complexes/chemistry , Coordination Complexes/chemical synthesis , Cell Line, Tumor , Mutation , Caenorhabditis elegans Proteins/genetics , Caenorhabditis elegans Proteins/metabolism , DNA/chemistry , MCF-7 Cells
10.
Sci Total Environ ; 934: 173214, 2024 Jul 15.
Article En | MEDLINE | ID: mdl-38754507

Zinc oxide nanoparticles (ZnO-NPs) are one of the most widely used metal oxide nanomaterials. The increased use of ZnO-NPs has exacerbated environmental pollution and raised the risk of neurological disorders in organisms through food chains, and it is urgent to look for detoxification strategies. γ-Aminobutyric acid (GABA) is an inhibitory neurotransmitter that has been shown to have anxiolytic, anti-aging and inhibitory effects on nervous system excitability. However, there are few reports on the prevention and control of the toxicity of nano-metal ions by GABA. In zebrafish, ZnO-NPs exposure led to increased mortality and behavioral abnormalities of larva, which could be moderated by GABA intervention. Similar results were investigated in Caenorhabditis elegans, showing lifespan extension, abnormal locomotor frequency and behavior recovery when worms fed with GABA under ZnO-NPs exposure. Moreover, GABA enhanced antioxidant enzyme activities by upregulating the expression of antioxidant-related genes and thus scavenged excessive O2-. In the case of ZnO-NPs exposure, inhibition of nuclear translocation of DAF-16 and SKN-1 was restored by GABA. Meanwhile, the protective effect of GABA was blocked in daf-16 (-) and skn-1 (-) mutant, suggesting that DAF-16/FoxO and SKN-1/Nrf2 pathways is the key targets of GABA. This study provides a new solution for the application of GABA and mitigation of metal nanoparticle neurotoxicity.


Caenorhabditis elegans Proteins , Caenorhabditis elegans , Forkhead Transcription Factors , NF-E2-Related Factor 2 , Oxidative Stress , Zebrafish , Zinc Oxide , gamma-Aminobutyric Acid , Zinc Oxide/toxicity , Animals , Oxidative Stress/drug effects , NF-E2-Related Factor 2/metabolism , Caenorhabditis elegans/drug effects , Caenorhabditis elegans/physiology , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans Proteins/genetics , gamma-Aminobutyric Acid/metabolism , Forkhead Transcription Factors/metabolism , Metal Nanoparticles/toxicity , Transcription Factors/metabolism , Transcription Factors/genetics , Signal Transduction/drug effects , Zebrafish Proteins/metabolism , Zebrafish Proteins/genetics , Nanoparticles/toxicity , DNA-Binding Proteins/metabolism
11.
PLoS One ; 19(5): e0295094, 2024.
Article En | MEDLINE | ID: mdl-38743782

Oxygen is essential to all the aerobic organisms. However, during normal development, disease and homeostasis, organisms are often challenged by hypoxia (oxygen deprivation). Hypoxia-inducible transcription factors (HIFs) are master regulators of hypoxia response and are evolutionarily conserved in metazoans. The homolog of HIF in the genetic model organism C. elegans is HIF-1. In this study, we aimed to understand short-term hypoxia response to identify HIF-1 downstream genes and identify HIF-1 direct targets in C. elegans. The central research questions were: (1) which genes are differentially expressed in response to short-term hypoxia? (2) Which of these changes in gene expression are dependent upon HIF-1 function? (3) Are any of these hif-1-dependent genes essential to survival in hypoxia? (4) Which genes are the direct targets of HIF-1? We combine whole genome gene expression analyses and chromatin immunoprecipitation sequencing (ChIP-seq) experiments to address these questions. In agreement with other published studies, we report that HIF-1-dependent hypoxia-responsive genes are involved in metabolism and stress response. Some HIF-1-dependent hypoxia-responsive genes like efk-1 and phy-2 dramatically impact survival in hypoxic conditions. Genes regulated by HIF-1 and hypoxia overlap with genes responsive to hydrogen sulfide, also overlap with genes regulated by DAF-16. The genomic regions that co-immunoprecipitate with HIF-1 are strongly enriched for genes involved in stress response. Further, some of these potential HIF-1 direct targets are differentially expressed under short-term hypoxia or are differentially regulated by mutations that enhance HIF-1 activity.


Caenorhabditis elegans Proteins , Caenorhabditis elegans , Hypoxia-Inducible Factor 1 , Transcription Factors , Animals , Binding Sites , Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism , Caenorhabditis elegans Proteins/genetics , Caenorhabditis elegans Proteins/metabolism , Gene Expression Profiling , Gene Expression Regulation , Hypoxia/genetics , Hypoxia/metabolism , Hypoxia-Inducible Factor 1/metabolism , Hypoxia-Inducible Factor 1/genetics , Transcription Factors/genetics , Transcription Factors/metabolism
12.
PLoS Genet ; 20(5): e1011253, 2024 May.
Article En | MEDLINE | ID: mdl-38722918

Synaptic vesicle proteins (SVps) are transported by the motor UNC-104/KIF1A. We show that SVps travel in heterogeneous carriers in C. elegans neuronal processes, with some SVp carriers co-transporting lysosomal proteins (SV-lysosomes). LRK-1/LRRK2 and the clathrin adaptor protein complex AP-3 play a critical role in the sorting of SVps and lysosomal proteins away from each other at the SV-lysosomal intermediate trafficking compartment. Both SVp carriers lacking lysosomal proteins and SV-lysosomes are dependent on the motor UNC-104/KIF1A for their transport. In lrk-1 mutants, both SVp carriers and SV-lysosomes can travel in axons in the absence of UNC-104, suggesting that LRK-1 plays an important role to enable UNC-104 dependent transport of synaptic vesicle proteins. Additionally, LRK-1 acts upstream of the AP-3 complex and regulates its membrane localization. In the absence of the AP-3 complex, the SV-lysosomes become more dependent on the UNC-104-SYD-2/Liprin-α complex for their transport. Therefore, SYD-2 acts to link upstream trafficking events with the transport of SVps likely through its interaction with the motor UNC-104. We further show that the mistrafficking of SVps into the dendrite in lrk-1 and apb-3 mutants depends on SYD-2, likely by regulating the recruitment of the AP-1/UNC-101. SYD-2 acts in concert with AP complexes to ensure polarized trafficking & transport of SVps.


Adaptor Protein Complex 3 , Caenorhabditis elegans Proteins , Caenorhabditis elegans , Lysosomes , Nerve Tissue Proteins , Synaptic Vesicles , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans Proteins/genetics , Animals , Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism , Synaptic Vesicles/metabolism , Synaptic Vesicles/genetics , Adaptor Protein Complex 3/metabolism , Adaptor Protein Complex 3/genetics , Lysosomes/metabolism , Lysosomes/genetics , Nerve Tissue Proteins/metabolism , Nerve Tissue Proteins/genetics , Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/genetics , Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/metabolism , Protein Transport , Protein Serine-Threonine Kinases/metabolism , Protein Serine-Threonine Kinases/genetics , Neurons/metabolism , Kinesins/metabolism , Kinesins/genetics , Intracellular Signaling Peptides and Proteins/metabolism , Intracellular Signaling Peptides and Proteins/genetics , Axons/metabolism , Intercellular Signaling Peptides and Proteins
13.
Mol Biol Cell ; 35(7): ar98, 2024 Jul 01.
Article En | MEDLINE | ID: mdl-38809582

C. elegans undergo age-dependent declines in muscle organization and function, similar to human sarcopenia. The chaperone UNC-45 is required to fold myosin heads after translation and is likely used for refolding after thermally- or chemically-induced unfolding. UNC-45's TPR region binds HSP-90 and its UCS domain binds myosin heads. We observe early onset sarcopenia when UNC-45 is reduced at the beginning of adulthood. There is sequential decline of HSP-90, UNC-45, and MHC B myosin. A mutation in age-1 delays sarcopenia and loss of HSP-90, UNC-45, and myosin. UNC-45 undergoes age-dependent phosphorylation, and mass spectrometry reveals phosphorylation of six serines and two threonines, seven of which occur in the UCS domain. Additional expression of UNC-45 results in maintenance of MHC B myosin and suppression of A-band disorganization in old animals. Our results suggest that increased expression or activity of UNC-45 might be a strategy for prevention or treatment of sarcopenia.


Aging , Caenorhabditis elegans Proteins , Caenorhabditis elegans , Molecular Chaperones , Myosins , Sarcomeres , Animals , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans Proteins/genetics , Caenorhabditis elegans/metabolism , Aging/metabolism , Aging/physiology , Molecular Chaperones/metabolism , Myosins/metabolism , Sarcomeres/metabolism , Phosphorylation , HSP90 Heat-Shock Proteins/metabolism , Humans , Mutation , Muscle, Skeletal/metabolism
14.
PLoS One ; 19(5): e0300190, 2024.
Article En | MEDLINE | ID: mdl-38814971

Histone variants are paralogs that replace canonical histones in nucleosomes, often imparting novel functions. However, how histone variants arise and evolve is poorly understood. Reconstruction of histone protein evolution is challenging due to large differences in evolutionary rates across gene lineages and sites. Here we used intron position data from 108 nematode genomes in combination with amino acid sequence data to find disparate evolutionary histories of the three H2A variants found in Caenorhabditis elegans: the ancient H2A.ZHTZ-1, the sperm-specific HTAS-1, and HIS-35, which differs from the canonical S-phase H2A by a single glycine-to-alanine C-terminal change. Although the H2A.ZHTZ-1 protein sequence is highly conserved, its gene exhibits recurrent intron gain and loss. This pattern suggests that specific intron sequences or positions may not be important to H2A.Z functionality. For HTAS-1 and HIS-35, we find variant-specific intron positions that are conserved across species. Patterns of intron position conservation indicate that the sperm-specific variant HTAS-1 arose more recently in the ancestor of a subset of Caenorhabditis species, while HIS-35 arose in the ancestor of Caenorhabditis and its sister group, including the genus Diploscapter. HIS-35 exhibits gene retention in some descendent lineages but gene loss in others, suggesting that histone variant use or functionality can be highly flexible. Surprisingly, we find the single amino acid differentiating HIS-35 from core H2A is ancestral and common across canonical Caenorhabditis H2A sequences. Thus, we speculate that the role of HIS-35 lies not in encoding a functionally distinct protein, but instead in enabling H2A expression across the cell cycle or in distinct tissues. This work illustrates how genes encoding such partially-redundant functions may be advantageous yet relatively replaceable over evolutionary timescales, consistent with the patchwork pattern of retention and loss of both genes. Our study shows the utility of intron positions for reconstructing evolutionary histories of gene families, particularly those undergoing idiosyncratic sequence evolution.


Amino Acid Sequence , Caenorhabditis elegans , Evolution, Molecular , Histones , Introns , Animals , Histones/genetics , Histones/metabolism , Introns/genetics , Caenorhabditis elegans/genetics , Phylogeny , Conserved Sequence , Caenorhabditis elegans Proteins/genetics , Male
15.
Sci Rep ; 14(1): 12280, 2024 05 29.
Article En | MEDLINE | ID: mdl-38811827

Loss of the tumor suppressor PTEN homolog daf-18 in Caenorhabditis elegans (C. elegans) triggers diapause cell division during L1 arrest. While prior studies have delved into established pathways, our investigation takes an innovative route. Through forward genetic screening in C. elegans, we pinpoint a new player, F12E12.11, regulated by daf-18, impacting cell proliferation independently of PTEN's typical phosphatase activity. F12E12.11 is an ortholog of human estradiol 17-beta-dehydrogenase 8 (HSD17B8), which converts estradiol to estrone through its NAD-dependent 17-beta-hydroxysteroid dehydrogenase activity. We found that PTEN engages in a physical interplay with HSD17B8, introducing a distinctive suppression mechanism. The reduction in estrone levels and accumulation of estradiol may arrest tumor cells in the G2/M phase of the cell cycle through MAPK/ERK. Our study illuminates an unconventional protein interplay, providing insights into how PTEN modulates tumor suppression by restraining cell division through intricate molecular interactions.


Caenorhabditis elegans Proteins , Caenorhabditis elegans , Cell Proliferation , PTEN Phosphohydrolase , PTEN Phosphohydrolase/metabolism , PTEN Phosphohydrolase/genetics , Animals , Caenorhabditis elegans/metabolism , Caenorhabditis elegans/genetics , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans Proteins/genetics , Humans , 17-Hydroxysteroid Dehydrogenases/metabolism , 17-Hydroxysteroid Dehydrogenases/genetics , Estradiol/metabolism , Estrone/metabolism
16.
J Cell Biol ; 223(9)2024 Sep 02.
Article En | MEDLINE | ID: mdl-38767515

Ciliopathies are often caused by defects in the ciliary microtubule core. Glutamylation is abundant in cilia, and its dysregulation may contribute to ciliopathies and neurodegeneration. Mutation of the deglutamylase CCP1 causes infantile-onset neurodegeneration. In C. elegans, ccpp-1 loss causes age-related ciliary degradation that is suppressed by a mutation in the conserved NEK10 homolog nekl-4. NEKL-4 is absent from cilia, yet it negatively regulates ciliary stability via an unknown, glutamylation-independent mechanism. We show that NEKL-4 was mitochondria-associated. Additionally, nekl-4 mutants had longer mitochondria, a higher baseline mitochondrial oxidation state, and suppressed ccpp-1∆ mutant lifespan extension in response to oxidative stress. A kinase-dead nekl-4(KD) mutant ectopically localized to ccpp-1∆ cilia and rescued degenerating microtubule doublet B-tubules. A nondegradable nekl-4(PEST∆) mutant resembled the ccpp-1∆ mutant with dye-filling defects and B-tubule breaks. The nekl-4(PEST∆) Dyf phenotype was suppressed by mutation in the depolymerizing kinesin-8 KLP-13/KIF19A. We conclude that NEKL-4 influences ciliary stability by activating ciliary kinesins and promoting mitochondrial homeostasis.


Caenorhabditis elegans Proteins , Caenorhabditis elegans , Cilia , Microtubules , Mitochondria , Neurons , Animals , Microtubules/metabolism , Microtubules/genetics , Mitochondria/metabolism , Mitochondria/genetics , Cilia/metabolism , Cilia/genetics , Caenorhabditis elegans/metabolism , Caenorhabditis elegans/genetics , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans Proteins/genetics , Neurons/metabolism , Mutation/genetics
17.
Cell ; 187(12): 3141-3160.e23, 2024 Jun 06.
Article En | MEDLINE | ID: mdl-38759650

Systematic functional profiling of the gene set that directs embryonic development is an important challenge. To tackle this challenge, we used 4D imaging of C. elegans embryogenesis to capture the effects of 500 gene knockdowns and developed an automated approach to compare developmental phenotypes. The automated approach quantifies features-including germ layer cell numbers, tissue position, and tissue shape-to generate temporal curves whose parameterization yields numerical phenotypic signatures. In conjunction with a new similarity metric that operates across phenotypic space, these signatures enabled the generation of ranked lists of genes predicted to have similar functions, accessible in the PhenoBank web portal, for ∼25% of essential development genes. The approach identified new gene and pathway relationships in cell fate specification and morphogenesis and highlighted the utilization of specialized energy generation pathways during embryogenesis. Collectively, the effort establishes the foundation for comprehensive analysis of the gene set that builds a multicellular organism.


Caenorhabditis elegans , Embryonic Development , Gene Expression Regulation, Developmental , Animals , Caenorhabditis elegans/embryology , Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans Proteins/genetics , Embryo, Nonmammalian/metabolism , Gene Expression Profiling/methods , Gene Knockdown Techniques , Phenotype
19.
ACS Chem Neurosci ; 15(11): 2182-2197, 2024 06 05.
Article En | MEDLINE | ID: mdl-38726817

Aggregative α-synuclein and incurring oxidative stress are pivotal cascading events, leading to dopaminergic (DAergic) neuronal loss and contributing to clinical manifestations of Parkinson's disease (PD). Our previous study demonstrated that 2-butoxytetrahydrofuran (2-BTHF), isolated from Holothuria scabra (H. scabra), could inhibit amyloid-ß aggregation and its ensuing toxicity, which leads to Alzheimer's disease. In the present study, we found that 2-BTHF also attenuated the aggregative and oxidative activities of α-synuclein and lessened its toxicity in a transgenic Caenorhabditis elegans (C. elegans) PD model. Such worms treated with 100 µM of 2-BTHF showed substantial reductions in α-synuclein accumulation and DAergic neurodegeneration. Mechanistically, 2-BTHF, at this concentration, significantly decreased aggregation of monomeric α-synuclein and restored locomotion and dopamine-dependent behaviors. Molecular docking exhibited potential bindings of 2-BTHF to HSF-1 and DAF-16 transcription factors. Additionally, 2-BTHF significantly increased the mRNA transcripts of genes encoding proteins involved in proteostasis, including the molecular chaperones hsp-16.2 and hsp-16.49, the ubiquitination/SUMOylation-related ubc-9 gene, and the autophagy-related genes atg-7 and lgg-1. Transcriptomic profiling revealed an additional mechanism of 2-BTHF in α-synuclein-expressing worms, which showed upregulation of PPAR signaling cascades that mediated fatty acid metabolism. 2-BTHF significantly restored lipid deposition, upregulated the fat-7 gene, and enhanced gcs-1-mediated glutathione synthesis in the C. elegans PD model. Taken together, this study demonstrated that 2-BTHF could abrogate aggregative and oxidative properties of α-synuclein and attenuate its toxicity, thus providing a possible therapeutic application for the treatment of α-synuclein-induced PD.


Animals, Genetically Modified , Caenorhabditis elegans , Disease Models, Animal , Furans , Holothuria , Oxidative Stress , alpha-Synuclein , Animals , Caenorhabditis elegans/drug effects , alpha-Synuclein/metabolism , Oxidative Stress/drug effects , Furans/pharmacology , Parkinson Disease/metabolism , Parkinson Disease/drug therapy , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans Proteins/genetics , Molecular Docking Simulation , Dopaminergic Neurons/drug effects , Dopaminergic Neurons/metabolism , Humans
20.
EMBO Rep ; 25(6): 2698-2721, 2024 Jun.
Article En | MEDLINE | ID: mdl-38744971

Centrioles organize centrosomes, the cell's primary microtubule-organizing centers (MTOCs). Centrioles double in number each cell cycle, and mis-regulation of this process is linked to diseases such as cancer and microcephaly. In C. elegans, centriole assembly is controlled by the Plk4 related-kinase ZYG-1, which recruits the SAS-5-SAS-6 complex. While the kinase activity of ZYG-1 is required for centriole assembly, how it functions has not been established. Here we report that ZYG-1 physically interacts with and phosphorylates SAS-5 on 17 conserved serine and threonine residues in vitro. Mutational scanning reveals that serine 10 and serines 331/338/340 are indispensable for proper centriole assembly. Embryos expressing SAS-5S10A exhibit centriole assembly failure, while those expressing SAS-5S331/338/340A possess extra centrioles. We show that in the absence of serine 10 phosphorylation, the SAS-5-SAS-6 complex is recruited to centrioles, but is not stably incorporated, possibly due to a failure to coordinately recruit the microtubule-binding protein SAS-4. Our work defines the critical role of phosphorylation during centriole assembly and reveals that ZYG-1 might play a role in preventing the formation of excess centrioles.


Caenorhabditis elegans Proteins , Caenorhabditis elegans , Cell Cycle Proteins , Centrioles , Caenorhabditis elegans/metabolism , Caenorhabditis elegans/genetics , Centrioles/metabolism , Phosphorylation , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans Proteins/genetics , Animals , Cell Cycle Proteins/metabolism , Cell Cycle Proteins/genetics , Protein Binding , Protein Serine-Threonine Kinases/metabolism , Protein Serine-Threonine Kinases/genetics , Serine/metabolism , Amino Acid Sequence , Protein Kinases
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