Rapid measurement of ageing by automated monitoring of movement of C. elegans populations

Finding new interventions that slow ageing and maintain human health is a huge challenge of our time. The nematode Caenorhabditis elegans offers a rapid in vivo method to determine whether a compound extends its 2 to 3-week lifespan. Measuring lifespan is the standard method to monitor ageing, but a compound that extends lifespan will not necessarily maintain health. Here, we describe the automated monitoring of C. elegans movement from early to mid-adulthood as a faster healthspan-based method to measure ageing. Using the WormGazer™ technology, multiple Petri dishes each containing several C. elegans worms are imaged simultaneously and non-invasively by an array of cameras that can be scaled easily. This approach demonstrates that most functional decline in C. elegans occurs during the first week of adulthood. We find 7 days of imaging is sufficient to measure the dose-dependent efficacy of sulfamethoxazole to slow ageing, compared to 40 days required for a parallel lifespan experiment. Understanding any negative consequences of interventions that slow ageing is important. We show that the long-lived mutant age-1(hx546) stays active for longer than the wild type but it moves slower in early adulthood. Thus, continuous analysis of movement can rapidly identify interventions that slow ageing while simultaneously revealing any negative effects on health.

Applying C. elegans to the Industrial Drug Discovery Process to Slow Aging

The increase in our molecular understanding of the biology of aging, coupled with a recent surge in investment, has led to the formation of several companies developing pharmaceuticals to slow aging. Research using the tiny nematode worm Caenorhabditis elegans was the first to show that mutations in single genes can extend lifespan, and subsequent research has shown that this model organism is uniquely suited to testing interventions to slow aging. Yet, with a few notable exceptions, C. elegans is not in the standard toolkit of longevity companies. Here we discuss the paths to overcome the barriers to using C. elegans in industrial drug discovery. We address the predictive power of C. elegans for human aging, how C. elegans research can be applied to specific challenges in the typical drug discovery pipeline, and how standardised and quantitative assays will help C. elegans fulfil its potential in the biotech and pharmaceutical industry. We argue that correct application of this model and its knowledge base will significantly accelerate progress to slow human aging.

Imaging Fluorescent Nuclear Pore Complex Proteins in C. elegans

C. elegans is a well-characterized and relatively simple model organism, making it attractive for studying nuclear pore complex proteins in cell and developmental biology. C. elegans is transparent and highly amendable to genetic manipulation. Therefore, it is possible to generate fluorescently tagged proteins and combine this with various light microscopy techniques to study protein behavior in space and time. Here, we provide protocols to prepare both fixed and live C. elegans for confocal and light sheet microscopy. This enables the analysis of nuclear pore complex proteins from embryonic stages to the aging adult.

Neuronal SKN-1B modulates nutritional signalling pathways and mitochondrial networks to control satiety

The feeling of hunger or satiety results from integration of the sensory nervous system with other physiological and metabolic cues. This regulates food intake, maintains homeostasis and prevents disease. In C. elegans, chemosensory neurons sense food and relay information to the rest of the animal via hormones to control food-related behaviour and physiology. Here we identify a new component of this system, SKN-1B which acts as a central food-responsive node, ultimately controlling satiety and metabolic homeostasis. SKN-1B, an ortholog of mammalian NF-E2 related transcription factors (Nrfs), has previously been implicated with metabolism, respiration and the increased lifespan incurred by dietary restriction. Here we show that SKN-1B acts in two hypothalamus-like ASI neurons to sense food, communicate nutritional status to the organism, and control satiety and exploratory behaviours. This is achieved by SKN-1B modulating endocrine signalling pathways (IIS and TGF-β), and by promoting a robust mitochondrial network. Our data suggest a food-sensing and satiety role for mammalian Nrf proteins.

Deciding when and how much to eat is important for maintaining health and preventing disease. It requires an intricate molecular level of communication between our nervous, physiological, and metabolic systems. These signals stimulate food intake, and afterwards the feeling of satiety which makes us stop eating. We have studied these phenomena using the simple nematode worm C. elegans which has a fully mapped nervous system and quantifiable food-related behaviours. In C. elegans, chemosensory neurons sense food and communicate this to the rest of the animal via hormones to control food-related behaviour and associated physiological changes. Here we identify a new central node of this system, the C. elegans gene SKN-1B, which acts in two sensory neurons to sense food, communicate food-status to the rest of the worm, and control satiety and exploratory behaviours. It does this by altering hormonal signalling (Insulin and Transforming Growth Factor-β), and by promoting a strong mitochondrial network. The mammalian equivalents of SKN-1B are the NF-E2 related transcription factors (Nrfs), which have previously been implicated with metabolism and respiration. Our data suggest a new food-sensing and satiety role for mammalian Nrf proteins.

Bacteria increase host micronutrient availability: mechanisms revealed by studies in C. elegans

Micronutrients cannot be synthesized by humans and are obtained from three different sources: diet, gut microbiota, and oral supplements. The microbiota generates significant quantities of micronutrients, but the contribution of these compounds to total uptake is unclear. The role of bacteria in the synthesis and uptake of micronutrients and supplements is widely unexplored and may have important implications for human health. The efficacy and safety of several micronutrient supplements, including folic acid, have been questioned due to some evidence of adverse effects on health. The use of the simplified animal-microbe model, Caenorhabditis elegans, and its bacterial food source, Escherichia coli, provides a controllable system to explore the underlying mechanisms by which bacterial metabolism impacts host micronutrient status. These studies have revealed mechanisms by which bacteria may increase the bioavailability of folic acid, B12, and iron. These routes of uptake interact with bacterial metabolism, with the potential to increase bacterial pathogenesis, and thus may be both beneficial and detrimental to host health.

Antioxidant and Antiaging Effects of Licorice on the Caenorhabditis elegans Model

The causative relationship between oxidative stress and aging remains controversial, but it is a fact that many of the pathologies of age-related diseases are associated with oxidative stress. Phytochemicals may reduce damage from oxidative stress; the intake of these through diet could represent a strategy to lessen their pathological consequences. The popular and widely consumed licorice (Glycyrrhiza glabra) is a rich source of potential antioxidants. The aim of this study was to investigate whether licorice increases the oxidative stress resistance and lifespan of the animal model Caenorhabditis elegans. Licorice roots ethanolic extract showed in vitro antioxidant activity, with an IC₅₀ of 51.17 μg/mL using 2,2-diphenyl-1-picrylhydrazyl (DPPH) as free radical. C. elegans pretreated with licorice showed an increase of survival rate when exposed to the oxidant juglone, being this increase up to ∼33.56%. This pretreated population also showed an increase in lifespan of 14.28% at a concentration of 250 μg/mL. In conclusion, we suggest that licorice has a high antioxidant capability both in vitro and in vivo and that this activity may explain the observed extension of lifespan.

Phosphatidylinositol-5-Phosphate 4-Kinases Regulate Cellular Lipid Metabolism By Facilitating Autophagy

While the majority of phosphatidylinositol-4, 5-bisphosphate (PI-4, 5-P₂) in mammalian cells is generated by the conversion of phosphatidylinositol-4-phosphate (PI-4-P) to PI-4, 5-P₂, a small fraction can be made by phosphorylating phosphatidylinositol-5-phosphate (PI-5-P). The physiological relevance of this second pathway is not clear. Here, we show that deletion of the genes encoding the two most active enzymes in this pathway, Pip4k2a and Pip4k2b, in the liver of mice causes a large enrichment in lipid droplets and in autophagic vesicles during fasting. These changes are due to a defect in the clearance of autophagosomes that halts autophagy and reduces the supply of nutrients salvaged through this pathway. Similar defects in autophagy are seen in nutrient-starved Pip4k2a^-/-Pip4k2b^-/- mouse embryonic fibroblasts and in C. elegans lacking the PI5P4K ortholog. These results suggest that this alternative pathway for PI-4, 5-P₂ synthesis evolved, in part, to enhance the ability of multicellular organisms to survive starvation.

On microbes, aging and the worm: an interview with David Weinkove

David Weinkove is an associate professor at Durham University, UK, studying host-microbe interactions in the model organism Caenorhabditis elegans. David has been focusing on the way microbes affect the physiology of their hosts, including the process of aging. In this interview, he discusses the questions shaping his research, how they evolved over the years, and his guiding principles for leading a lab.

A bacterial route for folic acid supplementation

Background

To prevent folate deficiencies, many countries supplement various foodstuffs with folic acid. This compound is a synthetic oxidised folate that differs from naturally occurring reduced folates in its metabolism and uptake. Notably, safety reviews of folic acid supplementation have not considered interactions with gut bacteria. Here, we use the Caenorhabditis elegans – Escherichia coli animal– microbe model to examine a possible bacterial route for folic acid uptake. It has been assumed that supplements are taken up directly by the worm, especially because E. coli is unable to take up folates. However, E. coli, like many other bacteria, can transport the folate breakdown product, para-aminobenzoate-glutamate (PABA-glu), via AbgT and use it for bacterial folate synthesis. This pathway may impact host health because inhibition of bacterial folate synthesis increases C. elegans lifespan.

Results

Folic acid supplementation was found to rescue a C. elegans developmental folate-deficient mutant; however, a much higher concentration was required compared to folinic acid, a reduced folate. Unlike folinic acid, the effectiveness of folic acid supplementation was dependent on the E. coli gene, abgT, suggesting a bacterial route with PABA-glu uptake by E. coli as a first step. Surprisingly, we found up to 4% PABA-glu in folic acid preparations, including in a commercial supplement. Via breakdown to PABA-glu, folic acid increases E. coli folate synthesis. This pathway restores folate synthesis in a bacterial mutant defective in PABA synthesis, reversing the ability of this mutant to increase C. elegans lifespan.

Conclusions

Folic acid supplementation in C. elegans occurs chiefly indirectly via bacterial uptake of breakdown products via E. coli AbgT, and can impact C. elegans development and longevity. Examining how folic acid supplementation affects bacterial folate synthesis in the human gut may help us to better understand the safety of folic acid supplementation.

Electronic supplementary material

The online version of this article (10.1186/s12915-018-0534-3) contains supplementary material, which is available to authorized users.

Folate Acts in E. coli to Accelerate C. elegans Aging Independently of Bacterial Biosynthesis

Folates are cofactors for biosynthetic enzymes in all eukaryotic and prokaryotic cells. Animals cannot synthesize folate and must acquire it from their diet or microbiota. Previously, we showed that inhibiting E. coli folate synthesis increases C. elegans lifespan. Here, we show that restriction or supplementation of C. elegans folate does not influence lifespan. Thus, folate is required in E. coli to shorten worm lifespan. Bacterial proliferation in the intestine has been proposed as a mechanism for the life-shortening influence of E. coli. However, we found no correlation between C. elegans survival and bacterial growth in a screen of 1,000+ E. coli deletion mutants. Nine mutants increased worm lifespan robustly, suggesting specific gene regulation is required for the life-shortening activity of E. coli. Disrupting the biosynthetic folate cycle did not increase lifespan. Thus, folate acts through a growth-independent route in E. coli to accelerate animal aging.

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Limiting folate in E. coli, not in C. elegans, increases worm lifespan

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An E. coli screen for worm longevity identifies folate synthesis as a target

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Folate synthesis influences E. coli physiology independently of growth

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Bacterial folate synthesis may be a sustainable target for chronic disease

Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children

Gut microbiota has been implicated as a pivotal contributing factor in diet-related obesity; however, its role in development of disease phenotypes in human genetic obesity such as Prader-Willi syndrome (PWS) remains elusive. In this hospitalized intervention trial with PWS (n = 17) and simple obesity (n = 21) children, a diet rich in non-digestible carbohydrates induced significant weight loss and concomitant structural changes of the gut microbiota together with reduction of serum antigen load and alleviation of inflammation. Co-abundance network analysis of 161 prevalent bacterial draft genomes assembled directly from metagenomic datasets showed relative increase of functional genome groups for acetate production from carbohydrates fermentation. NMR-based metabolomic profiling of urine showed diet-induced overall changes of host metabotypes and identified significantly reduced trimethylamine N-oxide and indoxyl sulfate, host-bacteria co-metabolites known to induce metabolic deteriorations. Specific bacterial genomes that were correlated with urine levels of these detrimental co-metabolites were found to encode enzyme genes for production of their precursors by fermentation of choline or tryptophan in the gut. When transplanted into germ-free mice, the pre-intervention gut microbiota induced higher inflammation and larger adipocytes compared with the post-intervention microbiota from the same volunteer. Our multi-omics-based systems analysis indicates a significant etiological contribution of dysbiotic gut microbiota to both genetic and simple obesity in children, implicating a potentially effective target for alleviation.

RESEARCH IN CONTEXT

Poorly managed diet and genetic mutations are the two primary driving forces behind the devastating epidemic of obesity-related diseases. Lack of understanding of the molecular chain of causation between the driving forces and the disease endpoints retards progress in prevention and treatment of the diseases. We found that children genetically obese with Prader-Willi syndrome shared a similar dysbiosis in their gut microbiota with those having diet-related obesity. A diet rich in non-digestible but fermentable carbohydrates significantly promoted beneficial groups of bacteria and reduced toxin-producers, which contributes to the alleviation of metabolic deteriorations in obesity regardless of the primary driving forces.

Metformin retards aging in C. elegans by altering microbial folate and methionine metabolism

The biguanide drug metformin is widely prescribed to treat type 2 diabetes and metabolic syndrome, but its mode of action remains uncertain. Metformin also increases lifespan in Caenorhabditis elegans cocultured with Escherichia coli. This bacterium exerts complex nutritional and pathogenic effects on its nematode predator/host that impact health and aging. We report that metformin increases lifespan by altering microbial folate and methionine metabolism. Alterations in metformin-induced longevity by mutation of worm methionine synthase (metr-1) and S-adenosylmethionine synthase (sams-1) imply metformin-induced methionine restriction in the host, consistent with action of this drug as a dietary restriction mimetic. Metformin increases or decreases worm lifespan, depending on E. coli strain metformin sensitivity and glucose concentration. In mammals, the intestinal microbiome influences host metabolism, including development of metabolic disease. Thus, metformin-induced alteration of microbial metabolism could contribute to therapeutic efficacy—and also to its side effects, which include folate deficiency and gastrointestinal upset.

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A casein kinase 1 and PAR proteins regulate asymmetry of a PIP(2) synthesis enzyme for asymmetric spindle positioning

Spindle positioning is an essential feature of asymmetric cell division. The conserved PAR proteins together with heterotrimeric G proteins control spindle positioning in animal cells, but how these are linked is not known. In C. elegans, PAR protein activity leads to asymmetric spindle placement through cortical asymmetry of Gα regulators GPR-1/2. Here, we establish that the casein kinase 1 gamma CSNK-1 and a PIP₂ synthesis enzyme (PPK-1) transduce PAR polarity to asymmetric Gα regulation. PPK-1 is posteriorly enriched in the one-celled embryo through PAR and CSNK-1 activities. Loss of CSNK-1 causes uniformly high PPK-1 levels, high symmetric cortical levels of GPR-1/2 and LIN-5, and increased spindle pulling forces. In contrast, knockdown of ppk-1 leads to low GPR-1/2 levels and decreased spindle forces. Furthermore, loss of CSNK-1 leads to increased levels of PIP₂. We propose that asymmetric generation of PIP₂ by PPK-1 directs the posterior enrichment of GPR-1/2 and LIN-5, leading to posterior spindle displacement.

Effects of resveratrol on lifespan in Drosophila melanogaster and Caenorhabditis elegans

It was recently reported that the plant polyphenol resveratrol, found, e.g., in grape berry skins, extended lifespan in the fruit fly Drosophila melanogaster and the nematode worm Caenorhabditis elegans. This lifespan extension was dependent on an NAD(+)-dependent histone deacetylase, Sir2 in Drosophila and SIR-2.1 in C. elegans. The extension of lifespan appeared to occur through a mechanism related to dietary restriction (DR), the reduction of available nutrients without causing malnutrition, an intervention that extends lifespan in diverse organisms from yeast to mammals. In Drosophila, lifespan extension by DR is associated with a reduction in fecundity. However, a slight increase in fecundity was reported upon treatment with resveratrol, suggesting a mode of action at least partially distinct from that of DR. To probe this mechanism further, we initiated a new study of the effects of resveratrol on Drosophila. We saw no significant effects on lifespan in seven independent trials. We analysed our resveratrol and found that its structure was normal, with no oxidative modifications. We therefore re-tested the effects of resveratrol in C. elegans, in both wild-type and sir-2.1 mutant worms. The results were variable, with resveratrol treatment resulting in slight increases in lifespan in some trials but not others, in both wild type and sir-2.1 mutant animals. We postulate that the effect of resveratrol upon lifespan in C. elegans could reflect induction of phase 2 drug detoxification or activation of AMP kinase.

Long-term starvation and ageing induce AGE-1/PI 3-kinase-dependent translocation of DAF-16/FOXO to the cytoplasm

Background

The provision of stress resistance diverts resources from development and reproduction and must therefore be tightly regulated. In Caenorhabditis elegans, the switch to increased stress resistance to promote survival through periods of starvation is regulated by the DAF-16/FOXO transcription factor. Reduction-of-function mutations in AGE-1, the C. elegans Class IA phosphoinositide 3-kinase (PI3K), increase lifespan and stress resistance in a daf-16 dependent manner. Class IA PI3Ks downregulate FOXOs by inducing their translocation to the cytoplasm. However, the circumstances under which AGE-1 is normally activated are unclear. To address this question we used C. elegans first stage larvae (L1s), which when starved enter a developmentally-arrested diapause stage until food is encountered.

Results

We find that in L1s both starvation and daf-16 are necessary to confer resistance to oxidative stress in the form of hydrogen peroxide. Accordingly, DAF-16 is localised to cell nuclei after short-term starvation. However, after long-term starvation, DAF-16 unexpectedly translocates to the cytoplasm. This translocation requires functional age-1. H₂O₂ treatment can replicate the translocation and induce generation of the AGE-1 product PIP₃. Because feeding reduces to zero in ageing adult C. elegans, these animals may also undergo long-term starvation. Consistent with our observation in L1s, DAF-16 also translocates to the cytoplasm in old adult worms in an age-1-dependent manner.

Conclusion

DAF-16 is activated in the starved L1 diapause. The translocation of DAF-16 to the cytoplasm after long-term starvation may be a feedback mechanism that prevents excessive expenditure on stress resistance. H₂O₂ is a candidate second messenger in this feedback mechanism. The lack of this response in age-1(hx546) mutants suggests a novel mechanism by which this mutation increases longevity.

The G-protein gamma subunit gpc-1 of the nematode C.elegans is involved in taste adaptation

Caenorhabditis elegans has two heterotrimeric G-protein gamma subunits, gpc-1 and gpc-2. Although GPC-1 is specifically expressed in sensory neurons, it is not essential for the detection of odorants or salts. To test whether GPC-1 is involved in sensory plasticity, we developed a water soluble compound adaptation assay. The behaviour of wild-type animals in this assay confirms that prolonged exposure to salts can abolish chemo-attraction to these compounds. This process is time and concentration dependent, partly salt specific and reversible. In contrast, gpc-1 mutant animals show clear deficits in their ability to adapt to NaAc, NaCl and NH4Cl, but normal wild-type adaptation to odorants. Two other loci previously implicated in odorant adaptation, adp-1 and osm-9, are also involved in adaptation to salts. Our finding that G proteins, OSM-9 and ADP-1 are involved in taste adaptation offer the first molecular insight into this process.

The genetic control of organ growth: insights from Drosophila

The genetic control of growth ensures that animals grow to reproducible sizes and that tumourous growth is rare. This year, the regulation of organ growth has been studied extensively in Drosophila imaginal discs, and a signalling pathway that regulates organ growth and size has been identified. Furthermore, the role of Drosophila homologues to human tumour suppressor genes and oncogenes in imaginal disc growth has been investigated.

Regulation of imaginal disc cell size, cell number and organ size by Drosophila class I(A) phosphoinositide 3-kinase and its adaptor

BACKGROUND

Class I(A) phosphoinositide 3-kinases (PI 3-kinases) have been implicated in the regulation of several cellular processes including cell division, cell survival and protein synthesis. The size of Drosophila imaginal discs (epithelial structures that give rise to adult organs) is maintained by factors that can compensate for experimentally induced changes in these PI 3-kinase-regulated processes. Overexpression of the gene encoding the Drosophila class I(A) PI 3-kinase, Dp110, in imaginal discs, however, results in enlarged adult organs. These observations have led us to investigate the role of Dp100 and its adaptor, p60, in the control of imaginal disc cell size, cell number and organ size.

RESULTS

Null mutations in Dp110 and p60 were generated and used to demonstrate that they are essential genes that are autonomously required for imaginal disc cells to achieve their normal adult size. In addition, modulating Dp110 activity increases or reduces cell size in the developing imaginal disc, and does so throughout the cell cycle. The inhibition of Dp110 activity reduces the rate of increase in cell number in the imaginal discs, suggesting that Dp110 normally promotes cell division and/or cell survival. Unlike direct manipulation of cell-cycle progression, manipulation of Dp110 activity in one compartment of the disc influences the size of that compartment and the size of the disc as a whole.

CONCLUSIONS

We conclude that during imaginal disc development, Dp110 and p60 regulate cell size, cell number and organ size. Our results indicate that Dp110 and p60 signalling can affect growth in multiple ways, which has important implications for the function of signalling through class I(A) PI 3-kinases.

Mutants of phycomyces with decreased gallic acid content

Most plants and some fungi accumulate phenols. Two hydroxybenzoic acids, gallic and protocatechuic acids, are abundant in the giant sporangiophores of the zygomycete Phycomyces blakesleeanus, much more so than in the basal mycelium or the culture medium. The actual concentrations vary with illumination, age of the culture, and composition of the medium. We devised a simple screening procedure to isolate hba mutants whose sporangiophores contained less gallic acid than the wild type. The most useful mutant had very low concentrations of hydroxybenzoic acids in the sporangiophores, but about the same as the wild type in the basal mycelium and the medium. The mutant was only slightly different from the wild type in growth and morphology. Mutant and wild-type sporangiophores grew away from ultraviolet C sources (260 nm) equally well. Contrary to previous conjectures, ultraviolet tropism does not depend on the ultraviolet absorption of gallic acid or other free hydroxybenzoic acids in the sporangiophore. Against expectations, phenols did not impair DNA extraction: sporangiophores produced better DNA preparations than basal mycelia and the hba mutant only slightly better than the wild type.

p60 is an adaptor for the Drosophila phosphoinositide 3-kinase, Dp110

The mammalian phosphoinositide 3-kinases (PI3Ks) p110alpha, beta, and delta form heterodimers with Src homology 2 (SH2) domain-containing adaptors such as p85alpha or p55(PIK). The two SH2 domains of these adaptors bind to phosphotyrosine residues (pY) found within the consensus sequence pYXXM. Here we show that a heterodimer of the Drosophila PI3K, Dp110, with an adaptor, p60, can be purified from S2 cells with a pYXXM phosphopeptide affinity matrix. Using amino acid sequence from the gel-purified protein, the gene encoding p60 was cloned and mapped to the genomic region 21B8-C1, and the exon/intron structure was determined. p60 contains two SH2 domains and an inter-SH2 domain but lacks the SH3 and breakpoint cluster region homology (BH) domains found in mammalian p85alpha and beta. Analysis of the sequence of p60 shows that the amino acids responsible for the SH2 domain binding specificity in mammalian p85alpha are conserved and predicts that the inter-SH2 domain has a coiled-coil structure. The Dp110.p60 complex was immunoprecipitated with p60-specific antisera and shown to possess both lipid and protein kinase activity. The complex was found in larvae, pupae, and adults, consistent with p60 functioning as the adaptor for Dp110 throughout the Drosophila life cycle.

The Drosophila phosphoinositide 3-kinase Dp110 promotes cell growth

Phosphoinositide 3-kinases (PI3Ks) have been identified in an evolutionarily diverse range of organisms, including mammals, Drosophila, yeast, plants and Dictyostelium. They are activated by a multitude of extracellular signals and implicated in mitogenesis, differentiation and cell survival, as well as in the control of the cytoskeleton and cell shape. Here we describe the molecular and functional analysis of Drosophila p110 (Dp110). A full-length Dp110 cDNA was isolated and found to encode a protein homologous throughout its length to the class I mammalian PI3Ks p110alpha and p110beta. Overexpression of Dp110 in wing or eye imaginal discs resulted in flies with enlarged wings or eyes respectively. In contrast, overexpression of Dp110 containing a mutation predicted to result in the loss of catalytic activity resulted in smaller wings and eyes. The alterations in wing size result from changes in both cell size and cell number, whereas in the eye only differences in cell size were detected. These data imply a role for Dp110 in growth control during Drosophila development and have implications for the function of class I PI3Ks in other organisms.