Effect of the diet type and temperature on the C. elegans transcriptome

Studying the mechanisms of neurodegeneration: C. elegans advantages and opportunities

Caenorhabditis elegans has been widely used as a model organism in neurodevelopment for several decades due to its simplicity, rapid growth, short life cycle, transparency, and rather simple genetics. It has been useful in modeling neurodegenerative diseases by the heterologous expression of the major proteins that form neurodegenerative-linked aggregates such as amyloid-β peptide, tau protein, and α-synuclein, among others. Furthermore, chemical treatments as well as the existence of several interference RNA libraries, transgenic worm lines, and the possibility of generating new transgenic strains create a magnificent range of possible tools to study the signaling pathways that could confer protection against protein aggregates or, on the contrary, are playing a detrimental role. In this review, we summarize the different C. elegans models of neurodegenerative diseases with a focus on Alzheimer's and Parkinson's diseases and how genetic tools could be used to dissect the signaling pathways involved in their pathogenesis mentioning several examples. Finally, we discuss the use of pharmacological agents in C. elegans models that could help to study these disease-associated signaling pathways and the powerful combinations of experimental designs with genetic tools. This review highlights the advantages of C. elegans as a valuable intermediary between in vitro and mammalian in vivo models in the development of potential new therapies.

Salmonella biofilm formation diminishes bacterial proliferation in the C. elegans intestine

Non-typhoidal Salmonella serovars are a significant global cause of foodborne infections, owing their transmission success to the formation of biofilms. While the role of these biofilms in Salmonella's persistence outside the host is well understood, their significance during infection remains elusive. In this study, we investigated the impact of Salmonella biofilm formation on host colonization and virulence using the nematode model Caenorhabditis elegans. This infection model enables us to isolate the effect of biofilm formation on gut colonization and proliferation, as no gut microbiome is present and Salmonella cannot invade the intestinal tissue of the nematode. We show that a biofilm-deficient ΔcsgD mutant enhances gut proliferation compared to the wild-type strain, while the pathogen's virulence, the host's immune signaling pathways, and host survival remain unaffected. Hence, our work suggests that biofilm formation does not significantly contribute to Salmonella infection in C. elegans. However, complementary assays in higher-order in vivo models are required to further characterize the role of biofilm formation during infection and to take into account the impact of biofilm formation on competition with gut microbiome and epithelial invasion.

Catalytic activities of wild-type C. elegans DAF-2 kinase and dauer-associated mutants

DAF-2, the Caenorhabditis elegans insulin-like receptor homolog, regulates larval development, metabolism, stress response, and lifespan. The availability of numerous daf-2 mutant alleles has made it possible to elucidate the genetic mechanisms underlying these physiological processes. The DAF-2 pathway is significantly conserved with the human insulin/IGF-1 signaling pathway; it includes proteins homologous to human IRS, GRB-2, and PI3K, making it an important model to investigate human pathological conditions. We expressed and purified the kinase domain of wild-type DAF-2 to examine the catalytic activity and substrate specificity of the enzyme. Like the human insulin receptor kinase, DAF-2 kinase phosphorylates tyrosines within specific YxN or YxxM motifs, which are important for recruiting downstream effectors. DAF-2 kinase phosphorylated peptides derived from the YxxM and YxN motifs located in the C-terminal extension of the receptor tyrosine kinase, consistent with the idea that the DAF-2 receptor may possess independent signaling capacity. Unlike the human insulin or IGF-1 receptor kinases, DAF-2 kinase was poorly inhibited by the small-molecule inhibitor linsitinib. We also expressed and purified mutant kinases corresponding to daf-2 alleles that result in partial loss-of-function phenotypes in C. elegans. These mutations caused a complete loss of kinase function in vitro. Our biochemical investigations provide new insights into DAF-2 kinase function, and the approach should be useful for studying other mutations to shed light on DAF-2 signaling in C. elegans physiology.

Caenorhabditis elegans as a Convenient Animal Model for Microbiome Studies

Microbes constitute the most prevalent life form on Earth, yet their remarkable diversity remains mostly unrecognized. Microbial diversity in vertebrate models presents a significant challenge for investigating host-microbiome interactions. The model organism Caenorhabditis elegans has many advantages for delineating the effects of host genetics on microbial composition. In the wild, the C. elegans gut contains various microbial species, while in the laboratory it is usually a host for a single bacterial species. There is a potential host-microbe interaction between microbial metabolites, drugs, and C. elegans phenotypes. This mini-review aims to summarize the current understanding regarding the microbiome in C. elegans. Examples using C. elegans to study host-microbe-metabolite interactions are discussed.

A novel endoplasmic reticulum adaptation is critical for the long-lived Caenorhabditis elegans rpn-10 proteasomal mutant

The loss of proteostasis due to reduced efficiency of protein degradation pathways plays a key role in multiple age-related diseases and is a hallmark of the aging process. Paradoxically, we have previously reported that the Caenorhabditis elegans rpn-10(ok1865) mutant, which lacks the RPN-10/RPN10/PSMD4 subunit of the 19S regulatory particle of the 26S proteasome, exhibits enhanced cytosolic proteostasis, elevated stress resistance and extended lifespan, despite possessing reduced proteasome function. However, the response of this mutant against threats to endoplasmic reticulum (ER) homeostasis and proteostasis was unknown. Here, we find that the rpn-10 mutant is highly ER stress resistant compared to the wildtype. Under unstressed conditions, the ER unfolded protein response (UPR) is activated in the rpn-10 mutant as signified by increased xbp-1 splicing. This primed response appears to alter ER homeostasis through the upregulated expression of genes involved in ER protein quality control (ERQC), including those in the ER-associated protein degradation (ERAD) pathway. Pertinently, we find that ERQC is critical for the rpn-10 mutant longevity. These changes also alter ER proteostasis, as studied using the C. elegans alpha-1 antitrypsin (AAT) deficiency model, which comprises an intestinal ER-localised transgenic reporter of an aggregation-prone form of AAT called ATZ. The rpn-10 mutant shows a significant reduction in the accumulation of the ATZ reporter, thus indicating that its ER proteostasis is augmented. Via a genetic screen for suppressors of decreased ATZ aggregation in the rpn-10 mutant, we then identified ecps-2/H04D03.3, a novel ortholog of the proteasome-associated adaptor and scaffold protein ECM29/ECPAS. We further show that ecps-2 is required for improved ER proteostasis as well as lifespan extension of the rpn-10 mutant. Thus, we propose that ECPS-2-proteasome functional interactions, alongside additional putative molecular processes, contribute to a novel ERQC adaptation which underlies the superior proteostasis and longevity of the rpn-10 mutant.

Caenorhabditis elegans for research on cancer hallmarks

After decades of research, our knowledge of the complexity of cancer mechanisms, elegantly summarized as 'hallmarks of cancer', is expanding, as are the therapeutic opportunities that this knowledge brings. However, cancer still needs intense research to diminish its tremendous impact. In this context, the use of simple model organisms such as Caenorhabditis elegans, in which the genetics of the apoptotic pathway was discovered, can facilitate the investigation of several cancer hallmarks. Amenable for genetic and drug screens, convenient for fast and efficient genome editing, and aligned with the 3Rs ('Replacement, Reduction and Refinement') principles for ethical animal research, C. elegans plays a significant role in unravelling the intricate network of cancer mechanisms and presents a promising option in clinical diagnosis and drug discovery.

Analyzing the postulated inhibitory effect of Manumycin A on farnesyltransferase

Manumycin A is postulated to be a specific inhibitor against the farnesyltransferase (FTase) since this effect has been shown in 1993 for yeast FTase. Since then, plenty of studies investigated Manumycin A in human cells as well as in model organisms like Caenorhabditis elegans. Some studies pointed to additional targets and pathways involved in Manumycin A effects like apoptosis. Therefore, these studies created doubt whether the main mechanism of action of Manumycin A is FTase inhibition. For some of these alternative targets half maximal inhibitory concentrations (IC₅₀) of Manumycin A are available, but not for human and C. elegans FTase. So, we aimed to 1) characterize missing C. elegans FTase kinetics, 2) elucidate the IC₅₀ and K_i values of Manumycin A on purified human and C. elegans FTase 3) investigate Manumycin A dependent expression of FTase and apoptosis genes in C. elegans. C. elegans FTase has its temperature optimum at 40°C with K_M of 1.3 µM (farnesylpyrophosphate) and 1.7 µM (protein derivate). Whilst other targets are inhibitable by Manumycin A at the nanomolar level, we found that Manumycin A inhibits cell-free FTase in micromolar concentrations (K_{i human} 4.15 μM; K_{i C. elegans} 3.16 μM). Furthermore, our gene expression results correlate with other studies indicating that thioredoxin reductase 1 is the main target of Manumycin A. According to our results, the ability of Manumycin A to inhibit the FTase at the micromolar level is rather neglectable for its cellular effects, so we postulate that the classification as a specific FTase inhibitor is no longer valid.

Neuronal temperature perception induces specific defenses that enable C. elegans to cope with the enhanced reactivity of hydrogen peroxide at high temperature

Hydrogen peroxide is the most common reactive chemical that organisms face on the microbial battlefield. The rate with which hydrogen peroxide damages biomolecules required for life increases with temperature, yet little is known about how organisms cope with this temperature-dependent threat. Here, we show that Caenorhabditis elegans nematodes use temperature information perceived by sensory neurons to cope with the temperature-dependent threat of hydrogen peroxide produced by the pathogenic bacterium Enterococcus faecium. These nematodes preemptively induce the expression of specific hydrogen peroxide defenses in response to perception of high temperature by a pair of sensory neurons. These neurons communicate temperature information to target tissues expressing those defenses via an insulin/IGF1 hormone. This is the first example of a multicellular organism inducing their defenses to a chemical when they sense an inherent enhancer of the reactivity of that chemical.

Caenorhabditis elegans as an emerging model in food and nutrition research: importance of standardizing base diet

As a model organism that has helped revolutionize life sciences, Caenorhabditis elegans has been increasingly used in nutrition research. Here we explore the tradeoffs between pros and cons of its use as a dietary model based primarily on literature review from the past decade. We first provide an overview of its experimental strengths as an animal model, focusing on lifespan and healthspan, behavioral and physiological phenotypes, and conservation of key nutritional pathways. We then summarize recent advances of its use in nutritional studies, e.g. food preference and feeding behavior, sugar status and metabolic reprogramming, lifetime and transgenerational nutrition tracking, and diet-microbiota-host interactions, highlighting cutting-edge technologies originated from or developed in C. elegans. We further review current challenges of using C. elegans as a nutritional model, followed by in-depth discussions on potential solutions. In particular, growth scales and throughputs, food uptake mode, and axenic culture of C. elegans are appraised in the context of food research. We also provide perspectives for future development of chemically defined nematode food ("NemaFood") for C. elegans, which is now widely accepted as a versatile and affordable in vivo model and has begun to show transformative potential to pioneer nutrition science.

Population bottleneck has only marginal effect on fitness evolution and its repeatability in dioecious Caenorhabditis elegans

The predictability of evolution is expected to depend on the relative contribution of deterministic and stochastic processes. This ratio is modulated by effective population size. Smaller effective populations harbor less genetic diversity and stochastic processes are generally expected to play a larger role, leading to less repeatable evolutionary trajectories. Empirical insight into the relationship between effective population size and repeatability is limited and focused mostly on asexual organisms. Here, we tested whether fitness evolution was less repeatable after a population bottleneck in obligately outcrossing populations of Caenorhabditis elegans. Replicated populations founded by 500, 50, or five individuals (no/moderate/strong bottleneck) were exposed to a novel environment with a different bacterial prey. As a proxy for fitness, population size was measured after one week of growth before and after 15 weeks of evolution. Surprisingly, we found no significant differences among treatments in their fitness evolution. Even though the strong bottleneck reduced the relative contribution of selection to fitness variation, this did not translate to a significant reduction in the repeatability of fitness evolution. Thus, although a bottleneck reduced the contribution of deterministic processes, we conclude that the predictability of evolution may not universally depend on effective population size, especially in sexual organisms.

Real age prediction from the transcriptome with RAPToR

Transcriptomic data is often affected by uncontrolled variation among samples that can obscure and confound the effects of interest. This variation is frequently due to unintended differences in developmental stages between samples. The transcriptome itself can be used to estimate developmental progression, but existing methods require many samples and do not estimate a specimen's real age. Here we present real-age prediction from transcriptome staging on reference (RAPToR), a computational method that precisely estimates the real age of a sample from its transcriptome, exploiting existing time-series data as reference. RAPToR works with whole animal, dissected tissue and single-cell data for the most common animal models, humans and even for non-model organisms lacking reference data. We show that RAPToR can be used to remove age as a confounding factor and allow recovery of a signal of interest in differential expression analysis. RAPToR will be especially useful in large-scale single-organism profiling because it eliminates the need for accurate staging or synchronisation before profiling.

The utility of alternative models in particulate matter air pollution toxicology

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Countless unique particulate matter (PM) samples with limited or no toxicity information.

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Alternative in vivo models offer greater throughput than traditional mammalian models.

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Use of zebrafish, fruit flies, and nematodes in PM toxicology lacks systematic review.

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Their utility in PM toxicity and mechanistic research and as screening tools is reviewed.

Exposure to particulate matter (PM) air pollution increases risk of adverse human health effects. As more attention is brought to bear on the problem of PM, traditional mammalian in vivo models struggle to keep up with the risk assessment challenges posed by the countless number of unique PM samples across air sheds with limited or no toxicity information. This review examines the utility of three higher throughput, alternative, in vivo animal models in PM toxicity research: Danio rerio (zebrafish), Caenorhabditis elegans (nematode), and Drosophila melanogaster (fruit fly). These model organisms vary in basic biology, ease of handling, methods of exposure to PM, number and types of available assays, and the degree to which they mirror human biology and responsiveness, among other differences. The use of these models in PM research dates back over a decade, with assessments of the toxicity of various PM sources including traffic-related combustion emissions, wildland fire smoke, and coal fly ash. This article reviews the use of these alternative model organisms in PM toxicity studies, their biology, the various assays developed, endpoints measured, their strengths and limitations, as well as their potential role in PM toxicity assessment and mechanistic research going forward.

Host age increased conjugal plasmid transfer in gut microbiota of the soil invertebrate Caenorhabditis elegans

Plasmid conjugation contributes greatly to the spread of antibiotic resistance genes (ARGs) in soils. However, the spread potential in the gut of soil fauna remains poorly studied, and little was known about the impact of host age on ARGs dissemination in the gut microbiota of soil animals. Here, the typical nematode-Caenorhabditis elegans was employed as the model soil animal, aiming to investigate transfer of broad-host-range IncP-1ɛ from Escherichia coli MG1655 to gut microbiota within 6 days under varied temperature gradients (15, 20 and 25 °C) using qPCR combined with plate screening. Results showed that conjugation rates increased with incubation time and rising temperature in the gut of C. elegans, sharing a similar trend with abundances of plasmid conjugation relevant genes such as trbBp (mating pair formation) and trfAp (plasmid replication). Incubation time and temperature significantly shaped the gut microbial community of C. elegans. Core microbiota in the gut of C. elegans, including Enterobacteriaceae, Lactobacillaceae and Leuconostocaceae, constituted a large part of transconjugal pool for plasmid IncP-1ɛ. Our results highlight an important sink of gut microbiota for ARGs dissemination and upregulation of ARGs transfer in the gut microbiota with host age, further potentially stimulating evolution of ARGs in terrestrial environments.

Towards a reporting guideline for developmental and reproductive toxicology testing in C. elegans and other nematodes

Implementation of reliable methodologies allowing Reduction, Refinement, and Replacement (3Rs) of animal testing is a process that takes several decades and is still not complete. Reliable methods are essential for regulatory hazard assessment of chemicals where differences in test protocol can influence the test outcomes and thus affect the confidence in the predictive value of the organisms used as an alternative for mammals. Although test guidelines are common for mammalian studies, they are scarce for non-vertebrate organisms that would allow for the 3Rs of animal testing. Here, we present a set of 30 reporting criteria as the basis for such a guideline for Developmental and Reproductive Toxicology (DART) testing in the nematode Caenorhabditis elegans. Small organisms like C. elegans are upcoming in new approach methodologies for hazard assessment; thus, reliable and robust test protocols are urgently needed. A literature assessment of the fulfilment of the reporting criteria demonstrates that although studies describe methodological details, essential information such as compound purity and lot/batch number or type of container is often not reported. The formulated set of reporting criteria for C. elegans testing can be used by (i) researchers to describe essential experimental details (ii) data scientists that aggregate information to assess data quality and include data in aggregated databases (iii) regulators to assess study data for inclusion in regulatory hazard assessment of chemicals.

Coordinated maintenance of H3K36/K27 methylation by histone demethylases preserves germ cell identity and immortality

Germ cells have evolved unique mechanisms to ensure the transmission of genetically and nongenetically encoded information, whose alteration compromises germ cell immortality. Chromatin factors play fundamental roles in these mechanisms. H3K36 and H3K27 methyltransferases shape and propagate a pattern of histone methylation essential for C. elegans germ cell maintenance, but the role of respective histone demethylases remains unexplored. Here, we show that jmjd-5 regulates H3K36me2 and H3K27me3 levels, preserves germline immortality, and protects germ cell identity by controlling gene expression. The transcriptional and biological effects of jmjd-5 loss can be hindered by the removal of H3K27demethylases, indicating that H3K36/K27 demethylases act in a transcriptional framework and promote the balance between H3K36 and H3K27 methylation required for germ cell immortality. Furthermore, we find that in wild-type, but not in jmjd-5 mutants, alterations of H3K36 methylation and transcription occur at high temperature, suggesting a role for jmjd-5 in adaptation to environmental changes.

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jmjd-5 is required for germ cell immortality at high temperature

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jmjd-5 sustains the expression of germline genes and represses somatic fate

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Mutations in jmjd-5 result in a global increase of H3K36me2 and H3K27me3

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Ablation of H3K27 demethylases counteracts the effects of jmjd-5 mutations

Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans

To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell autonomous. We have discovered that, in Caenorhabditis elegans, neuronal heat shock factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR), causes extensive fat remodeling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine and a global shift in the saturation levels of plasma membrane's phospholipids. The observed remodeling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least 6 TAX-2/TAX-4 cyclic guanosine monophosphate (cGMP) gated channel expressing sensory neurons, and transforming growth factor ß (TGF-β)/bone morphogenetic protein (BMP) are required for signaling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodeling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell nonautonomously coordinate membrane saturation and composition across tissues in a multicellular animal.

Review of Biological Effects of Acute and Chronic Radiation Exposure on Caenorhabditis elegans

Knowledge regarding complex radiation responses in biological systems can be enhanced using genetically amenable model organisms. In this manuscript, we reviewed the use of the nematode, Caenorhabditis elegans (C. elegans), as a model organism to investigate radiation’s biological effects. Diverse types of experiments were conducted on C. elegans, using acute and chronic exposure to different ionizing radiation types, and to assess various biological responses. These responses differed based on the type and dose of radiation and the chemical substances in which the worms were grown or maintained. A few studies compared responses to various radiation types and doses as well as other environmental exposures. Therefore, this paper focused on the effect of irradiation on C. elegans, based on the intensity of the radiation dose and the length of exposure and ways to decrease the effects of ionizing radiation. Moreover, we discussed several studies showing that dietary components such as vitamin A, polyunsaturated fatty acids, and polyphenol-rich food source may promote the resistance of C. elegans to ionizing radiation and increase their life span after irradiation.

The Mitochondrial Na+/Ca2+ Exchanger Inhibitor CGP37157 Preserves Muscle Structure and Function to Increase Lifespan and Healthspan in Caenorhabditis elegans

We have reported recently that the mitochondrial Na⁺/Ca²⁺ exchanger inhibitor CGP37157 extends lifespan in Caenorhabditis elegans by a mechanism involving mitochondria, the TOR pathway and the insulin/IGF1 pathway. Here we show that CGP37157 significantly improved the evolution with age of the sarcomeric regular structure, delaying development of sarcopenia in C. elegans body wall muscle and increasing the average and maximum speed of the worms. Similarly, CGP37157 favored the maintenance of a regular mitochondrial structure during aging. We have also investigated further the mechanism of the effect of CGP37157 by studying its effect in mutants of aak-1;aak-2/AMP-activated kinase, sir-2.1/sirtuin, rsks-1/S6 kinase and daf-16/FOXO. We found that this compound was still effective increasing lifespan in all these mutants, indicating that these pathways are not involved in the effect. We have then monitored pharynx cytosolic and mitochondrial Ca²⁺ signalling and our results suggest that CGP37157 is probably inhibiting not only the mitochondrial Na⁺/Ca²⁺ exchanger, but also Ca²⁺ entry through the plasma membrane. Finally, a transcriptomic study detected that CGP37157 induced changes in lipid metabolism enzymes and a four-fold increase in the expression of ncx-6, one of the C. elegans mitochondrial Na⁺/Ca²⁺ exchangers. In summary, CGP37157 increases both lifespan and healthspan by a mechanism involving changes in cytosolic and mitochondrial Ca²⁺ homeostasis. Thus, Ca²⁺ signalling could be a promising target to act on aging.

Association with a novel protective microbe facilitates host adaptation to a stressful environment

Protective symbionts can allow hosts to occupy otherwise uninhabitable niches. Despite the importance of symbionts in host evolution, we know little about how these associations arise. Encountering a microbe that can improve host fitness in a stressful environment may favor persistent interactions with that microbe, potentially facilitating a long-term association. The bacterium Bacillus subtilis protects Caenorhabditis elegans nematodes from heat shock by increasing host fecundity compared to the nonprotective Escherichia coli. In this study, we ask how the protection provided by the bacterium affects the host's evolutionary trajectory. Because of the stark fitness contrast between hosts heat shocked on B. subtilis versus E. coli, we tested whether the protection conferred by the bacteria could increase the rate of host adaptation to a stressful environment. We passaged nematodes on B. subtilis or E. coli, under heat stress or standard conditions for 20 host generations of selection. When assayed under heat stress, we found that hosts exhibited the greatest fitness increase when evolved with B. subtilis under stress compared to when evolved with E. coli or under standard (nonstressful) conditions. Furthermore, despite not directly selecting for increased B. subtilis fitness, we found that hosts evolved to harbor more B. subtilis as they adapted to heat stress. Our findings demonstrate that the context under which hosts evolve is important for the evolution of beneficial associations and that protective microbes can facilitate host adaptation to stress. In turn, such host adaptation can benefit the microbe.

Alternative model organisms for toxicological fingerprinting of relevant parameters in food and nutrition

In the field of (food) toxicology, there is a strong trend of replacing animal trials with alternative methods for the assessment of adverse health effects in humans. The replacement of animal trials is not only driven by ethical concerns but also by the number of potential testing substances (food additives, packaging material, contaminants, and toxicants), which is steadily increasing. In vitro 2D cell culture applications in combination with in silico modeling might provide an applicable first response. However, those systems lack accurate predictions of metabolic actions. Thus, alternative in vivo models could fill the gap between cell culture and animal trials. In this review, we highlight relevant studies in the field and spotlight the applicability of alternative models, including C. elegans, D. rerio, Drosophila, HET-CAM and Lab-on-a-chip.

Temporally regulated cell migration is sensitive to variation in body size

Few studies have measured the robustness to perturbations of the final position of a long-range migrating cell. In the nematode Caenorhabditis elegans, the QR neuroblast migrates anteriorly, while undergoing three division rounds. We study the final position of two of its great-granddaughters, the end of migration of which was previously shown to depend on a timing mechanism. We find that the variance in their final position is similar to that of other long-range migrating neurons. As expected from the timing mechanism, the position of QR descendants depends on body size, which we varied by changing maternal age or using body size mutants. Using a mathematical model, we show that body size variation is partially compensated for. Applying environmental perturbations, we find that the variance in final position increased following starvation at hatching. The mean position is displaced upon a temperature shift. Finally, highly significant variation was found among C. elegans wild isolates. Overall, this study reveals that the final position of these neurons is quite robust to stochastic variation, shows some sensitivity to body size and to external perturbations, and varies in the species.This article has an associated 'The people behind the papers' interview.

The secreted endoribonuclease ENDU-2 from the soma protects germline immortality in C. elegans

Multicellular organisms coordinate tissue specific responses to environmental information via both cell-autonomous and non-autonomous mechanisms. In addition to secreted ligands, recent reports implicated release of small RNAs in regulating gene expression across tissue boundaries. Here, we show that the conserved poly-U specific endoribonuclease ENDU-2 in C. elegans is secreted from the soma and taken-up by the germline to ensure germline immortality at elevated temperature. ENDU-2 binds to mature mRNAs and negatively regulates mRNA abundance both in the soma and the germline. While ENDU-2 promotes RNA decay in the soma directly via its endoribonuclease activity, ENDU-2 prevents misexpression of soma-specific genes in the germline and preserves germline immortality independent of its RNA-cleavage activity. In summary, our results suggest that the secreted RNase ENDU-2 regulates gene expression across tissue boundaries in response to temperature alterations and contributes to maintenance of stem cell immortality, probably via retaining a stem cell specific program of gene expression.

The question as to how the soma regulates the germline has been much studied. Here, the authors show in C. elegans that the poly-U specific endoribonuclease ENDU-2 is secreted from the soma and taken-up by the germline, binding mature mRNA, repressing expression of somatic transcripts and maintaining germline immortality.

Bacterial diets differentially alter lifespan and healthspan trajectories in C. elegans

Diet is one of the more variable aspects in life due to the variety of options that organisms are exposed to in their natural habitats. In the laboratory, C. elegans are raised on bacterial monocultures, traditionally the E. coli B strain OP50, and spontaneously occurring microbial contaminants are removed to limit experimental variability because diet-including the presence of contaminants-can exert a potent influence over animal physiology. In order to diversify the menu available to culture C. elegans in the lab, we have isolated and cultured three such microbes: Methylobacterium, Xanthomonas, and Sphingomonas. The nutritional composition of these bacterial foods is unique, and when fed to C. elegans, can differentially alter multiple life history traits including development, reproduction, and metabolism. In light of the influence each food source has on specific physiological attributes, we comprehensively assessed the impact of these bacteria on animal health and devised a blueprint for utilizing different food combinations over the lifespan, in order to promote longevity. The expansion of the bacterial food options to use in the laboratory will provide a critical tool to better understand the complexities of bacterial diets and subsequent changes in physiology and gene expression.

Intergenerational Pathogen-Induced Diapause in Caenorhabditis elegans Is Modulated by mir-243

Persistent infection of the bacterivore nematode C. elegans with bacteria such as P. aeruginosa and S. enterica makes the worm diapause or hibernate. By doing this, the worm closes its mouth, avoiding infection. This response takes two generations to be implemented. In this work, we looked for genes expressed upon infection that could mediate the worm diapause triggered by pathogens. We identify mir-243-3p as the only transcript commonly upregulated when animals feed on P. aeruginosa and S. enterica for two consecutive generations. Moreover, we demonstrate that mir-243-3p is required for pathogen-induced dauer formation, a new function that has not been previously described for this microRNA (miRNA). We also find that the transcriptional activators DAF-16, PQM-1, and CRH-2 are necessary for the expression of mir-243 under pathogenesis. Here we establish a relationship between a small RNA and a developmental change that ensures the survival of a percentage of the progeny.

The interaction and communication between bacteria and their hosts modulate many aspects of animal physiology and behavior. Dauer entry as a response to chronic exposure to pathogenic bacteria in Caenorhabditis elegans is an example of a dramatic survival response. This response is dependent on the RNA interference (RNAi) machinery, suggesting the involvement of small RNAs (sRNAs) as effectors. Interestingly, dauer formation occurs after two generations of interaction with two unrelated moderately pathogenic bacteria. Therefore, we sought to discover the identity of C. elegans RNAs involved in pathogen-induced diapause. Using transcriptomics and differential expression analysis of coding and long and small noncoding RNAs, we found that mir-243-3p (the mature form of mir-243) is the only transcript continuously upregulated in animals exposed to both Pseudomonas aeruginosa and Salmonella enterica for two generations. Phenotypic analysis of mutants showed that mir-243 is required for dauer formation under pathogenesis but not under starvation. Moreover, DAF-16, a master regulator of defensive responses in the animal and required for dauer formation was found to be necessary for mir-243 expression. This work highlights the role of a small noncoding RNA in the intergenerational defensive response against pathogenic bacteria and interkingdom communication.

Tissue-specific effects of temperature on proteasome function

Variation in ambient growth temperature can cause changes in normal animal physiology and cellular functions such as control of protein homeostasis. A key mechanism for maintaining proteostasis is the selective degradation of polyubiquitinated proteins, mediated by the ubiquitin-proteasome system (UPS). It is still largely unsolved how temperature changes affect the UPS at the organismal level. Caenorhabditis elegans nematodes are normally bred at 20 °C, but for some experimental conditions, 25 °C is often used. We studied the effect of 25 °C on C. elegans UPS by measuring proteasome activity and polyubiquitinated proteins both in vitro in whole animal lysates and in vivo in tissue-specific transgenic reporter strains. Our results show that an ambient temperature shift from 20 to 25 °C increases the UPS activity in the intestine, but not in the body wall muscle tissue, where a concomitant accumulation of polyubiquitinated proteins occurs. These changes in the UPS activity and levels of polyubiquitinated proteins were not detectable in whole animal lysates. The exposure of transgenic animals to 25 °C also induced ER stress reporter fluorescence, but not the fluorescence of a heat shock responsive reporter, albeit detection of a mild induction in hsp-16.2 mRNA levels. In conclusion, C. elegans exhibits tissue-specific responses of the UPS as an organismal strategy to cope with a rise in ambient temperature.

ZAKα Recognizes Stalled Ribosomes through Partially Redundant Sensor Domains

Impairment of ribosome function activates the MAPKKK ZAK, leading to activation of mitogen-activated protein (MAP) kinases p38 and JNK and inflammatory signaling. The mechanistic basis for activation of this ribotoxic stress response (RSR) remains completely obscure. We show that the long isoform of ZAK (ZAKα) directly associates with ribosomes by inserting its flexible C terminus into the ribosomal intersubunit space. Here, ZAKα binds helix 14 of 18S ribosomal RNA (rRNA). An adjacent domain in ZAKα also probes the ribosome, and together, these sensor domains are critically required for RSR activation after inhibition of both the E-site, the peptidyl transferase center (PTC), and ribotoxin action. Finally, we show that ablation of the RSR response leads to organismal phenotypes and decreased lifespan in the nematode Caenorhabditis elegans (C. elegans). Our findings yield mechanistic insight into how cells detect ribotoxic stress and provide experimental in vivo evidence for its physiological importance.

A Cell Fate Switch in the Caenorhabditis elegans Seam Cell Lineage Occurs Through Modulation of the Wnt Asymmetry Pathway in Response to Temperature Increase

Populations often display consistent developmental phenotypes across individuals despite inevitable biological stochasticity. Nevertheless, developmental robustness has limits, and systems can fail upon change in the environment or the genetic background. We use here the seam cells, a population of epidermal stem cells in Caenorhabditis elegans, to study the influence of temperature change and genetic variation on cell fate. Seam cell development has mostly been studied so far in the laboratory reference strain (N2), grown at 20° temperature. We demonstrate that an increase in culture temperature to 25° introduces variability in the wild-type seam cell lineage, with a proportion of animals showing an increase in seam cell number. We map this increase to lineage-specific symmetrization events of normally asymmetric cell divisions at the fourth larval stage, leading to the retention of seam cell fate in both daughter cells. Using genetics and single-molecule imaging, we demonstrate that this symmetrization occurs via changes in the Wnt asymmetry pathway, leading to aberrant Wnt target activation in anterior cell daughters. We find that intrinsic differences in the Wnt asymmetry pathway already exist between seam cells at 20° and this may sensitize cells toward a cell fate switch at increased temperature. Finally, we demonstrate that wild isolates of C. elegans display variation in seam cell sensitivity to increased culture temperature, although their average seam cell number is comparable at 20°. Our results highlight how temperature can modulate cell fate decisions in an invertebrate model of stem cell patterning.

Caenorhabditis elegans ADAR editing and the ERI-6/7/MOV10 RNAi pathway silence endogenous viral elements and LTR retrotransposons

Silencing of transposable elements and viruses is critical for the maintenance of genome integrity, cellular homeostasis, and organismal health. Here we describe multiple factors that control different types of transposable elements, providing insight into how they are regulated. We also identify stress response pathways that are triggered upon misregulation of these transposable elements. The conservation of these factors and pathways in human suggests that our studies in Caenorhabditis elegans can provide general insight into the regulation of and response to transposable elements and viruses.

Endogenous retroviruses and long terminal repeat (LTR) retrotransposons are mobile genetic elements that are closely related to retroviruses. Desilenced endogenous retroviruses are associated with human autoimmune disorders and neurodegenerative diseases. Caenorhabditis elegans and related Caenorhabditis spp. contain LTR retrotransposons and, as described here, numerous integrated viral genes including viral envelope genes that are part of LTR retrotransposons. We found that both LTR retrotransposons and endogenous viral elements are silenced by ADARs [adenosine deaminases acting on double-stranded RNA (dsRNA)] together with the endogenous RNA interference (RNAi) factor ERI-6/7, a homolog of MOV10 helicase, a retrotransposon and retrovirus restriction factor in human. siRNAs corresponding to integrated viral genes and LTR retrotransposons, but not to DNA transposons, are dependent on the ADARs and ERI-6/7. siRNAs corresponding to palindromic repeats are independent of the ADARs and ERI-6/7, and are in fact increased in adar- and eri-6/7–defective mutants because of an antiviral RNAi response to dsRNA. Silencing of LTR retrotransposons is dependent on downstream RNAi factors and P granule components but is independent of the viral sensor DRH-1/RIG-I and the nuclear Argonaute NRDE-3. The activation of retrotransposons in the ADAR- and ERI-6/7/MOV10–defective mutant is associated with the induction of the unfolded protein response (UPR), a common response to viral infection. The overlap between genes induced upon viral infection and infection with intracellular pathogens and genes coexpressed with retrotransposons suggests that there is a common response to different types of foreign elements that includes a response to proteotoxicity presumably caused by the burden of replicating pathogens and expressed retrotransposons.

Reduction of mRNA export unmasks different tissue sensitivities to low mRNA levels during Caenorhabditis elegans development

Animal development requires the execution of specific transcriptional programs in different sets of cells to build tissues and functional organs. Transcripts are exported from the nucleus to the cytoplasm where they are translated into proteins that, ultimately, carry out the cellular functions. Here we show that in Caenorhabditis elegans, reduction of mRNA export strongly affects epithelial morphogenesis and germline proliferation while other tissues remain relatively unaffected. Epithelialization and gamete formation demand a large number of transcripts in the cytoplasm for the duration of these processes. In addition, our findings highlight the existence of a regulatory feedback mechanism that activates gene expression in response to low levels of cytoplasmic mRNA. We expand the genetic characterization of nuclear export factor NXF-1 to other members of the mRNA export pathway to model mRNA export and recycling of NXF-1 back to the nucleus. Our model explains how mutations in genes involved in general processes, such as mRNA export, may result in tissue-specific developmental phenotypes.

Biology is the root of variability: cautionary tales in Caenorhabditis elegans biology

Reproducibility is critical for the standardization, interpretation, and progression of research. However, many factors increase variability and reduce reproducibility. In Caenorhabditis elegans research, there are many possible causes of variability that may explain why experimental outcomes sometimes differ between laboratories and between experiments. Factors contributing to experimental variability include the genetic background of both C. elegans and its bacterial diet, differences in media composition, intergenerational and transgenerational effects that may be carried over for generations, and the use of chemicals or reagents that may have unexpected consequences. This review summarizes sources of variability in C. elegans research and serves to identify laboratory practices that could influence reproducibility.

Histone acetylation promotes long-lasting defense responses and longevity following early life heat stress

Early exposure to some mild stresses can slow down the aging process and extend lifespan, raising the question of how early life stress might impact the somatic health of aged animals. Here, we reveal that early life heat experience triggers the establishment of epigenetic memory in soma, which promotes long-lasting stress responses and longevity in C. elegans. Unlike lethal heat shock, mild heat activates a unique transcriptional program mimicking pathogen defense responses, characterized by the enhanced expression of innate immune and detoxification genes. Surprisingly, the expression of defense response genes persists long after heat exposure, conferring enhanced stress resistance even in aged animals. Further studies identify the histone acetyltransferase CBP-1 and the chromatin remodeling SWI/SNF complex as epigenetic modulators of the long-lasting defense responses. Histone acetylation is elevated by heat stress and maintained into agedness thereafter. Accordingly, histone acetylation levels were increased on the promoters of defense genes. Moreover, disruption of epigenetic memory abrogates the longevity response to early hormetic heat stress, indicating that long-lasting defense responses are crucial for the survival of aged animals. Together, our findings provide mechanistic insights into how temperature stress experienced in early life provides animals with lifetime health benefits.

Organism aging is a deleterious process characterized by the progressive decline of cellular and tissue functions in the late life stage. However, the rate of aging is often determined by an organism’s historic experiences that occur in early life. For example, some mild stresses experienced in early life can extend animal lifespan, implying that early stresses might impact the health of aged animals, the mechanisms of which remain largely unknown. Here, by using the model organism C. elegans, we reveal a mechanism of how early life heat stress impacts the health of aged animals and promotes longevity. We find that early exposure to mild heat activates basal innate immune and detoxification responses, which are surprisingly maintained long after temperature drop, even into agedness, and therefore contribute to lifespan extension. Remarkably, the long-lasting defense responses require epigenetic memory established by histone acetyltransferase CBP-1 and chromatin remodeling complex SWI/SNF. As a previous study has reported high temperature-induced transgenerational epigenetic effects in germline that involve histone methylation, our findings suggest that temperature may trigger distinct epigenetic changes in soma and germline, conferring adaptations in both the parental generation and their offspring.

Disruption of the Caenorhabditis elegans Integrator complex triggers a non-conventional transcriptional mechanism beyond snRNA genes

Gene expression is generally regulated by recruitment of transcription factors and RNA polymerase II (RNAP II) to specific sequences in the gene promoter region. The Integrator complex mediates processing of small nuclear RNAs (snRNAs) as well as the initiation and release of paused RNAP II at specific genes in response to growth factors. Here we show that in C. elegans, disruption of the Integrator complex leads to transcription of genes located downstream of the snRNA loci via a non-conventional transcription mechanism based on the lack of processing of the snRNAs. RNAP II read-through generates long chimeric RNAs containing snRNA, the intergenic region and the mature mRNA of the downstream gene located in sense. These chimeric sn-mRNAs remain as untranslated long non-coding RNAs, in the case of U1- and U2-derived sn-mRNAs, but can be translated to proteins in the case of SL-derived sn-mRNAs. The transcriptional effect caused by disruption of the Integrator complex is not restricted to genes located downstream of the snRNA loci but also affects key regulators of signal transduction such as kinases and phosphatases. Our findings highlight that these transcriptional alterations may be behind the correlation between mutations in the Integrator complex and tumor transformation.