The C. elegans dauer larva as a paradigm to study metabolic suppression and desiccation tolerance

Protecting Proteins from Desiccation Stress Using Molecular Glasses and Gels

Faced with desiccation stress, many organisms deploy strategies to maintain the integrity of their cellular components. Amorphous glassy media composed of small molecular solutes or protein gels present general strategies for protecting against drying. We review these strategies and the proposed molecular mechanisms to explain protein protection in a vitreous matrix under conditions of low hydration. We also describe efforts to exploit similar strategies in technological applications for protecting proteins in dry or highly desiccated states. Finally, we outline open questions and possibilities for future explorations.

Periodic ethanol supply as a path toward unlimited lifespan of Caenorhabditis elegans dauer larvae

The dauer larva is a specialized stage of worm development optimized for survival under harsh conditions that have been used as a model for stress resistance, metabolic adaptations, and longevity. Recent findings suggest that the dauer larva of Caenorhabditis elegans may utilize external ethanol as an energy source to extend their lifespan. It was shown that while ethanol may serve as an effectively infinite source of energy, some toxic compounds accumulating as byproducts of its metabolism may lead to the damage of mitochondria and thus limit the lifespan of larvae. A minimal mathematical model was proposed to explain the connection between the lifespan of a dauer larva and its ethanol metabolism. To explore theoretically if it is possible to extend even further the lifespan of dauer larvae, we incorporated two natural mechanisms describing the recovery of damaged mitochondria and elimination of toxic compounds, which were previously omitted in the model. Numerical simulations of the revised model suggested that while the ethanol concentration is constant, the lifespan still stays limited. However, if ethanol is supplied periodically, with a suitable frequency and amplitude, the dauer could survive as long as we observe the system. Analytical methods further help to explain how feeding frequency and amplitude affect lifespan extension. Based on the comparison of the model with experimental data for fixed ethanol concentration, we proposed the range of feeding protocols that could lead to even longer dauer survival and it can be tested experimentally.

The Endocannabinoid System in Caenorhabditis elegans

The existence of a formal Endocannabinoid System in C. elegans has been questioned due to data showing the absence of typical cannabinoid receptors in the worm; however, the presence of a full metabolism for endocannabinoids, alternative ligands, and receptors for these agents and a considerable number of orthologous and homologous genes regulating physiological cannabinoid-like signals and responses - several of which are similar to those of mammals - demonstrates a well-structured and functional complex system in nematodes. In this review, we describe and compare similarities and differences between the Endocannabinoid System in mammals and nematodes, highlighting the basis for the integral study of this novel system in the worm.

Deciphering the mechanism of anhydrobiosis in the entomopathogenic nematode Heterorhabditis indica through comparative transcriptomics

The entomopathogenic nematode, Heterorhabditis indica, is a popular biocontrol agent of high commercial significance. It possesses tremendous genetic architecture to survive desiccation stress by undergoing anhydrobiosis to increase its lifespan-an attribute exploited in the formulation technology. The comparative transcriptome of unstressed and anhydrobiotic H. indica revealed several previously concealed metabolic events crucial for adapting towards the moisture stress. During the induction of anhydrobiosis in the infective juveniles (IJ), 1584 transcripts were upregulated and 340 downregulated. As a strategy towards anhydrobiotic survival, the IJ showed activation of several genes critical to antioxidant defense, detoxification pathways, signal transduction, unfolded protein response and molecular chaperones and ubiquitin-proteasome system. Differential expression of several genes involved in gluconeogenesis - β-oxidation of fatty acids, glyoxylate pathway; glyceroneogenesis; fatty acid biosynthesis; amino-acid metabolism - shikimate pathway, sachharopine pathway, kyneurine pathway, lysine biosynthesis; one-carbon metabolism-polyamine pathway, transsulfuration pathway, folate cycle, methionine cycle, nucleotide biosynthesis; mevalonate pathway; and glyceraldehyde-3-phosphate dehydrogenase were also observed. We report the role of shikimate pathway, sachharopine pathway and glyceroneogenesis in anhydrobiotes, and seven classes of repeat proteins, specifically in H. indica for the first time. These results provide insights into anhydrobiotic survival strategies which can be utilized to strengthen the development of novel formulations with enhanced and sustained shelf-life.

Integrative Proteomic and Phosphoproteomic Analyses Revealed Complex Mechanisms Underlying Reproductive Diapause in Bombus terrestris Queens

Reproductive diapause is an overwintering strategy for Bombus terrestris, which is an important pollinator for agricultural production. However, the precise mechanisms underlying reproductive diapause in bumblebees remain largely unclear. Here, a combination analysis of proteomics and phosphoproteomics was used to reveal the mechanisms that occur during and after diapause in three different phases: diapause (D), postdiapause (PD), and founder postdiapause (FPD). In total, 4655 proteins and 10,600 phosphorylation sites of 3339 proteins were identified. Diapause termination and reactivation from D to the PD stage were characterized by the upregulation of proteins associated with ribosome assembly and biogenesis, transcription, and translation regulation in combination with the upregulation of phosphoproteins related to neural signal transmission, hormone biosynthesis and secretion, and energy-related metabolism. Moreover, the reproductive program was fully activated from PD to the FPD stage, as indicated by the upregulation of proteins related to fat digestion and absorption, the biosynthesis of unsaturated fatty acids, fatty acid elongation, protein processing in the endoplasmic reticulum, and the upregulation of energy-related metabolism at the phosphoproteome level. We also predicted a kinase-substrate interaction network and constructed protein-protein networks of proteomic and phosphoproteomic data. These results will help to elucidate the mechanisms underlying the regulation of diapause in B. terrestris for year-round mass breeding.

Small-Molecule Mn Antioxidants in Caenorhabditis elegans and Deinococcus radiodurans Supplant MnSOD Enzymes during Aging and Irradiation

Denham Harman's oxidative damage theory identifies superoxide (O₂^•-) radicals as central agents of aging and radiation injury, with Mn²⁺-dependent superoxide dismutase (MnSOD) as the principal O₂^•--scavenger. However, in the radiation-resistant nematode Caenorhabditis elegans, the mitochondrial antioxidant enzyme MnSOD is dispensable for longevity, and in the model bacterium Deinococcus radiodurans, it is dispensable for radiation resistance. Many radiation-resistant organisms accumulate small-molecule Mn²⁺-antioxidant complexes well-known for their catalytic ability to scavenge O₂^•-, along with MnSOD, as exemplified by D. radiodurans. Here, we report experiments that relate the MnSOD and Mn-antioxidant content to aging and oxidative stress resistances and which indicate that C. elegans, like D. radiodurans, may rely on Mn-antioxidant complexes as the primary defense against reactive oxygen species (ROS). Wild-type and ΔMnSOD D. radiodurans and C. elegans were monitored for gamma radiation sensitivities over their life spans while gauging Mn²⁺-antioxidant content by electron paramagnetic resonance (EPR) spectroscopy, a powerful new approach to determining the in vivo Mn-antioxidant content of cells as they age. As with D. radiodurans, MnSOD is dispensable for radiation survivability in C. elegans, which hyperaccumulates Mn-antioxidants exceptionally protective of proteins. Unexpectedly, ΔMnSOD mutants of both the nematodes and bacteria exhibited increased gamma radiation survival compared to the wild-type. In contrast, the loss of MnSOD renders radiation-resistant bacteria sensitive to atmospheric oxygen during desiccation. Our results support the concept that the disparate responses to oxidative stress are explained by the accumulation of Mn-antioxidant complexes which protect, complement, and can even supplant MnSOD. IMPORTANCE The current theory of cellular defense against oxidative damage identifies antioxidant enzymes as primary defenders against ROS, with MnSOD being the preeminent superoxide (O₂^•-) scavenger. However, MnSOD is shown to be dispensable both for radiation resistance and longevity in model organisms, the bacterium Deinococcus radiodurans and the nematode Caenorhabditis elegans. Measured by electron paramagnetic resonance (EPR) spectroscopy, small-molecule Mn-antioxidant content was shown to decline in unison with age-related decreases in cell proliferation and radioresistance, which again are independent of MnSOD presence. Most notably, the Mn-antioxidant content of C. elegans drops precipitously in the last third of its life span, which links with reports that the steady-state level of oxidized proteins increases exponentially during the last third of the life span in animals. This leads us to propose that global responses to oxidative stress must be understood through an extended theory that includes small-molecule Mn-antioxidants as potent O₂^•--scavengers that complement, and can even supplant, MnSOD.

A Primeval Mechanism of Tolerance to Desiccation Based on Glycolic Acid Saves Neurons in Mammals from Ischemia by Reducing Intracellular Calcium-Mediated Excitotoxicity

Stroke is the second leading cause of death and disability worldwide. Current treatments, such as pharmacological thrombolysis or mechanical thrombectomy, reopen occluded arteries but do not protect against ischemia-induced damage that occurs before reperfusion or neuronal damage induced by ischemia/reperfusion. It has been shown that disrupting the conversion of glyoxal to glycolic acid (GA) results in a decreased tolerance to anhydrobiosis in Caenorhabditis elegans dauer larva and that GA itself can rescue this phenotype. During the process of desiccation/rehydration, a metabolic stop/start similar to the one observed during ischemia/reperfusion occurs. In this study, the protective effect of GA is tested in different ischemia models, i.e., in commonly used stroke models in mice and swine. The results show that GA, given during reperfusion, strongly protects against ischemic damage and improves functional outcome. Evidence that GA exerts its effect by counteracting the glutamate-dependent increase in intracellular calcium during excitotoxicity is provided. These results suggest that GA treatment has the potential to reduce mortality and disability in stroke patients.

Genome-Wide Role of HSF1 in Transcriptional Regulation of Desiccation Tolerance in the Anhydrobiotic Cell Line, Pv11

The Pv11, an insect cell line established from the midge Polypedilum vanderplanki, is capable of extreme hypometabolic desiccation tolerance, so-called anhydrobiosis. We previously discovered that heat shock factor 1 (HSF1) contributes to the acquisition of desiccation tolerance by Pv11 cells, but the mechanistic details have yet to be elucidated. Here, by analyzing the gene expression profiles of newly established HSF1-knockout and -rescue cell lines, we show that HSF1 has a genome-wide effect on gene regulation in Pv11. The HSF1-knockout cells exhibit a reduced desiccation survival rate, but this is completely restored in HSF1-rescue cells. By comparing mRNA profiles of the two cell lines, we reveal that HSF1 induces anhydrobiosis-related genes, especially genes encoding late embryogenesis abundant proteins and thioredoxins, but represses a group of genes involved in basal cellular processes, thus promoting an extreme hypometabolism state in the cell. In addition, HSF1 binding motifs are enriched in the promoters of anhydrobiosis-related genes and we demonstrate binding of HSF1 to these promoters by ChIP-qPCR. Thus, HSF1 directly regulates the transcription of anhydrobiosis-related genes and consequently plays a pivotal role in the induction of anhydrobiotic ability in Pv11 cells.

Transgenic expression of late embryogenesis abundant proteins improves tolerance to water stress in Drosophila melanogaster

Four lines of Drosophila melanogaster were created that expressed transgenes encoding selected late embryogenesis abundant (LEA) proteins originally identified in embryos of the anhydrobiote Artemia franciscana The overall aim was to extend our understanding of the protective properties of LEA proteins documented with isolated cells to a desiccation-sensitive organism during exposure to drying and hyperosmotic stress. Embryos of D. melanogaster were dried at 57% relative humidity to promote a loss of 80% tissue water and then rehydrated. Embryos that expressed AfrLEA2 or AfrLEA3m eclosed 2 days earlier than wild-type embryos or embryos expressing green fluorescent protein (Gal4GFP control). For the third instar larval stage, all Afrlea lines and Gal4GFP controls experienced substantial drops in survivorship as desiccation proceeded. When results for all Afrlea lines were combined, Kaplan-Meier survival curves indicated a significant improvement in survivorship in fly lines expressing AfrLEA proteins compared with Gal4GFP controls. The percent water lost at the LT₅₀ (lethal time for 50% mortality) for the AfrLEA lines was 78% versus 52% for Gal4GFP controls. Finally, offspring of fly lines that expressed AfrLEA2, AfrLEA3m or AfrLEA6 exhibited significantly greater success in reaching pupation, compared with wild-type flies, when adults were challenged with hyperosmotic stress (NaCl-fortified medium) and progeny forced to develop under these conditions. In conclusion, the gain of function studies reported here show that LEA proteins can improve tolerance to water stress in a desiccation-sensitive species that normally lacks these proteins, and, simultaneously, underscore the complexity of desiccation tolerance across multiple life stages in multicellular organisms.

Initial response of ovarian tissue transcriptome to vitrification or microwave-assisted dehydration in the domestic cat model

Background

Long term preservation of living ovarian tissues is a critical approach in human reproductive medicine as well as in the conservation of rare animal genotypes. Compared to single cell preservation, optimization of protocols for tissues is highly complex because of the diversity of cells responding differently to non-physiological conditions. Using the prepubertal domestic cat as a model, the objective was to study immediate effects of vitrification or microwave-assisted dehydration on the global transcriptome dynamics in the ovarian cortex. RNA sequencing was performed on ovarian tissues (n = 6 individuals) from different conditions: fresh tissue after dissection (F), vitrified/warmed tissue (V), tissue dehydrated for 5 min (D5) or 10 min (D10) followed by rehydration. Differential gene expression analysis was performed for comparison pairs V vs. F, D10 vs. F, D5 vs. F and D10 vs. D5, and networks were built based on results of functional enrichment and in silico protein-protein interactions.

Results

The impact of the vitrification protocol was already measurable within 20 min after warming and involved upregulation of the expression of seven mitochondrial DNA genes related to mitochondrial respiration. The analysis of D10 vs. F revealed, 30 min after rehydration, major downregulation of gene expression with enrichment of in silico interacting genes in Ras, Rap1, PI3K-Akt and MAPK signaling pathways. However, comparison of D5 vs. F showed negligible effects of the shorter dehydration protocol with two genes enriched in Ras signaling. Comparison of D10 vs. D5 showed downregulation of only seven genes. Vitrification and dehydration protocols mainly changed the expression of different genes and functional terms, but some of the differentially expressed genes formed a major in silico protein-protein interaction cluster enriched for mitochondrial respiration and Ras/MAPK signaling pathways.

Conclusions

Our results showed, for the first time, different effects of vitrification and microwave-assisted dehydration protocols on the global transcriptome of the ovarian cortex (using the domestic cat as a biomedical model). Acquired data and networks built on the basis of differentially expressed genes (1) can help to better understand stress responses to non-physiological stresses and (2) can be used as directions for future preservation protocol optimizations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07236-z.

Mechanisms of Desiccation Tolerance: Themes and Variations in Brine Shrimp, Roundworms, and Tardigrades

Water is critical for the survival of most cells and organisms. Remarkably, a small number of multicellular animals are able to survive nearly complete drying. The phenomenon of anhydrobiosis, or life without water, has been of interest to researchers for over 300 years. In this review we discuss advances in our understanding of protectants and mechanisms of desiccation tolerance that have emerged from research in three anhydrobiotic invertebrates: brine shrimp (Artemia), roundworms (nematodes), and tardigrades (water bears). Discovery of molecular protectants that allow each of these three animals to survive drying diversifies our understanding of desiccation tolerance, and convergent themes suggest mechanisms that may offer a general model for engineering desiccation tolerance in other contexts.

Exogenous ethanol induces a metabolic switch that prolongs the survival of Caenorhabditis elegans dauer larva and enhances its resistance to desiccation

The dauer larva of Caenorhabditis elegans, destined to survive long periods of food scarcity and harsh environment, does not feed and has a very limited exchange of matter with the exterior. It was assumed that the survival time is determined by internal energy stores. Here, we show that ethanol can provide a potentially unlimited energy source for dauers by inducing a controlled metabolic shift that allows it to be metabolized into carbohydrates, amino acids, and lipids. Dauer larvae provided with ethanol survive much longer and have greater desiccation tolerance. On the cellular level, ethanol prevents the deterioration of mitochondria caused by energy depletion. By modeling the metabolism of dauers of wild‐type and mutant strains with and without ethanol, we suggest that the mitochondrial health and survival of an organism provided with an unlimited source of carbon depends on the balance between energy production and toxic product(s) of lipid metabolism.

Survival of Pratylenchus brachyurus under dry soil conditions

Pratylenchus brachyurus, a root-lesion nematode, depends on host plants for growth and survival. Weeds, volunteer plants, and crop root residues may act as reservoirs for the parasite in the field, but little is known about the ability of P. brachyurus to survive in the absence of a host. This study aimed to evaluate P. brachyurus survival and infectivity in artificially and naturally infested soil under dry conditions. Two experiments were conducted, the first using artificially infested soil and the second using naturally infested soil. Soil samples were inoculated with a nematode suspension or infected root fragments. At 0, 30, 60, and 90 days post-inoculation, pots were planted with nematode-susceptible maize and soybean. Fallow pots were also analyzed. Nematode survival, infectivity, and morphology were determined 30 days after planting. P. brachyurus showed enhanced survival in soil in the presence of root fragments. However, inoculation method had no effect on the ability of surviving nematodes to infect host roots. Parasites showed signs of anhydrobiosis (C-shaped or tightly coiled body) after 90 and 120 days under dry conditions.

C. elegans possess a general program to enter cryptobiosis that allows dauer larvae to survive different kinds of abiotic stress

All organisms encounter abiotic stress but only certain organisms are able to cope with extreme conditions and enter into cryptobiosis (hidden life). Previously, we have shown that C. elegans dauer larvae can survive severe desiccation (anhydrobiosis), a specific form of cryptobiosis. Entry into anhydrobiosis is preceded by activation of a set of biochemical pathways by exposure to mild desiccation. This process called preconditioning induces elevation of trehalose, intrinsically disordered proteins, polyamines and some other pathways that allow the preservation of cellular functionality in the absence of water. Here, we demonstrate that another stress factor, high osmolarity, activates similar biochemical pathways. The larvae that acquired resistance to high osmotic pressure can also withstand desiccation. In addition, high osmolarity significantly increases the biosynthesis of glycerol making larva tolerant to freezing. Thus, to survive abiotic stress, C. elegans activates a combination of genetic and biochemical pathways that serve as a general survival program.

A metabolic switch regulates the transition between growth and diapause in C. elegans

BACKGROUND

Metabolic activity alternates between high and low states during different stages of an organism's life cycle. During the transition from growth to quiescence, a major metabolic shift often occurs from oxidative phosphorylation to glycolysis and gluconeogenesis. We use the entry of Caenorhabditis elegans into the dauer larval stage, a developmentally arrested stage formed in response to harsh environmental conditions, as a model to study the global metabolic changes and underlying molecular mechanisms associated with growth to quiescence transition.

RESULTS

Here, we show that the metabolic switch involves the concerted activity of several regulatory pathways. Whereas the steroid hormone receptor DAF-12 controls dauer morphogenesis, the insulin pathway maintains low energy expenditure through DAF-16/FoxO, which also requires AAK-2/AMPKα. DAF-12 and AAK-2 separately promote a shift in the molar ratios between competing enzymes at two key branch points within the central carbon metabolic pathway diverting carbon atoms from the TCA cycle and directing them to gluconeogenesis. When both AAK-2 and DAF-12 are suppressed, the TCA cycle is active and the developmental arrest is bypassed.

CONCLUSIONS

The metabolic status of each developmental stage is defined by stoichiometric ratios within the constellation of metabolic enzymes driving metabolic flux and controls the transition between growth and quiescence.

Nematicidal actions of the marigold exudate α-terthienyl: oxidative stress-inducing compound penetrates nematode hypodermis

α-terthienyl is an allelochemical derived from the roots of marigold (Tagetes spp.), which is used to suppress plant parasitic nematodes. We investigated the nematicidal activity of α-terthienyl against the model organism Caenorhabditis elegans and the root-knot nematode, Meloidogyne incognita. As reported previously, α-terthienyl action was much higher after photoactivation, but was still effective against C. elegans dauer larvae and M. incognita second stage juveniles, even without photoactivation. Expression induction of two major enzymes, glutathione S-transferase (GST) and superoxide dismutase (SOD), was restricted in C. elegans hypodermis following treatment with α-terthienyl. The susceptibility of nematodes to α-terthienyl changed when the expression of GST and SOD was induced or suppressed. From these results, under dark conditions (without photoactivation), α-terthienyl is an oxidative stress-inducing chemical that effectively penetrates the nematode hypodermis and exerts nematicidal activity, suggesting high potential for its use as a practicable nematode control agent in agriculture.

Infective larvae of Anisakis simplex (Nematoda) accumulate trehalose and glycogen in response to starvation and temperature stress

Anisakis simplex L3 larvae infect fish and other seafood species such as squid or octopi; therefore, humans consuming raw or undercooked fish may become accidental hosts for this parasite. These larvae are induced to enter hypometabolism by cold temperatures. It is assumed that sugars (in particular trehalose and glycogen) are instrumental for survival under environmental stress conditions. To elucidate the mechanisms of environmental stress response in A. simplex, we observed the effects of starvation and temperature on trehalose and glycogen content, the activity of enzymes metabolizing those sugars, and the relative expression of genes of trehalose and glycogen metabolic pathways. The L3 of A. simplex synthesize trehalose both in low (0°C) and high temperatures (45°C). The highest content of glycogen was observed at 45°C at 36 h of incubation. On the second day of incubation, tissue content of trehalose depended on the activity of the enzymes: TPS was more active at 45°C, and TPP was more active at 0°C. The changes in TPP activity were consistent with the transcript level changes of the TPP gene, and the trehalose level, while glycogen synthesis correlates with the expression of glycogen synthase gene at 45°C; this suggests that the synthesis of trehalose is more essential. These results show that trehalose plays a key role in providing energy during the thermotolerance and starvation processes through the molecular and biochemical regulation of trehalose and glycogen metabolism.

C. elegans collectively forms dynamical networks

Understanding physical rules underlying collective motions requires perturbation of controllable parameters in self-propelled particles. However, controlling parameters in animals is generally not easy, which makes collective behaviours of animals elusive. Here, we report an experimental system in which a conventional model animal, Caenorhabditis elegans, collectively forms dynamical networks of bundle-shaped aggregates. We investigate the dependence of our experimental system on various extrinsic parameters (material of substrate, ambient humidity and density of worms). Taking advantage of well-established C. elegans genetics, we also control intrinsic parameters (genetically determined motility) by mutations and by forced neural activation via optogenetics. Furthermore, we develop a minimal agent-based model that reproduces the dynamical network formation and its dependence on the parameters, suggesting that the key factors are alignment of worms after collision and smooth turning. Our findings imply that the concepts of active matter physics may help us to understand biological functions of animal groups.

Understanding collective motions in a group of interacting animal is a challenge owing to the lack of control over, for example, real fish schools. Here, the authors study the aggregation of C. elegans at controllable conditions and reproduce the experimental observations using a minimal model.

Immunometabolic Crosstalk: An Ancestral Principle of Trained Immunity?

Memory was traditionally considered an exclusive hallmark of adaptive immunity. This dogma was challenged by recent reports that myeloid cells can retain 'memory' of earlier challenges, enabling them to respond strongly to a secondary stimulus. This process, designated 'trained immunity', is initiated by modulation of precursors of myeloid cells in the bone marrow. The ancestral innate immune system of lower organisms (e.g., Caenorhabditis elegans) can build long-lasting memory that modifies responses to secondary pathogen encounters. We posit that changes in cellular metabolism may be a common denominator of innate immune memory from lower animals to mammals. We discuss evidence from C. elegans and murine/human systems supporting the concept of an ancestral principle regulating innate immune memory by controlling cellular metabolism.

Automated classification of synaptic vesicles in electron tomograms of C. elegans using machine learning

Synaptic vesicles (SVs) are a key component of neuronal signaling and fulfil different roles depending on their composition. In electron micrograms of neurites, two types of vesicles can be distinguished by morphological criteria, the classical “clear core” vesicles (CCV) and the typically larger “dense core” vesicles (DCV), with differences in electron density due to their diverse cargos. Compared to CCVs, the precise function of DCVs is less defined. DCVs are known to store neuropeptides, which function as neuronal messengers and modulators [1]. In C. elegans, they play a role in locomotion, dauer formation, egg-laying, and mechano- and chemosensation [2]. Another type of DCVs, also referred to as granulated vesicles, are known to transport Bassoon, Piccolo and further constituents of the presynaptic density in the center of the active zone (AZ), and therefore are important for synaptogenesis [3].

To better understand the role of different types of SVs, we present here a new automated approach to classify vesicles. We combine machine learning with an extension of our previously developed vesicle segmentation workflow, the ImageJ macro 3D ART VeSElecT. With that we reliably distinguish CCVs and DCVs in electron tomograms of C. elegans NMJs using image-based features. Analysis of the underlying ground truth data shows an increased fraction of DCVs as well as a higher mean distance between DCVs and AZs in dauer larvae compared to young adult hermaphrodites. Our machine learning based tools are adaptable and can be applied to study properties of different synaptic vesicle pools in electron tomograms of diverse model organisms.

Gluconeogenesis: An ancient biochemical pathway with a new twist

Synthesis of sugars from simple carbon sources is critical for survival of animals under limited nutrient availability. Thus, sugar-synthesizing enzymes should be present across the entire metazoan spectrum. Here, we explore the evolution of glucose and trehalose synthesis using a phylogenetic analysis of enzymes specific for the two pathways. Our analysis reveals that the production of trehalose is the more ancestral biochemical process, found in single cell organisms and primitive metazoans, but also in insects. The gluconeogenic-specific enzyme glucose-6-phosphatase (G6Pase) first appears in Cnidaria, but is also present in Echinodermata, Mollusca and Vertebrata. Intriguingly, some species of nematodes and arthropods possess the genes for both pathways. Moreover, expression data from Drosophila suggests that G6Pase and, hence, gluconeogenesis, initially had a neuronal function. We speculate that in insects-and possibly in some vertebrates-gluconeogenesis may be used as a means of neuronal signaling.

The Future of Cell Biology: Emerging Model Organisms

Most current research in cell biology uses just a handful of model systems including yeast, Arabidopsis, Drosophila, Caenorhabditis elegans, zebrafish, mouse, and cultured mammalian cells. And for good reason - for many biological questions, the best system for the question is likely to be found among these models. However, in some cases, and particularly as the questions that engage scientists broaden, the best system for a question may be a little-studied organism. Modern research tools are facilitating a renaissance for unusual and interesting organisms as emerging model systems. As a result, we predict that an ever-expanding breadth of model systems may be a hallmark of future cell biology.

Molecular characterization of Tps1 and Treh genes in Drosophila and their role in body water homeostasis

In insects, trehalose serves as the main sugar component of haemolymph. Trehalose is also recognized as a mediator of desiccation survival due to its proposed ability to stabilize membranes and proteins. Although the physiological role of trehalose in insects has been documented for decades, genetic evidence to support the importance of trehalose metabolism remains incomplete. We here show on the basis of genetic and biochemical evidence that the trehalose synthesis enzyme Tps1 is solely responsible for the de novo synthesis of trehalose in Drosophila. Conversely, a lack of the gene for the trehalose hydrolyzing enzyme Treh causes an accumulation of trehalose that is lethal during the pupal period, as is observed with Tps1 mutants. Lack of either Tps1 or Treh results in a significant reduction in circulating glucose, suggesting that the maintenance of glucose levels requires a continuous turnover of trehalose. Furthermore, changes in trehalose levels are positively correlated with the haemolymph water volume. In addition, both Tps1 and Treh mutant larvae exhibit a high lethality after desiccation stress. These results demonstrate that the regulation of trehalose metabolism is essential for normal development, body water homeostasis, and desiccation tolerance in Drosophila.

The glyoxylate shunt is essential for desiccation tolerance in C. elegans and budding yeast

Many organisms, including species from all kingdoms of life, can survive desiccation by entering a state with no detectable metabolism. To survive, C. elegans dauer larvae and stationary phase S. cerevisiae require elevated amounts of the disaccharide trehalose. We found that dauer larvae and stationary phase yeast switched into a gluconeogenic mode in which metabolism was reoriented toward production of sugars from non-carbohydrate sources. This mode depended on full activity of the glyoxylate shunt (GS), which enables synthesis of trehalose from acetate. The GS was especially critical during preparation of worms for harsh desiccation (preconditioning) and during the entry of yeast into stationary phase. Loss of the GS dramatically decreased desiccation tolerance in both organisms. Our results reveal a novel physiological role for the GS and elucidate a conserved metabolic rewiring that confers desiccation tolerance on organisms as diverse as worm and yeast.

Integration of carbohydrate metabolism and redox state controls dauer larva formation in Caenorhabditis elegans

Under adverse conditions, Caenorhabditis elegans enters a diapause stage called the dauer larva. External cues signal the nuclear hormone receptor DAF-12, the activity of which is regulated by its ligands: dafachronic acids (DAs). DAs are synthesized from cholesterol, with the last synthesis step requiring NADPH, and their absence stimulates dauer formation. Here we show that NADPH levels determine dauer formation in a regulatory mechanism involving key carbohydrate and redox metabolic enzymes. Elevated trehalose biosynthesis diverts glucose-6-phosphate from the pentose phosphate pathway, which is the major source of cellular NADPH. This enhances dauer formation due to the decrease in the DA level. Moreover, DAF-12, in cooperation with DAF-16/FoxO, induces negative feedback of DA synthesis via activation of the trehalose-producing enzymes TPS-1/2 and inhibition of the NADPH-producing enzyme IDH-1. Thus, the dauer developmental decision is controlled by integration of the metabolic flux of carbohydrates and cellular redox potential.

Introduction to desiccation biology: from old borders to new frontiers

A special issue reviews the recent progress made in our understanding of desiccation tolerance across various plant and animal kingdoms. It has been known for a long time that seeds can survive near absolute protoplasmic dehydration through air drying and complete germination upon rehydration because of their desiccation tolerance. This property is present both in prokaryotes and eukaryotes across all life kingdoms. These dry organisms suspend their metabolism when dry, are extremely tolerant to acute environmental stresses and are relatively stable during long periods of desiccation. Studies aiming at understanding the mechanisms of survival in the dry state have emerged during the past 40 years, moving from in vitro to genomic models and comparative genomics, and from a view that tolerance is an all-or-nothing phenomenon to a quantitative trait. With the prospect of global climate change, understanding the mechanisms of desiccation tolerance appears to be a promising avenue as a prelude to engineering crops for improved drought tolerance. Understanding desiccation is also useful for seed banks that rely on dehydration tolerance to preserve plant genetic resources in the form of these propagules. Articles in this special issue explore the recent progress in our understanding of desiccation tolerance, including the evolutionary mechanisms that have been adopted across various plant (algae, lichens, seeds, resurrection plants) and animal model systems (Caenorhabditis elegans, brine shrimp). We propose that the term desiccation biology defines the discipline dedicated to understand the desiccation tolerance in living organisms as well as the limits and time constraints thereof.