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Sommer, R. J.

Publications and source records attributed to Sommer, R. J..

34 records · Page 2Linked to original sources

Glutamate, GABA, and dense-core vesicle secretion regulate predatory feeding in the nematode Pristionchus pacificus

Nematodes are one of the most diverse groups of organisms, found in various environments, and exhibit various feeding behaviours. Pristionchus pacificus displays two types of feeding behaviours: predatory and bacterial feeding. Previously, we showed that the neurotransmitter serotonin plays important roles in regulating predatory feeding in P. pacificus. However, the role of other neurotransmitters in predatory feeding remains unclear. Using the CRISPR/Cas9 system, we generated mutants of the dense-core vesicle (DCV)-based neuropeptide secretion system and genes related to seven neurotransmitters. Predatory assays revealed that the vesicular glutamate transporter Ppa-EAT-4, glutamic acid decarboxylase Ppa-UNC-25 which is involved in GABA synthesis, and the calcium-dependent activator protein for DCV secretion Ppa-UNC-31, play roles in predatory feeding behaviour. We assessed the pharyngeal movement necessary for predation as well as locomotion rate in these mutants. While the Ppa-eat-4 and Ppa-unc-31 mutants decreased predation movement, the Ppa-unc-25 mutant showed a reduction only in bacterial events compared to wild type animals. Additionally, Ppa-unc-25 and Ppa-unc-31 decreased in motor movement, potentially reducing predation efficiency. Together, these results suggest that glutamate, GABA and DCV secretion modulate feeding behaviours in P. pacificus. Our mutant collection of neurotransmitter-related genes will be useful for future analysis of neurobiology and behavioural evolution.

animal behavior and cognition↗

Comparative connectomics of two distantly related nematode species reveals patterns of nervous system evolution

Understanding the evolution of the bilaterian brain requires a detailed exploration of the precise nature of cellular and subcellular differences between related brains. To define the anatomical substrates of evolutionary change in the nervous system, we undertook an electron micrographic reconstruction of the brain of the predatory nematode Pristionchus pacificus. A comparison with the brain of Caenorhabditis elegans, which diverged at least 100 million years ago, reveals a conserved nematode core connectome and a wide range of specific substrates of evolutionary change. These changes include differences in neuronal cell death, neuronal cell position, axo-dendritic projection patterns and many changes in synaptic connectivity of homologous neurons that display no obvious changes in overall neurite morphology and projection patterns. Arguing against specific hot spots of evolutionary change, connectivity differences are distributed throughout the nervous system and extend to glia as well. We observed examples of apparent circuit drift, where changes in morphology and connectivity of a neuron do not appear to alter its behavioral output. In conclusion, our comprehensive comparison of distantly related nematode species provides novel vistas on patterns of conservation as well as the substrates of evolutionary change in the brain that span multiple organizational levels.

neuroscience↗

Feeding-structure morphogenesis in rhabditid and diplogastrid nematodes is not controlled by a conserved genetic module

Disentangling the evolution of the molecular processes and genetic networks that facilitate the emergence of morphological novelties is one of the main objectives in evolutionary developmental biology. Here, we investigated the evolutionary history of a gene regulatory network controlling the development of novel tooth-like feeding-structures in diplogastrid nematodes. Focusing on NHR-1 and NHR-40, the two transcription factors that regulate the morphogenesis of these feeding structures in Pristionchus pacificus, we sought to determine whether they have a similar function in out-group nematode Caenorhabditis elegans, which has typical "rhabditid" flaps instead of teeth. Contrary to our initial expectations, we found that they do not have a similar function. While both receptors are co-expressed in the tissues that produce the feeding structures in the two nematodes, genetic inactivation of either receptor had no impact on feeding-structure morphogenesis in C. elegans. Transcriptomic experiments revealed that NHR-1 and NHR-40 have highly species-specific regulatory targets. These results suggest two possible evolutionary scenarios: either the genetic module responsible for feeding-structure morphogenesis in Diplogastridae already existed in the last common ancestor of C. elegans and P. pacificus, and subsequently disintegrated in the former as NHR-1 and NHR-40 acquired new targets, or it evolved in conjunction with teeth in Diplogastridae. These findings indicate that feeding-structure morphogenesis is regulated by different genetic programs in P. pacificus and C. elegans, hinting at developmental systems drift during the flap-to-tooth transformation. Further research in other "rhabditid" species is needed to fully reconstruct the developmental genetic changes which facilitated the evolution of novel feeding structures in Diplogastridae. Research HighlightsCombining CRISPR-based mutagenesis, geometric morphometrics, and transcriptomics, we found that the genetic module governing the morphogenesis of novel feeding structures in diplogastrid nematodes is not conserved in the "rhabditid" C. elegans.

zoology↗

Conserved switch genes regulate a novel cannibalistic morph after whole genome duplication

Developmental plasticity facilitates morphological and behavioural novelty, but associated regulatory mechanisms remain elusive. Nematodes have emerged as a powerful model to study developmental plasticity and its evolution. Here, we show the predatory nematode Allodiplogaster sudhausi evolved an additional third mouth morph, concomitant with whole genome duplication (WGD) and a strong increase in body size. The three mouth morphs are induced by different diets; bacteria, fungi and nematodes. CRISPR experiments indicate that regulation of the third morph involves co-option of a conserved developmental switch gene, which through WGD resulted in two mouth-form regulators. Gene dosage studies revealed a diverged role of these developmental switches, with functional redundancy and quantitative effects in the two mouth-form decisions, respectively. The third morph is cannibalistic and kills kin, whereas the other two morphs do not. Thus, the recent evolution of a new morph relies on pre-existing regulatory mechanisms and adds behavioural and social complexity. One-Sentence SummaryExperimental genetics in a nematode reveals a key role for developmental plasticity in the evolution of nutritional diversity

evolutionary biology↗

Starvation resistance in the nematode Pristionchus pacificus requires a conserved supplementary nuclear receptor

Nuclear hormone receptors (NHRs) are a deeply-conserved superfamily of metazoan transcription factors, which fine-tune the expression of their regulatory target genes in response to a plethora of sensory inputs. In nematodes, NHRs underwent an explosive expansion and many species have hundreds of nhr genes, most of which remain functionally uncharacterized. However, recent studies elucidated that two sister receptors, Ppa-NHR-1 and Ppa-NHR-40, are crucial regulators of feeding-structure morphogenesis in the diplogastrid model nematode Pristionchus pacificus. In this study, we functionally characterize Ppa-NHR-10, the sister paralog of Ppa-NHR-1 and Ppa-NHR-40, aiming to reveal whether it too regulates aspects of feeding-structure development. We used CRISPR/CAS9-mediated mutagenesis to create knock-out mutations of this receptor and applied a combination of geometric morphometrics and unsupervised clustering to characterize potential mutant phenotypes. However, we found that Ppa-NHR-10 does not affect feeding-structures morphogenesis. Instead, multiple RNA-seq experiments revealed that many of the target genes of this receptor are involved in lipid catabolic processes. We hypothesized that their mis-regulation could affect the survival of mutant worms during starvation, where lipid catabolism is often essential. Indeed, using novel survival assays, we found that mutant worms show drastically decreased starvation resistance, both as young adults and as dauer larvae. We also characterized genome-wide changes to the transcriptional landscape in P. pacificus when exposed to 24hrs of acute starvation, and found that Ppa-NHR-10 partially regulates some of these responses. Taken together, we were able to demonstrate that Ppa-NHR-10 is broadly required for starvation resistance and regulates different biological processes than its closest paralogs Ppa-NHR-1 and Ppa-NHR-40.

evolutionary biology↗

Microbiota Succession Influences Nematode Physiology in a Beetle Microcosm Ecosystem

Research during the last decade has generated a substantial understanding of the role of microbiota in animal development, metabolism and immunity, including humans. However, many organismal interactions involve microbial successions, such as in animal decay but also human health and disease. The complexity of most microbiota makes it difficult to obtain insight into such microbial successions, resulting in a limited understanding of microbiota for ecosystem functioning. One potential, relatively simple, model system for the analysis of microbial successions is insect decay in soil ecosystems, a highly abundant process that has however, not been investigated in detail. For example, microbiota and nematodes are the two most abundant groups of organisms in soil systems, but their interplay and successions during the decomposition of insects are currently unknown. Here, we use a semi-artificial decaying rose chafer grub microcosm to study the reciprocal interactions between microbiota and nematodes through metagenomics and transcriptomic studies. We show that the controlled addition of nematodes to beetle grub carcasses will strongly influence the microbial succession and result in a massive increase in microbial diversity. Nematodes select microbes of high nutritional value for consumption, thereby influencing the composition of microbiota on the decaying insect. Reciprocally, the activity of nematode metabolic pathways strongly responds to their microbial diet and affects fat metabolism and the formation of dauer larvae, the nematode dispersal stage. These results indicate the importance of microbial successions and their reciprocal interactions with nematodes for insect decay in soil ecosystems.

microbiology↗

Histone 4 lysine 5/12 acetylation provides a plasticity code with epigenetic memory of environmental exposure

Development can be altered to match phenotypes with the environment, and the genetic mechanisms that direct such alternative phenotypes are beginning to be elucidated1,2. Yet, the rules that govern environmental sensitivity vs. invariant development (canalization), and potential epigenetic memory, remain unknown. Here, we show that plasticity of nematode mouth forms is determined by histone 4 lysine 5 and 12 acetylation (H4K5/12ac). Acetylation in early larval stages provides a permissive chromatin state at specific switch genes, which is susceptible to induction during the critical window of environmental sensitivity. As development proceeds deacetylation shuts off switch gene expression to end the critical period. We show that inhibiting deacetylase enzymes leads to long-term epigenetic memory, demonstrating that histone modifications in juveniles can carry environmental information to affect organismal traits in adults. This epigenetic regulation of plasticity appears to be derived from an ancient mechanism of licensing developmental speed that is conserved between flies and nematodes. Thus, H4K5/12ac provides a histone plasticity code with epigenetic potential that can be stored and erased by acetylation and deacetylation, respectively. HighlightsO_LIReciprocal transplant experiments reveal a critical time window of mouth-form plasticity. C_LIO_LIEntry and exit of the critical window is determined by H4K5/12ac at the switch gene eud-1. C_LIO_LIH4K12ac maintains transcriptional competence by supporting elongation. C_LIO_LIInhibition of deacetylation freezes an initial developmental trajectory, resulting in long-term epigenetic memory. C_LIO_LIH4K5/12 acetylation control of plasticity was co-opted from an ancestral role in controlling developmental speed. C_LI

developmental biology↗

Experimental and theoretical support for costs of plasticity and phenotype in a nematode cannibalistic trait

Developmental plasticity is the ability of a genotype to express multiple phenotypes under different environmental conditions and has been shown to facilitate the evolution of novel traits. However, while the associated cost of plasticity, i.e., the loss in fitness due to the plastic response to environment, and the cost of phenotype, i.e., the loss of fitness due to expressing a fixed phenotype across environments, have been theoretically predicted, empirically such costs remain poorly documented and little understood. Here, we use a plasticity model system, hermaphroditic nematode Pristionchus pacificus, to experimentally measure these costs in wild isolates under controlled laboratory conditions. P. pacificus can develop either a bacterial feeding or predatory mouth morph in response to different external stimuli, with natural variation of mouth-morph ratios between strains. We first demonstrated the cost of phenotype by analyzing fecundity and developmental speed in relation to mouth morphs across the P. pacificus phylogenetic tree. Then, we exposed P. pacificus strains to two distinct microbial diets that induce strain-specific mouth-form ratios. Our results indicate that the plastic strain does shoulder a cost of plasticity, i.e., the diet-induced predatory mouth morph is associated with reduced fecundity and slower developmental speed. In contrast, the non-plastic strain suffers from the cost of phenotype since its phenotype does not change to match the unfavorable bacterial diet, but shows increased fitness and higher developmental speed on the favorable diet. Furthermore, using a stage-structured population model based on empirically-derived life history parameters, we show how population structure can alleviate the cost of plasticity in P. pacificus. The results of the model illustrate the extent to which the costs associated with plasticity and its effect of competition depend on ecological factors. This study provides comprehensive support for the costs of plasticity and phenotype based on empirical and modeling approaches. Impact SummaryA genotype able to express a range of phenotypes in response to environmental conditions, that is to demonstrate developmental plasticity, would be a Darwinian demon, able to infinitely adapt and outcompete those genotypes that require genetic change to express a phenotype fit to an environment. It has been suggested that the absence of such demons in nature is due to the cost of plasticity, i.e., developmental plasticity results in a reduction of biological fitness compared to a genotype that facultatively expresses a phenotype matching the environment. While conceptually simple, measuring the cost of plasticity in nature has proven a major challenge. We use the nematode P. pacificus to measure the cost of plasticity. During its development, P. pacificus can assume one of two possible mouth forms: predatory or non-predatory. The likelihood developing any of these two mouth forms is determined by a gene regulatory network, which itself is affected by a wide range on environmental conditions, including diet. We used two strains of P. pacificus and grew them on two different bacterial diets. The plastic strain was capable of switching from non-predatory to predatory mouth form depending on the diet, while the non-plastic strain could only express the predatory mouth form on either of the diets. By measuring the number eggs laid in both strain on each diet, we show that the plastic response is associated with a reduction in fecundity, thus providing a clear example of the cost of plasticity. We then use a stage-structured model to simulate the population dynamics of the plastic and the non-plastic strains. Our simulation show that the cost of plasticity is highly context dependent and its ecological ramifications can be greatly influenced by biotic and abiotic factors.

evolutionary biology↗

Influence of environmental temperature on mouth-form plasticity in Pristionchus pacificus acts through daf-11-dependent cGMP signaling

Mouth-form plasticity in the nematode Pristionchus pacificus has become a powerful system to identify the genetic and molecular mechanisms associated with phenotypic (developmental) plasticity. In particular, the identification of developmental switch genes that can sense environmental stimuli and reprogram developmental processes has confirmed long-standing evolutionary theory. Together with the associated gene regulatory networks, these developmental switch genes have been important to show that plasticity is consistent with the Modern Synthesis of evolution. However, how these genes are involved in the direct sensing of the environment, or if the switch genes act downstream of another, primary environmental sensing mechanism, remains currently unknown. Here, we study the influence of environmental temperature on mouth-form plasticity. Using forward and reverse genetic technology including CRISPR/Cas9, we show that mutations in the guanylyl cyclase Ppa-daf-11, the Ppa-daf-25/AnkMy2 and the cyclic nucleotide-gated channel Ppa-tax-2 eliminate the response to elevated temperatures. Together, our study indicates that DAF-11, DAF-25 and TAX-2 have been co-opted for environmental sensing during mouth-form plasticity regulation in P. pacificus. This work suggests that developmental switch genes integrate environmental signals including perception by cGMP signaling.

genetics↗

Tissue-specific safety mechanism results in opposite protein aggregation patterns during aging

During aging, proteostasis capacity declines and aggregation-prone proteins become instable, accumulating in protein aggregates both inside and outside cells. Both in disease and during aging, proteins selectively aggregate in certain tissues and not others. Yet, tissue-specific regulation of protein aggregation remains poorly understood. Surprisingly, we found that the inhibition of three core protein quality control systems, i.e. chaperones, proteasome and macroautophagy, leads to lower levels of age-dependent protein aggregation in C. elegans pharyngeal muscles, but higher levels in body-wall muscles. We describe a novel safety mechanism called SAPA that selectively targets newly synthesized aggregation-prone proteins to suppress aggregation and proteotoxicity. vha-12 and scav-3 mutants reveal that SAPA relies on macroautophagy-independent lysosomal degradation. Furthermore, SAPA involves several previously uncharacterized components of the intracellular pathogen response. We propose that SAPA represents an anti-aggregation machinery targeting aggregation-prone proteins for lysosomal degradation.

cell biology↗

Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus

BackgroundNematode model organisms such as Caenorhabditis elegans and Pristionchus pacificus are powerful systems for studying the evolution of gene function at a mechanistic level. However, the identification of P. pacificus orthologs of candidate genes known from C. elegans is complicated by the discrepancy in the quality of gene annotations, a common problem in nematode and invertebrate genomics. ResultsHere, we combine comparative genomic screens for suspicious gene models with community-based curation to further improve the quality of gene annotations in P. pacificus. We extend previous curations of one-to-one orthologs to larger gene families and also orphan genes. Cross-species comparisons of protein lengths and screens for atypical domain combinations and species-specific orphan genes resulted in 4,221 candidate genes that were subject to community-based curation. Corrections for 2,851 gene models were implemented in a new version of the P. pacificus gene annotations. The new set of gene annotations contains 28,896 genes and has a single copy ortholog completeness level of 97.6%. ConclusionsOur work demonstrates the effectiveness of comparative genomic screens to identify suspicious gene models and the scalability of community-based approaches to improve the quality of thousands of gene models. Similar community-based approaches can help to improve the quality of gene annotations in other invertebrate species, including parasitic nematodes.

genomics↗

Museum phylogenomics of extinct Oryctes beetles from the Mascarene Islands

The evolution of island systems is characterized by processes that result in extreme morphological diversity, high endemism and high extinction rates. These dynamics can make phylogenetic reconstruction difficult, i.e. the extinct flightless Dodo from Mauritius was assigned to the family of doves only through DNA analysis of subfossils. Many insect species on islands have gone extinct through habitat loss, and face similar challenges to decipher their evolutionary history, however historical specimens have not yet been harnessed for phylogenomic reconstructions. Here, we employed historical museum specimens from the Mascarene Islands to generate the first whole-genome based phylogeny of three presumably extinct species of the rhinoceros beetle genus Oryctes. We compared their genomes with those of an extant Oryctes species from the island of Reunion, as well as a flightless Reunion-based species previously placed into the supposedly unrelated genus Marronus. We found that Marronus borbonicus belongs instead to the genus Oryctes and that the two Reunion-based species (O. borbonicus and M. borbonicus) are not sister taxa, suggesting two independent colonizations. The divergence time between them (<3Myr) overlaps with the volcanic formation of Reunion, likely indicating that M. borbonicus became flightless in situ. Our study showcases the power of genomes from insect museum specimens to address evolutionary questions in light of increasing extinction rates.

evolutionary biology↗

Conserved nuclear receptors controlling a novel trait target fast-evolving genes expressed in a single cell

Environment shapes development through a phenomenon called developmental plasticity. Deciphering its genetic basis has implications for understanding evolution and adaptation to novel environments, yet molecular studies are scarce. Here, we expanded the gene regulatory network controlling predatory vs. non-predatory morphology in the nematode Pristionchus pacificus. First, we isolated a mutant in the nuclear hormone receptor nhr-1 with a previously unseen phenotypic effect. It disrupts mouth-form determination and results in animals combining features of both wild-type morphs. Further, we identified common targets of NHR-1 and the previously identified nuclear hormone receptor NHR-40 through transcriptomics. Unlike their highly conserved regulators, the target genes have no orthologs in Caenorhabditis elegans and likely result from lineage-specific expansions. An array of transcriptional reporters revealed co-expression of all tested targets in the same pharyngeal gland cell. The morphological remodeling of this cell accompanied the evolution of teeth and predation, linking rapid gene turnover with morphological innovations.

developmental biology↗

Bacterial derived vitamin B12 enhances predatory behaviors in nematodes

The microbiome is known to affect host development, metabolism and immunity, however, its impact on behaviors is only beginning to be understood. Here, we investigate how bacteria modulate complex behaviors in the nematode model organism Pristionchus pacificus. P. pacificus is a predator feeding on the larvae of other nematodes including Caenorhabditis elegans. Growing P. pacificus on different bacteria and testing their ability to kill C. elegans reveals drastic differences in killing efficiencies with a Novosphingobium species showing the strongest enhancement. Strikingly, increased killing was not accompanied by an increase in feeding, a phenomenon known as surplus-killing whereby predators kill more prey than necessary for sustenance. RNA-seq revealed widespread metabolic rewiring upon exposure to Novosphingobium, which facilitated the screening for bacterial mutants leading to an altered transcriptional response. This identified bacterial derived vitamin B12 as a major micronutrient enhancing predatory behaviors. Vitamin B12 is an essential cofactor for detoxification and metabolite biosynthesis and has previously been shown to accelerate development in C. elegans. In P. pacificus vitamin B12 supplementation amplified, whereas mutants in vitamin B12-dependent pathways reduced surplus-killing. This demonstrates that bacterial vitamin B12 affects complex behaviors and thus establishes a connection between microbial diet and the nervous system.

microbiology↗

Evolution of neuronal anatomy and circuitry in two highly divergent nematode species

The nematodes C. elegans and P. pacificus populate diverse habitats and display distinct patterns of behavior. To understand how their nervous systems have diverged, we undertook a detailed examination of the neuroanatomy of the chemosensory system of P. pacificus. Using independent features such as cell body position, axon projections and lipophilic dye uptake, we have assigned homologies between the amphid neurons, their first-layer interneurons, and several internal receptor neurons of P. pacificus and C. elegans. We found that neuronal number and soma position are highly conserved. However, the morphological elaborations of several amphid cilia are different between them, most notably in the absence of winged cilia morphology in P. pacificus. We established a synaptic wiring diagram of amphid sensory neurons and amphid interneurons in P. pacificus and found striking patterns of conservation and divergence in connectivity relative to C. elegans, but very little changes in relative neighborhood of neuronal processes.\n\nImpact StatementThe substrate for evolutionary divergence does not lie in changes in neuronal cell number or targeting, but rather in sensory perception and synaptic partner choice within invariant, prepatterned neuronal processes.

neuroscience↗

Adult-specific pheromones differently influence malthusian escape strategies of younger generations

Many animal and plant species respond to high or low population densities by phenotypic plasticity. To investigate if specific age classes and/or cross-generational signaling affect(s) phenotypic plasticity, we developed a dye-based method to differentiate co-occurring nematode age classes. We applied this method to Pristionchus pacificus, which develops a predatory mouth form to exploit alternative resources and kill competitors in response to high population densities. Remarkably, only adult, but not juvenile, crowding induces the predatory morph in other juveniles. Profiling of secreted metabolites throughout development with HPLC-MS combined with genetic mutants traced this result to the production of adult-specific pheromones. Specifically, the P. pacificus-specific di-ascaroside#1 that induces the predatory morph exhibits a binary induction in adults, even though mouth form is no longer plastic in adults. This cross-generational signaling between adults and juveniles may serve as an indication of rapidly increasing population size. Thus, phenotypic plasticity depends on critical age classes.

ecology↗