Search bioRxiv⌕ Search

Biology subjects

Witte, H.

Publications and source records attributed to Witte, H..

At least 19 recordsLinked to original sources

Terminal selector and subtype selector function across 200 million years of nematode evolution

The evolution of brains is subject to investigation in many different animal groups, each offering unique advantages to advance our understanding of the cellular, molecular and regulatory substrates of evolutionary change. Here, we use two nematode species, C. elegans and P. pacificus, separated by more than 200 million years of evolution to explore how neuronal cell types and the regulatory programs instructing the identity of these cell types have evolved over time. Using gene expression pattern analysis, we compare the differentiation programs of over half of all nematode neuron classes. To explore how the gene regulatory architecture of neuronal differentiation programs evolves, we apply our deep understanding of neuronal differentiation programs, controlled by terminal selectors and subtype selectors in C. elegans. Through mutant analysis of orthologous P. pacificus regulatory factors, we elucidate patterns of conservation and novelties over such substantial evolutionary distance. We discovered striking similarities in terminal selector expression and activities throughout the nervous system but also observed that terminal selectors can acquire novel sites of expression and distinct regulatory capabilities, manifested by changes in effector gene expression and, hence, neuronal phenotypes. Our mutant analysis argues for a buffering of terminal selector function and for an evolutionary lability of differences in closely related neuronal subtypes. Taken together, our analysis reveals molecular substrates of evolutionary change in nervous systems.

neuroscience↗

A multifunctional polyketide synthase in nematodes produces divergent families of signaling molecules that control different developmental arrests

To improve their chances of reproductive success, nematodes not only must arrest their development in response to adverse growth conditions but also must quickly recover if conditions improve. A polyketide synthase (PKS)-nonribosomal peptide synthetase (NRPS) hybrid assembly line that is expressed in the canal-associated neurons (CANs) of Caenorhabditis elegans promotes recovery from starvation-induced larval arrest. Here, we show that in the predatory nematode Pristionchus pacificus this assembly line produces a suite of secondary metabolites, including a family of hybrid polyketide-nonribosomal peptides known as the nemamides, the related nemaketides, and a family of ascarylose-modified polyketides named ascarenes. Depending on the starter unit that is loaded onto the PKS, the assembly line can produce dramatically different downstream products. Whereas the nemamides promote recovery from starvation-induced larval arrest, the ascarenes inhibit development of the dauer larval stage and promote recovery. This dichotomy suggests that the PKS-NRPS megasynthetase serves as a signaling hub in the CANs, controlling multiple developmental events. The PKS-NRPS assembly line is highly conserved across many nematode species, and identification of these chemical signals will help to elucidate the signaling pathways that control development in the worm and lead to novel anthelmintics.

biochemistry↗

Plasticity in nonsense-mediated decay and translation initiation regulate polyphenism

Developmental plasticity is increasingly recognised as facilitator of evolutionary novelty. However, how plasticity itself evolves and how variation in plastic trait expression is structured in populations remain unknown1,2. The predatory nematode Pristionchus pacificus exhibits mouth-form plasticity with underlying molecular mechanisms being increasingly identified3. We investigate the temporal scale of natural variation of mouth-form plasticity. An 11-year survey characterised Adoretus beetle-derived isolates from Colorado, La Reunion Island and revealed a gradual shift in mouth-form preference. Quantitative trait locus mapping of mouth-form preferences identified a single peak harbouring the developmental switch gene eud-1. Through CRISPR-engineering and biochemical assays, we show that plasticity in nonsense-mediated decay coupled with alternative start codon selection resulting in different N-terminal proteoforms of EUD-1 are associated with natural variation of mouth-form preference. This work provides molecular explanations for variation in plastic trait expression and links nonsense variants in the major developmental switch locus to ecological and evolutionary processes.

evolutionary biology↗

A unique Cysteine-type protein domain regulates cuticular extracellular matrix assembly in nematodes

Apical extracellular matrices (aECMs) act as barriers against pathogens and shape tissue organization throughout animals. In nematodes, the cuticle is the aECM performing this function, representing a defining feature of this largest animal phylum. Morphological and molecular evidence supports that worm cuticles extend from the head into the mouth, the latter contributing to the large diversity of nematode feeding structures. However, the biochemical understanding of the compositions of nematode cuticles and head structures is largely limited to collagens. Here, we characterized a recently identified mucin-type protein DPY-6 as a constituent of the cuticle and mouth in the model organisms Pristionchus pacificus and Caenorhabditis elegans. Utilizing bioinformatic tools, we discover a unique cysteine-consisting motif at the N-terminus of DPY-6 with the amino acid sequence CxCxCxC. We demonstrate through in vitro biophysical experiments that this cysteine motif facilitates the intermolecular dimerization of DPY-6 proteins. In vivo studies in both species reveal that this motif is involved in the proper localization of the protein in the cuticle, but functions synergistically with other protein domains in a species-specific manner. Given that dpy-6 transcriptomic expression precedes other cuticle components, we speculate that DPY-6 acts as scaffold molecule for nematode cuticular aECM formation.

biochemistry↗

An Evolutionarily Conserved N-terminal Domain of RRF-3 Governs GTSF-1 Binding in Nematodes

GTSF1 is an essential activating cofactor for PIWI proteins in many metazoans. In the nematode Caenorhabditis elegans, however, GTSF-1 does not bind PIWI, but associates with the RNA-dependent RNA polymerase RRF-3, supporting endo-siRNA (26G-RNA) biogenesis. Here, we demonstrate that this rewiring is deeply conserved across nematodes. For C. briggsae and Pristionchus pacificus we show that GTSF-1 interacts with RRF-3 and is essential for 26G-RNA production and fertility. We map this interaction to an N-terminal domain of RRF-3, termed the GTSF-1 interacting domain (GID), and show that the GTSF-1 zinc finger region alone is sufficient for binding. Mutagenesis identifies critical residues mediating this interaction and reveals that GTSF-1 stability depends on RRF-3. Other RdRPs possess GID-like domains, which we propose to bind GTSF-1-related proteins. Phylogenomic and structural analyses support GTSF-1-RRF-3 interactions across all major nematode lineages and map the shift in GTSF-1 activity to the last common nematode ancestor. We propose that binding of GTSF-1 induces conformational changes in RRF-3 that facilitate ERI complex assembly and activate RdRP function, paralleling its role as a PIWI activator.

molecular biology↗

Poly(UG)-tailed RNAs are involved in the control of thousands of genes predominantly in the germline in Pristionchus pacificus

In the nematode Caenorhabditis elegans, the terminal transferase RDE-3 adds a poly(UG)-tail to the free 3 end of RNA molecules generated by the action of primary siRNAs or piRNAs. The tailed RNA serves as a template for RNA-dependent RNA polymerases (RdRp) to generate secondary siRNAs, thereby reinforcing the RNAi effect. In this iterative process, progressively shorter tailed RNAs are formed. In C. elegans, injection of poly(UG)-tailed single-stranded RNA (ssRNA) leads to RNAi-mediated gene silencing, thereby bypassing the need for the processing of double-stranded RNA into siRNAs. We wondered if poly(UG)-tailed ssRNAs could also be used for experimental gene knockdown in nematodes where long dsRNA-mediated RNAi does not work reliably, such as the satellite model organism Pristionchus pacificus or parasitic nematodes of the genus Strongyloides. Here we show that injection of poly(UG)-tailed RNA leads to gene knock down in P. pacificus and that the injected RNA, as well as the corresponding endogenous RNA, serve as substrate for the formation of new poly(UG)-tailed RNAs. Different from C. elegans, in P. pacificus, the knockdown effect depends on the redundant activity of the three rde-1 paralogs present in this species. We detected endogenously occurring poly(UG)-tailed RNAs derived from thousands of genes, more than half of which belong to germline-specific co-expression clusters. Mutations in Ppa-rde-3, lead to sterility. In contrast, in Strongyloides spp., we found poly(UG)-tailed RNAs to be much less abundant, if not absent. Our results show that poly(UG)-tailed RNAs are not restricted to C. elegans and suggest that they play an important function in the germ line in P. pacificus.

molecular biology↗

Conceptualization and Feasibility Testing of a Vibro-Acoustic Solution for Tumor Detection

Accurate detection of tumors is critical for the success of oncologic surgical intervention. Along with any modality for the localization of tumors, surgeons achieve important information with direct palpation as long as direct touch of the tumor is possible. However, often due to using surgical tools in confined cavities or employing robotic endeffectors, direct palpation is not possible. We propose a low-frequency vibro-acoustic vibration sensing method to identify tumors based on their mechanical properties. The tumor detection problem was cast into a binary classification as a complementary modality. The method involves a wavelet-based multilayer perceptron neural network that is trained in a supervised manner. Some phantoms of healthy tissue with tumor model inclusion were used for experiments and data collection. From the 120 overall number of experiments, 18 data (15% of the whole data samples) were used as test data to evaluate the performance. The results show an 83.3% accuracy related to the confusion matrix, reflecting the model performance on previously unseen data. Performance of the classifier was evaluated using the confusion matrix and the receiver operating characteristic (ROC). It is discussed that the advantage of the proposed system is that the sensor is not directly touching the specimen and can be integrated into the probe end due to its small dimension.

bioengineering↗

Diet-derived vitamin B12 induces transgenerational inheritance of nematode predation through elevated vitellogenin provisioning

Dietary and nutritional effects can alter organismal phenotypes and influence trait inheritance over generations, so-called transgenerational epigenetic inheritance. However, the chemical nature of the stimuli and the downstream events inducing such memory remain largely elusive. The nematode Pristionchus pacificus exhibits mouth-form plasticity including predation and was recently shown to respond to a multigenerational Novosphingobium diet with the induction and subsequent transgenerational inheritance of the predatory morph. Here, we show that bacteria-derived vitamin B12 is both necessary and sufficient for transgenerational memory. Different vitamin B12 concentrations are required for the original induction and the subsequent transgenerational inheritance of the predatory morph. Mutant analysis revealed that vitamin B12 functions through methionine-synthase and involves methionine but not vitamin B9. The inherited effect acts through increased multigenerational vitellogenin transcription indicating elevated nutrient provisioning. Consistently, mutants in the vitellogenin receptor Ppa-rme-2 are memory-defective. Thus, vitamin B12 induces vitellogenin provisioning to control organismal physiology and behavior.

genetics↗

Biosynthesis of modular signaling molecules requires functional diversification of carboxylesterases in Pristionchus pacificus

The model nematode Pristionchus pacificus produces four types of complex ascaroside pheromones named UBAS, DASC, NPAR, and PASC. However, the exact biosynthetic pathways of these modular signaling molecules remain enigmatic. We have previously identified a carboxylesterase Ppa-UAR-1 for the biosynthesis of UBAS, enabling the attachment of ureidoisobutyric acid at the 4-position of simple ascarosides. Here, we report three new carboxylesterases Ppa-UAR-5, Ppa-UAR-6 and Ppa-UAR-12 from P. pacificus. Ppa-UAR-5 functions downstream of Ppa-UAR-1 to furnish the biosynthesis of ubas#1 and ubas#2, whereas Ppa-UAR-12 specifically links two ascr#1 at the 4-position to synthesize dasc#1. Finally, Ppa-UAR-6 is essential for the biosynthesis of npar#1-3 and part#9. The expression patterns of Ppa-uar-6 and Ppa-uar-12 in the intestinal and epidermal cells suggest pheromone biosynthesis to be restricted to specific tissues. These findings indicate that the expansion and functional diversification of carboxylesterases plays a crucial role in the evolution of complex pheromones in nematodes. SIGNIFICANCEOur study identified three new carboxylesterase genes (Ppa-uar-5, Ppa-uar-12 and Ppa-uar-6) from P. pacificus. The encoded enzymes separately regulated the biosynthesis of three types of modular pheromones (UBAS, DASC, and NPAR-types) in worms intestinal cells and exhibited extremely high substrate-specificity. For example, we verified that Ppa-UAR-12 specifically linked one ascr#1 to the 4-position of another ascr#1 to finally furnish the biosynthesis of ascaroside dimer dasc#1. These new discoveries largely clarify the delicate biosynthetic mechanisms of how diversification of carboxylesterases functions in P. pacificus to build up enormous complexity of modular signaling molecules. Such a biosynthetic mechanism of nematode pheromones might be widely conserved in the phylum Nematoda.

biochemistry↗

EBAX-1/ZSWIM8 destabilizes miRNAs resulting in transgenerational memory of a predatory trait

Environmental influences on traits and associated transgenerational epigenetic inheritance have widespread implications, but remain controversial and underlying mechanisms poorly understood. We introduce long-term environmental induction experiments on alternative diets in Pristionchus pacificus, a nematode exhibiting mouth-form plasticity including predation, by propagating 110 isogenic lines for 101 generations with associated food-reversal experiments. We found dietary induction and subsequent transgenerational memory of the predatory morph and identified a role of ubiquitin ligase EBAX-1/ZSWIM8 in this process. Ppa-ebax-1 mutants have no memory and Ppa-EBAX-1 destabilizes the clustered microRNA family miR-2235a/miR-35. Deletions of a cluster of 44 identical miR-2235a copies resulted in precocious and extended transgenerational inheritance of the predatory morph. These findings indicate that EBAX-1/ZSWIM8 destabilizes miRNAs resulting in transgenerational memory, suggesting a role for target-directed miRNA degradation.

genetics↗

Functional divergence of conserved developmental plasticity genes between two distantly related nematodes

Genes diverge in form and function in multiple ways over time; they can be conserved, acquire new roles, or eventually be lost. However, the way genes diverge at the functional level is little understood, particularly in plastic systems. We investigated this process using two distantly related nematode species, Allodiplogaster sudhausi and Pristionchus pacificus. Both these nematodes display environmentally-influenced developmental plasticity of mouth-form feeding structures. This phenotype can be manipulated by growth on particular diets, making them ideal traits to investigate functional divergence of developmental plasticity genes between organisms. Using CRISPR-engineered mutations in A. sudhausi mouth-form genes, we demonstrate examples of the various ways ancestral genes regulate developmental plasticity and how these roles can progressively diverge. We examined four ancestral genes, revealing distinct differences in their conservation and functional divergence in regulating the mouth phenotype in both species. Specifically, certain genes retain the same characteristics, while others have acquired a new function. Additionally, two ancestral genes retain their functions as switch genes, which completely prevent a phenotype, and the other two display quantitative effects, with knockouts in these genes displaying intermediate phenotypes. Remarkably, despite the evolutionary distance, all genes examined were involved in mouth-form regulation. Finally, multiple gene knock-out mutants were engineered, with key sulfatase-encoding genes acting downstream of all others, suggesting they play a major role in mouth-form plasticity. Together, this study represents the first mutant-based functional analysis of the evolution of developmental plasticity between two highly diverged species, offering new insights into the genetic mechanisms underlying phenotypic evolution. Article SummaryWhile evolutionary divergence of genes is well-studied at the sequence level, the resulting functional and phenotypic consequences are less known, particularly in plastic systems. Here, we examined functional divergence of a set of genes involved in developmental plasticity of mouth-form between two highly diverged nematode species. We found that all studied genes control mouth-form plasticity in both species; however, with strong functional divergence and gene-specific quantitative effects or even novel functions. Thus, there is a spectrum from full conservation, partial conservation to the gain of a new function; with genes involved in sulfation showing the strongest conservation during evolution.

evolutionary biology↗

High nutritional conditions influence feeding plasticity in Pristionchus pacificus and render worms non-predatory

Developmental plasticity, the ability of a genotype to produce different phenotypes in response to environmental conditions, has been subject to intense studies in the last four decades. The self-fertilizing nematode Pristionchus pacificus has been developed as a genetic model system for studying developmental plasticity due to its mouth-form polyphenism that results in alternative feeding strategies with a facultative predatory and a non-predatory mouth form. Many studies linked molecular aspects of the regulation of mouth-form polyphenism with investigations of its evolutionary and ecological significance. Also, several environmental factors influencing P. pacificus feeding structure expression were identified including temperature, culture condition and population density. However, the nutritional plasticity of the mouth form has never been properly investigated although polyphenisms are known to be influenced by changes in nutritional conditions. For instance, studies in eusocial insects and scarab beetles have provided significant mechanistic insights into the nutritional regulation of polyphenisms but also other forms of plasticity. Here, we study the influence of nutrition on mouth-form polyphenism in P. pacificus through experiments with monosaccharide and fatty acid supplementation. We show that in particular glucose supplementation renders worms non-predatory. Subsequent transcriptomic and mutant analyses indicate that de novo fatty acid synthesis and peroxisomal beta-oxidation pathways play an important role in the mediation of this plastic response. Finally, the analysis of fitness consequences through fecundity counts suggests that non-predatory animals have an advantage over predatory animals grown in the glucose-supplemented condition. Research highlightsThis study represents the first systematic attempt to investigate the influence of nutrition on mouth-form polyphenism in the genetic model organism Pristionchus pacificus. Through glucose and oleic acid supplementation we show that high nutritional conditions influence feeding plasticity and render worms non-predatory. Mutant analysis indicates a role of de novo fatty acid synthesis and peroxisomal beta-oxidation pathways for these responses.

evolutionary biology↗

Developmental small RNA transcriptomics reveals divergent evolution of the conserved microRNA miR-100 and the let-7-complex in nematodes

BackgroundOver the last three decades, small RNAs have emerged as one of the key post-transcriptional regulators, and are categorised into microRNAs (miRNAs), small interfering RNAs (siRNAs), and PIWI-interacting RNAs (piRNAs). Since their discovery as regulators of developmental timing in the nematode Caenorhabditis elegans, some miRNAs have been found to be highly conserved throughout animal evolution. miR-100 is one such highly conserved miRNA, possibly predating the origin of bilaterians. Furthermore, mir-100 is a member of the conserved let-7-complex, a locus containing three conserved miRNA-coding genes (mir-100, let-7, and mir-125/lin-4) that does not exist in the same arrangement in C. elegans. ResultsWe performed small RNA sequencing across four developmental time-points in the satellite nematode Pristionchus pacificus, identifying 64 novel and ontogenically specifically expressed miRNAs. We also identified miR-100 as the most abundant miRNA in post-embryonic juvenile stages. Additionally, P. pacificus exhibited a novel constellation of the let-7-complex, wherein mir-100 is closely linked to let-7, but without mir-125/lin-4 in the same locus. Mutants of mir-100 and let-7, individually as well as simultaneously, resulted in viable but developmentally defective worms, showing misregulation in collagen and astacin gene families. Interestingly, lin-4 mutants showed a delayed but otherwise normal development. ConclusionThis study provides the first developmental small RNA transcriptome of P. pacificus, providing a community resource for future evo-devo studies. Furthermore, we identify miR-100 as the most abundant ontogenically-specific miRNA, which, along with let-7, regulates normal development in P. pacificus. Lastly, we observe two alternative arrangements of the highly conserved miRNA locus let-7-complex.

evolutionary biology↗

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↗

Positions of pivot points in quadrupedal locomotion: limbs and trunk global control in four different dog breeds.

Dogs (Canis familiaris) prefer the walk at lower speeds and the more economical trot at speeds ranging from 0.5 Fr up to 3 Fr. Important works were carried out to understand these gaits at the levels of center of mass, joint mechanics, and muscular control. However, less is known about the global control goals for limbs and overall locomotion, and of whether these global control goals are gait or breed specific. For walk and trot, we analyzed dog global dynamics based on motion capture and single leg kinetic data recorded from treadmill locomotion of French Bulldog (N = 4), Whippet (N = 5), Malinois (N = 4) and Beagle (N = 5). Dogs displayed two virtual pivot points (VPP) during walk and trot each. One resembles control of both thoracic (fore) limbs and is roughly located above and caudally to the scapular pivot, while the second is located roughly above and cranially to the hip and mirrors the control of the pelvic (hind-) limbs. The positions of VPPs and the patterns of the legs axial and tangential functions were gait and breed related. However, breed related changes were mainly exposed by the French Bulldog. The position of VPPs relative to the proximal pivots explains the propulsive and breaking forces observed in quadrupedal locomotion and may help to reduce limb work. In combination with former work, from the present study the VPP template emerges as the expression of a simple and general global control rule for both bipeds and quadrupeds.

animal behavior and cognition↗

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↗

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↗

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↗