Biology subjects

Holstein, T. W.

Publications and source records attributed to Holstein, T. W..

12 recordsLinked to original sources

bioRxiv2024

The dynamic genomes of Hydra and the anciently active repeat complement of animal chromosomes

Many animal genomes are characterized by highly conserved chromosomal homologies that pre-date the ancient origin of this clade. Despite such conservation, the evolutionary forces behind the retention, expansion, and contraction of chromosomal elements, and the resulting macro-evolutionary implications, are unknown. Here we present a comprehensive stem-cell resolved genomic and transcriptomic study of the fresh-water cnidarian Hydra, an animal characterized by its high regenerative capacity, the ability to propagate clonally, and an apparent lack of aging. Using single-haplotype telomere-to-telomere genome assemblies of two recently diverged hydra strains, we show how the macro-evolutionary history of chromosomal elements is shaped by both old and recent transposable element (TE) expansions. Unique features of hydra biology allowed us to compare the individual genomes of hydras three stem cell lineages. We show that distinct TE families are active at both transcriptional and genomic levels via non-random insertions in the genomes of each of these lineages. In transcriptomes, over 14,000 transcripts were composed of nearly complete TE sequences, and further classification into families, subfamilies, and individual loci reveals cell type-specific TE expression. The active TEs include elements that differentially contribute to changes in the genome size as well as persistent structural variants around loci associated with cell proliferation. Our study reveals 14 active TE families that primarily act in this role and are predominantly composed of DNA elements. Evolutionary analysis revealed that these families constitute a highly conserved TE core in eukaryotic and metazoan genomes. Our results suggest an ancient role for these core TEs as self-renewing genomic components that persist beyond ancient chromosomal homologies.

genomics↗

bioRxiv2023

Spatio-temporal Coordination of Active Deformation Forces and Wnt / Hippo-Yap Signaling in Hydra Regeneration

Ample evidence suggests that Wnt signaling and tissue deformation are key determinants for pattern formation in animals. The coordination of these biochemical and biomechanical spatio-temporal asymmetries is often unknown or controversial. We investigated this relationship by studying regeneration in the freshwater polyp Hydra. In both reaggregates of dissociated cells and tissue regenerates, we found significant tissue contraction waves and upregulation of Wnt signaling. Applying a simple mechanical model to the mode analysis of the active deformations, we quantitatively defined the phase reversal of size change and axial deformation in those oscillations as the time point of "biomechanical" symmetry breaking. Moreover, overexpression and inhibition of canonical Wnt signaling modulated the timing of this biomechanical symmetry breaking. A direct comparison with the RNAseq data indicates that the biomechanical symmetry breaking occurs only after the upregulation of canonical Wnt signaling. Further data suggest that biochemical signaling and biomechanical active deformation synergistically stabilize the body axis and hence the following head structure formation by Hippo-Yap signaling. The symmetry breaking mechanism identified here in Hydra most likely represents a patterning module that is evolutionary conserved from early metazoan to bilaterian animals.

biophysics↗

bioRxiv2023

An ancient split of germline and somatic stem cell lineages in Hydra

In many animals, germ cell segregation occurs during early embryogenesis to protect the genome, but its origin in basal metazoans is controversial. Here, we show in the freshwater polyp Hydra by clonal analysis and transgenic animals that interstitial stem cells comprise two separate stem cell populations, i.e., germline and multipotent somatic stem cells. We isolated genetically labelled stem cells for a global transcriptome study and discovered a broad set of germline-specific/enriched genes including Prdm9, Pax5, Dmrt1. In an alternative splicing analysis, we identified many genes with germline-specific isoforms; among them, male-specific isoforms of Dmrt1 and Snf5. The somatic interstitial stem cell lineage was characterized by numerous neuronal control genes like Neurog. But all stem cells in Hydra also share a core of stemness genes that has its roots in unicellular eukaryotes. This suggests an evolutionary scenario in which, at the emergence of animal multicellularity, there was an early split into a stable germline and different somatic stem cell lineages.

developmental biology↗

bioRxiv2023

A predatory gastrula leads to symbiosis-independent settlement in Aiptasia

The planulae larvae of cnidarians (jellyfish, hydras, anemones, corals) have attracted interest since Haeckels 150-year-old postulation of the gastrula developmental stage of sponges and corals as the terminal lifeform of primitive multicellular metazoans. Widely viewed as primarily particle feeders, the planulae larvae of the anemone Exaiptasia pallida (commonly Aiptasia) have not been reported to undergo settlement and metamorphosis to adult morphology, and the lack of a closed lifecycle has been a major obstacle in this increasingly popular model system for coral-dinoflagellate endosymbiosis. Here we studied Aiptasia larvae feeding behavior and show its indispensability to trigger the first reports of settlement and metamorphosis in the system, finally closing the Aiptasia lifecycle. Surprisingly, the young gastrula-like planulae at just two days post fertilization actively feed on living crustacean nauplii, preferentially to heat-killed ones. Predation is dependent on functional stinging cells (nematocytes), indicative of complex neuronal control. Larvae fed daily dramatically increase in size and at 14 days post fertilization begin to morphologically change prior to settlement at high efficiency. Strikingly, dinoflagellate endosymbionts are neither required for larval growth nor measurably affect settlement dynamics, but are essential for spawning of the mature adult polyps. Our data show for the first time that gastrula-like planulae were capable of prey capture, suggesting carnivory in addition to filter feeding as a common strategy of this terminal life form. These data are discussed in the context of recent revelations on the evolution of basal metazoans.

zoology↗

bioRxiv2023

A new look at the architecture and dynamics of the Hydra nerve net

The Hydra nervous system is the paradigm of a "simple nerve net". Nerve cells in Hydra, as in many cnidarian polyps, are organized in a nerve net extending throughout the body column. This nerve net is required for control of spontaneous behavior: elimination of nerve cells leads to polyps that do not move and are incapable of capturing and ingesting prey (Campbell, 1976). We have re-examined the structure of the Hydra nerve net by immunostaining fixed polyps with a novel antibody that stains all nerve cells in Hydra. Confocal imaging shows that there are two distinct nerve nets, one in the ectoderm and one in the endoderm, with the unexpected absence of nerve cells in the endoderm of the tentacles. The nerve nets in the ectoderm and endoderm do not contact each other. High-resolution TEM and serial block face SEM show that the nerve nets consist of bundles of parallel overlapping neurites. Results from transgenic lines show that neurite bundles include different neural circuits and hence that neurites in bundles require circuit-specific recognition. Nerve cell-specific innexins indicate that gap junctions can provide this specificity. The occurrence of bundles of neurites supports a model for continuous growth and differentiation of the nerve net by lateral addition of new nerve cells to the existing net. This model was confirmed by tracking newly differentiated nerve cells.

neuroscience↗

bioRxiv2021

How Dickkopf molecules and Wnt/beta-catenin interplay to self-organise the Hydra body axis

The antagonistic interplay between canonical Wnt signalling and Dickkopf (Dkk) proteins is fundamental to tissue organisation, including stem cell differentiation and body-axis formation. Disruptions in this interaction are linked to various human diseases, yet the mechanisms enabling robust body-axis formation through {beta}-catenin/Wnt-Dkk interactions remain unclear. A key model system for Wnt-driven pattern formation is the pre-bilaterian organism Hydra, where two ancestral Dkk proteins interact with Wnt signalling to self-organise the body axis. While Hydra patterning has been extensively studied using the activator-inhibitor framework, a model integrating experimentally identified molecules has been lacking. Here, we introduce a mathematical model that incorporates both Dkks and their experimentally observed interactions with Wnt signalling. Numerical and analytical studies show that this network alone is sufficient to drive de novo body-axis formation across a broad parameter range. Our mutual inhibition model provides a biologically grounded realization of the general local-activation/long-range-inhibition (LALI) principle of de novo pattern formation, offering a mechanistic explanation for the observed Dkk and Wnt expression patterns under various conditions. Unlike previous models, it is directly grounded in experimental data, links injury response to pattern formation, and remains robust against perturbations. Author SummaryHow organisms form and regenerate complex body structures is a fundamental question in biology. In the freshwater animal Hydra, which can regenerate its entire body from a small tissue fragment, a molecular signalling system involving Wnt proteins and their inhibitors, the Dickkopf (Dkk) family, plays a central role in organising the body axis. While these molecules are known to interact, their exact roles and how they collectively shape large-scale patterns have remained unclear--especially since their activity does not fully align with established pattern formation models. In this study, we present a new mathematical model that captures the observed interactions between Wnt and two Dkk molecules in Hydra. We show that a mechanism based on mutual inhibition--rather than the traditional interplay between activator and inhibitor molecules--can explain the emergence of a stable body axis and the results of various perturbation experiments. Our work offers new insights into the design principles of biological pattern formation and emphasizes the importance of exploring alternative mechanisms beyond classical theories.

developmental biology↗

bioRxiv2021

β-Catenin and canonical Wnts control two separate pattern formation systems in Hydra: Insights from mathematical modelling

The formation of body axes and apical termini is crucial for animal development. In Hydra, nuclear {beta}-catenin and Wnt3 play key roles and were previously thought to be part of a single mechanism for axis and head formation. This study challenges this view by combining mathematical modeling with experimental data. We show that {beta}-catenin and Wnt3 patterning in Hydra operate at two different scales, requiring distinct inhibitory mechanisms. {beta}-catenin, possibly interacting with other Wnts, co-ordinates axis formation, whereas Wnt3 is involved in small-scale head patterning. A double-loop reaction-diffusion model was developed, demonstrating the ability to describe patterns with divergent shapes, which single-loop models could not achieve. The previously proposed threshold mechanism for Wnt3 expression based on {beta}-catenin prepatterns could not explain the data. Our results suggest a more complex patterning mechanism in other animals, where axis and head formation may not be controlled by a single process.

developmental biology↗

bioRxiv2020

A Wnt-specific astacin proteinase controls head formation in Hydra

The Hydra head organizer acts as a signaling center that initiates and maintains the primary body axis in steady state polyps and during budding or regeneration. Wnt/beta-Catenin signaling functions as a primary cue controlling this process, but how Wnt ligand activity is locally restricted at the protein level is poorly understood. Here we report the identification of an astacin family proteinase as a Wnt processing factor. Hydra astacin-7 (HAS-7) is expressed from gland cells as an apical-distal gradient in the body column, peaking close beneath the tentacle zone. HAS-7 siRNA knockdown abrogates HyWnt3 proteolysis in the head tissue and induces a robust double axis phenotype, which is rescued by simultaneous HyWnt3 knockdown. Accordingly, double axes are also observed in conditions of increased Wnt levels as in transgenic actin::HyWnt3 and HyDkk1/2/4 siRNA treated animals. HyWnt3-induced double axes in Xenopus embryos could be rescued by co-injection of HAS-7 mRNA. Mathematical modelling combined with experimental promotor analysis indicate an indirect regulation of HAS-7 by beta-Catenin, expanding the classical Turing-type activator-inhibitor model. Our data suggest a negative regulatory function of Wnt processing astacin proteinases in the global patterning of the oral-aboral axis in Hydra.

developmental biology↗

bioRxiv2020

MAPK signaling links the injury response to Wnt-regulated patterning in Hydra regeneration

Hydra has a long history as an informative model to study pattern formation and regeneration. Wnt signaling is a critical component of Hydra patterning that must be activated during regeneration, but it is largely unknown how the injury stimulus ultimately leads to this activation. In a proteomic screen we previously identified mitogen protein kinases (MAPKs) among the earliest injury response factors in Hydra regeneration, making them attractive candidates to transmit injury-response signals to the initial steps of patterning, which in Hydra includes Wnt signaling. Our data demonstrate that three MAPKs, p38, c-Jun N-terminal kinases (JNKs), and extracellular signal-regulated kinases (ERK), are essential to initiate regeneration in Hydra. This activation occurs in response to an injury signal, which consists of calcium and reactive oxygen species (ROS) signaling. Phosphorylated MAPKs exhibit cross-talk with a mutual antagonism between the ERK1/2 pathway and the stress induced MAPKs. The activation of these MAPK pathways, as well as the induction of apoptosis, occurs in all injuries regardless of the position of the wound. MAPK phosphorylation is required for the transcriptional activation of position independent Wnt3 and Wnt9/10c ligands. In summary, our data show that the activation of MAPKs is an essential component of the wound response which transmits the injury signal to induce the transcriptional activation of Wnt ligands, which are essential for patterning the regenerating tissue. Given the high level of evolutionary conservation of MAPKs and Wnts in the injury response, this likely represents a deeply conserved pathway in animals.

developmental biology↗

bioRxiv2018

Membrane capacitance recordings resolve dynamics and complexity of receptor-mediated endocytosis in Wnt signalling

Receptor-mediated endocytosis is an essential process in signaling pathways for an activation of intracellular signaling cascades. One example is the Wnt signaling pathway, which seems to depend on endocytosis of the ligand-receptor complex for initiation of Wnt signal transduction. So far, the role of different endocytic pathways in Wnt signaling, the molecular players and the kinetics of this process are unclear. Here, we monitor endocytosis in Wnt3a and Wnt5a mediated signaling by membrane capacitance recordings of HEK293 cells. Our measurements revealed a fast and substantial increase in the number of endocytic vesicles. This endocytotic activity is specifically elicited by extracellular Wnt ligands; it starts immediately upon ligand binding and ceases over a period of ten minutes. By using specific inhibitors, we can dissect Wnt induced endocytosis into two independent pathways, where canonical Wnt3a is taken up mainly by clathrin-independent endocytosis and Wnt5a exclusively by clathrin-mediated endocytosis.

cell biology↗

bioRxiv2017

Genetic knockdown and knockout approaches in Hydra

Hydra is a member of the Cnidaria, an ancient phylum at the base of metazoan evolution and sister group to all bilaterian animals. The regeneration capacity of Hydra, mediated by its stem cell systems is unparalleled in the animal kingdom. The recent sequencing of the Hydra genome and that of other cnidarians has drawn new attention to this well-known model organism. In spite of this, the establishment of methods to manipulate gene expression in Hydra have remained a major challenge. Here we report a CRISPR-Cas9 based targeted mutation approach as well as an optimized, reproducible strategy for the delivery of siRNAs. Both approaches are based on a refined electroporation protocol for adult Hydra polyps. We demonstrate that these strategies provide reliable genetic interference with target gene expression, facilitating functional studies and genome editing in Hydra.

developmental biology↗

bioRxiv2017

Spatio-temporal elasticity patterns in extracellular matrix during Hydra morphogenesis

Albeit ample evidence has suggested the remodeling of extracellular matrix (ECM) in animals plays crucial roles in development and diseases, little is understood how ECM mechanics correlates with tissue morphogenesis. In this study, we quantitatively determined how spatio-temporal elasticity patterns in ECM change during the asexual reproduction of freshwater polyp Hydra. We first determined the mesoscopic protein arrangement in Hydra ECM (mesoglea) by grazing-incidence small-angle X-ray scattering with nano-beam (nano-GISAXS). Our data unraveled fibrillar type I collagen in Hydra mesoglea (Hcol-I) takes an anisotropic, more strongly distorted hexagonal lattice compared to those in vertebrates that could be attributed to the lower proline content and lack of lysin-crosslinks in Hcol-1 fibers. Then, we "mapped" the spatio-temporal changes in ECM stiffness ex vivo with aid of nano-indentation. We identified three representative elasticity patterns during tissue growth along the oral-aboral body axis of the animals. Our complementary proteome analysis demonstrated that the elasticity patterns of the ECM correlate with a gradient like distribution of proteases. Perturbations of the oral Wnt/{beta}-catenin signaling center further indicated that ECM elasticity patterns are governed by Wnt/{beta}-catenin signaling. The ex vivo biomechanical phenotyping of Hydra mesoglea established in this study will help us gain comprehensive insights into the spatio-temporal coordination of biochemical and biomechanical cues in tissue morphogenesis in vivo.

developmental biology↗