Biology subjects

Martindale, M. Q.

Publications and source records attributed to Martindale, M. Q..

15 recordsLinked to original sources

bioRxiv2025

Notch expression during ctenophore development gives insight into its ancestral function

The canonical Notch pathway is a juxtacrine signaling module with widely conserved roles maintaining progenitor cell populations, promoting binary cell fate decisions, and establishing tissue boundaries. This pathway emerged in Metazoan lineages, although many molecular components and regulators existed prior to that divergence. Given that the vast majority of Notch studies focus on bilaterians, it is unclear when or how Notch gained its developmental signaling functions. To clarify the ancestral function of Notch, we turned to an early branching Metazoan -- the ctenophore Mnemiopsis leidyi -- and conducted structural analyses of putative Notch components to evaluate predicted signaling potential. We characterized gene expression of these components with in situ hybridization and show they are expressed during late embryogenesis. Using hybridization chain reaction (HCRTM), we examine MlNotch expression relative to canonical transcriptional targets and putative stem cell markers and identify differential expression patterns at a cellular resolution. Pharmacological inhibition reveals zones of active and inactive MlNotch during late embryonic development. Our results suggest that Notch evolved its signaling potential by the Metazoan divergence and is likely involved in regulating progenitor cell populations and coordinating developmental fate decisions.

developmental biology↗

bioRxiv2024

The Nematostella Wnt/β-catenin destruction complex provides insight into the evolution of the regulation of a major metazoan signal transduction pathway

The genesis of signaling pathways likely drove metazoan evolution, but the origins of these pathways and how they acquired signaling activity is poorly understood. Here, we studied functional evolution of the Wnt/{beta}-catenin (cWnt) pathway destruction-complex (DC) that regulates {beta}-catenin signaling. Bilaterian DC function requires {beta}-catenin binding to Axin and APC proteins, and Axin-APC heterodimerization. However, bioinformatic analyses predicted that Axin and APC-like homologs in early-branching non-bilaterians lack important previously defined bilaterian {beta}-catenin binding domains, questioning if they have functional cWnt-DCs. We demonstrate that both Axin and APC proteins in the cnidarian Nematostella vectensis (a representative of the sister taxon to bilaterians) can regulate cWnt signaling indicating an active cWnt-DC. Using in vitro analyses, we show that NvAxin binds Nv{beta}-catenin weakly despite lacking the conserved bilaterian Axin {beta}-catenin-binding motif ({beta}catBM). Using AlphaFold3, we identified two predicted {beta}catBM-like sequences in NvAxin, one within the Axin-RGS domain and another towards the C-terminus. Similar analysis of placozoan, poriferan, and ctenophore Axin identified single {beta}catBM-like sequences located within Axin-RGS. We show that ctenophore Axin and {beta}-catenin do not interact and changing a conserved leucine on NvAxin-{beta}catBM-like motifs to resemble the ctenophore sequence abolished NvAxin-Nv{beta}-catenin interactions. We propose that an ancestral Axin-RGS sequence acquired low-affinity {beta}-catenin binding early in metazoan evolution, followed by motif duplication in the cnidarian-bilaterian ancestor. In bilaterians, the duplicated {beta}catBM evolved higher-affinity for {beta}-catenin, while the ancestral sequence was lost. Our results demonstrate how phylogenetic insights, AI tools and functional assays can be used to reconstruct the evolution of complex signaling pathways.

developmental biology↗

bioRxiv2024

β-catenin localization in the ctenophore Mnemiopsis leidyi suggests an ancestral role in cell adhesion and nuclear function

The emergence of multicellularity in animals marks a pivotal evolutionary event which was likely enabled by molecular innovations in the way cells adhere and communicate with one another. {beta}-catenin is significant to this transition due to its dual role as both a structural component in the cadherin-catenin complex and as a transcriptional coactivator involved in the Wnt/{beta}-catenin signaling pathway. However, our knowledge of how this protein functions in ctenophores, one of the earliest diverging metazoans, is limited. To study {beta}-catenin function in the ctenophore Mnemiopsis leidyi, we generated affinity-purified polyclonal antibodies targeting Ml{beta}-catenin. We then used this tool to observe {beta}-catenin protein localization in developing Mnemiopsis embryos. In this article we provide evidence of consistent {beta}-catenin protein enrichment at cell-cell interfaces in Mnemiopsis embryos, suggesting that Ml{beta}-catenin had an ancestral role in cell adhesion. Additionally, we found {beta}-catenin enrichment in some nuclei, particularly restricted to the oral pole around the time of gastrulation, suggesting Ml{beta}-catenin may have a nuclear function in Mnemiopsis embryos. The Ml{beta}-catenin affinity-purified antibodies now provide us with a powerful reagent to study the ancestral functions of {beta}-catenin in cell adhesion and transcriptional regulation.

developmental biology↗

bioRxiv2023

A novel in vivo system to study coral biomineralization in the starlet sea anemone (Nematostella vectensis)

Coral reefs are important for maintaining healthy marine ecosystems and are declining rapidly due to increasing environmental stresses. Coral conservation efforts require a mechanistic understanding of how these stresses may disrupt biomineralization, but progress in this area has been slow primarily because corals are not easily amenable to laboratory research. Some cellular characteristics of biomineralization are well characterized, such as the role of carbonic anhydrases, the polarized secretion of ions, and the secretion of "intrinsically disordered proteins" (IDPs) into extracellular microenvironments. We highlight how the starlet sea anemone (Nematostella vectensis) can serve as a tractable model to interrogate the cellular mechanisms of coral biomineralization. We have developed transgenic constructs using genes involved in biomineralization from several animal phyla that can be injected into Nematostella zygotes. These constructs are designed so translated proteins may be purified using TEV protease or Histidine tags to study their physicochemical properties. Using a fluorescent tag, we confirm ectopic expression of the coral biomineralizing protein SpCARP1 in live Nematostella embryos and adults and demonstrate via calcein staining that calcium ions co-localize with SpCARP1 in carbonate and calcium enriched seawater. Our findings suggest that SpCARP1 can induce the formation of amorphous calcium carbonate precursors in N. vectensis, consistent with its suspected role in the early stages of coral biomineralization. These results lay a fundamental groundwork for establishing N. vectensis as a novel in vivo system to explore the evolutionary and cellular mechanisms of biomineralization, improve coral conservation efforts, and even develop novel biomaterials. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/560932v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@1170b4eorg.highwire.dtl.DTLVardef@1e7491corg.highwire.dtl.DTLVardef@1710cd1org.highwire.dtl.DTLVardef@100743b_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

Nematostella vectensis exemplifies the exceptional expansion and diversity of opsins in the eyeless Hexacorallia

BackgroundOpsins are the primary proteins responsible for light detection in animals. Cnidarians (jellyfish, sea anemones, corals) have diverse visual systems that have evolved in parallel with bilaterians (squid, flies, fish) for hundreds of millions of years. Medusozoans (e.g. jellyfish, hydroids) have evolved eyes multiple times, each time independently incorporating distinct opsin orthologs. Anthozoans (e.g. corals, sea anemones,) have diverse light-mediated behaviors and, despite being eyeless, exhibit more extensive opsin duplications than medusozoans. To better understand the evolution of photosensitivity in animals without eyes we increased anthozoan representation in the phylogeny of animal opsins and investigated the large but poorly characterized opsin family in the sea anemone Nematostella vectensis. ResultsWe analyzed genomic and transcriptomic data from 16 species of cnidarians to generate a large opsin phylogeny (708 sequences) with the largest sampling of anthozoan sequences to date. We identified 29 opsins from N. vectensis (NvOpsins) with high confidence, using transcriptomic and genomic datasets. We found that lineage-specific opsin duplications are common across Cnidaria, with anthozoan lineages exhibiting among the highest numbers of opsins in animals. To establish putative photosensory function of NvOpsins, we identified canonically conserved protein domains and amino acid sequences essential for opsin function in other animal species. We show high sequence diversity among NvOpsins at sites important for photoreception and transduction, suggesting potentially diverse functions. We further examined the spatiotemporal expression of NvOpsins and found both dynamic expression of opsins during embryonic development and sexually dimorphic opsin expression in adults. ConclusionsThese data show that lineage-specific duplication and divergence has led to expansive diversity of opsins in eyeless cnidarians, suggesting opsins from these animals may exhibit novel biochemical functions. The variable expression patterns of opsins in N. vectensis suggest opsin gene duplications allowed for a radiation of unique sensory cell types with tissue-and stage-specific functions. This diffuse network of distinct sensory cell types could be an adaptive solution for varied sensory tasks experienced in distinct life history stages in Anthozoans.

evolutionary biology↗

bioRxiv2023

Cytoplasmic polyadenylation is an ancestral hallmark of early development in animals

Differential regulation of gene expression has produced the astonishing diversity of life on Earth. Understanding the origin and evolution of mechanistic innovations for control of gene expression is therefore integral to evolutionary and developmental biology. Cytoplasmic polyadenylation is the biochemical extension of polyadenosine at the 3-end of cytoplasmic mRNAs. This process regulates the translation of specific maternal transcripts and is mediated by the Cytoplasmic Polyadenylation Element Binding Protein family (CPEBs). Genes that code for CPEBs are amongst a very few that are present in animals but missing in non-animal lineages. Whether cytoplasmic polyadenylation is present in non bilaterian animals (i.e., sponges, ctenophores, placozoans, cnidarians) remains unknown. We have conducted phylogenetic analyses of CPEBs and our results show that CPEB1 and CPEB2 subfamilies originated in the animal stem lineage. Our assessment of expression in the sea anemone, Nematostella vectensis (Cnidaria), and the comb jelly, Mnemiopsis leidyi (Ctenophora), demonstrates that maternal expression of CPEB1 and the catalytic subunit of the cytoplasmic polyadenylation machinery (GLD2) is an ancient feature that is conserved across animals. Furthermore, our measurements of poly(A)-tail elongation reveal that key targets of cytoplasmic polyadenylation are shared between vertebrates, cnidarians, and ctenophores, indicating that this mechanism orchestrates a regulatory network that is conserved throughout animal evolution. We postulate that cytoplasmic polyadenylation through CPEBs was a fundamental innovation that contributed to animal evolution from unicellular life.

evolutionary biology↗

bioRxiv2022

Independent innexin radiation shaped signaling in ctenophores.

Innexins facilitate cell-cell communication by forming gap junctions or non-junctional hemichannels, which play important roles in metabolic, chemical, ionic, and electrical coupling. The lack of knowledge regarding the evolution and role of these channels in ctenophores (comb jellies), the likely sister group to the rest of animals, represents a substantial gap in our understanding of the evolution of intercellular communication in animals. Here we identify and phylogenetically characterize the complete set of innexins of four ctenophores: Mnemiopsis leidyi, Hormiphora californensis, Pleurobrachia bachei, and Beroe ovata. Our phylogenetic analyses suggest that ctenophore innexins diversified independently from those of other animals and were established early in the emergence of ctenophores. We identified a four-innexin genomic cluster, which was present in the last common ancestor of these four species and has been largely maintained in these lineages. Evidence from correlated spatial and temporal gene expression of the M. leidyi innexin cluster suggest that this cluster has been maintained due to constraints related to gene regulation. We describe basic electrophysiological properties of putative ctenophore hemichannels from muscle cells using intracellular recording techniques, showing substantial overlap with the properties of bilaterian innexin channels. Together, our results suggest that the last common ancestor of animals had gap junctional channels also capable of forming functional innexin hemichannels, and that innexin genes have independently evolved in major lineages throughout Metazoa.

evolutionary biology↗

bioRxiv2020

On the origin and evolution of RNA editing in metazoans

Extensive adenosine-to-inosine (A-to-I) editing of nuclear-transcribed RNAs is the hallmark of metazoan transcriptional regulation, and is fundamental to numerous biochemical processes. Here we explore the origin and evolution of this regulatory innovation, by quantifying its prevalence in 22 species that represent all major transitions in metazoan evolution. We provide substantial evidence that extensive RNA editing emerged in the common ancestor of extant metazoans. We find the frequency of RNA editing varies across taxa in a manner independent of metazoan complexity. Nevertheless, cis-acting features that guide A-to-I editing are under strong constraint across all metazoans. RNA editing seems to preserve an ancient mechanism for suppressing the more recently evolved repetitive elements, and is generally nonadaptive in protein-coding regions across metazoans, except for Drosophila and cephalopods. Interestingly, RNA editing preferentially target genes involved in neurotransmission, cellular communication and cytoskeleton, and recodes identical amino acid positions in several conserved genes across diverse taxa, emphasizing broad roles of RNA editing in cellular functions during metazoan evolution that have been previously underappreciated.

evolutionary biology↗

bioRxiv2019

Molecular patterning during the development of Phoronopsis harmeri reveals similarities to rhynchonelliform brachiopods

BackgroundAnswering the question how conserved patterning systems are across evolutionary lineages requires a broad taxon sampling. Phoronid development has previously been studied using fate mapping and morphogenesis, yet molecular descriptions are missing. Here we report the expression patterns of the evolutionarily conserved anterior (otx, gsc, six3/6, nk2.1), posterior (cdx, bra) and endomesodermal (foxA, gata4/5/6, twist) markers in the phoronid Phoronopsis harmeri.\n\nResultsThe transcription factors foxA, gata4/5/6 and cdx show conserved expression in patterning the development and regionalization of the phoronid embryonic gut, with foxA expressed in the presumptive foregut, gata4/5/6 demarcating the midgut and cdx confined to the hindgut. Surprisingly, brachyury, an evolutionary conserved transcription factor often associated with gastrulation movements and patterning of the mouth and hindgut, seems to be unrelated with gastrulation and mouth patterning in phoronids. Furthermore, six3/6, a well-conserved anterior marker, shows a remarkably dynamic expression, demarcating not only the apical organ and the oral ectoderm, but also clusters of cells of the developing midgut and the anterior mesoderm, similar to what has been reported for brachiopods, bryozoans and some deuterostome Bilateria.\n\nConclusionsOur comparison of gene expression patterns with other studied Bilateria reveals that the timing of axis determination and cell fate distribution of the phoronid shows highest similarities to rhynchonelliform brachiopods. Despite these similarities, the phoronid P. harmeri shows also particularities in its development, which hint to divergences in the arrangement of gene regulatory networks responsible for germ layer formation and axis specification.

developmental biology↗

bioRxiv2019

Evolutionary dynamics of the trypsin superfamily and the origins of novel secretory cell function in the internalized ectoderm of the sea anemone Nematostella vectensis

Understanding the drivers of morphological diversity is a persistent challenge in evolutionary biology. Here, we investigate functional diversification of secretory cells in the sea anemone Nematostella vectensis to understand the mechanisms promoting cellular specialization across animals. We demonstrate regionalized expression of gland cell subtypes in the internal ectoderm of N. vectensis and show that adult gland cell identity is acquired very early in development. A phylogenetic survey of trypsins across animals suggests this gene family has undergone numerous expansions. We reveal unexpected diversity in trypsin protein structure and show that trypsin diversity arose through independent acquisitions of non-trypsin domains. Finally, we show that trypsin diversification in N. vectensis was effected through a combination of tandem duplication, exon shuffling, and retrotransposition. Together we reveal that numerous evolutionary mechanisms drove trypsin duplication and divergence during the morphological specialization of cell types and suggest the secretory cell phenotype is highly adaptable as a vehicle for novel secretory products.

evolutionary biology↗

bioRxiv2019

β-catenin has an ancestral role in cell fate specification but not cell adhesion

The {beta}-catenin protein has two major known functions in animal cells. It keeps epithelial tissue homeostasis by its connection with Adherens Junctions (AJ), and it serves as a transcriptional cofactor along with Lef/Tcf to enter the nucleus and regulate target genes of the Wnt/{beta}-catenin (cWnt) signaling pathway. To assess the ancestral role of {beta}-catenin during development we examined its distribution and function in the ctenophore Mnemiopsis leidyi (one of the earliest branching animal phyla) by using ctenophore-specific antibodies and mRNA injection. We found that {beta}-catenin protein never localizes to cell-cell contacts during embryogenesis as it does in other metazoans, most likely because ctenophore-cadherins do not have the cytoplasmic domain required for interaction with the catenin proteins. Downregulation of zygotic Ml{beta}-catenin signaling led to the loss of endodermal and mesodermal tissues indicating that nuclear {beta}-catenin may have a deep role in germ-layer evolution. Our results indicate that the ancestral role for {beta}-catenin was in the cell-fate specification and not in cell adhesion and also further emphasizes the critical role of this protein in the evolution of tissue layers in metazoans.

developmental biology↗

bioRxiv2018

Par-Cteno-Genesis or Cteno Par-Genesis

In bilaterians and cnidarians, embryonic and epithelial cell-polarity are regulated by the interactions between Par proteins, Wnt/PCP signaling pathway, and cell-cell adhesion. Par proteins are highly conserved across Metazoa, including ctenophores. But strikingly, ctenophore genomes lack components of the Wnt/PCP pathway and cell-cell adhesion complexes; raising the question if ctenophore cells are polarized by mechanisms involving Par proteins. Here, by using immunohistochemistry and live-cell imaging overexpression of specific mRNAs, we describe for the first time the subcellular localization of selected Par proteins in blastomeres and epithelial cells during the embryogenesis of the ctenophore Mnemiopsis leidyi. We show that these proteins distribute differently compared to what has been described for other animals, even though they segregate in a host-specific fashion when expressed in cnidarian embryos. This differential localization might be related to the emergence of different junctional complexes during metazoan evolution. Data obtained here challenge the ancestry of the apicobasal cell polarity and raise questions about the homology of epithelial tissue across the Metazoa.

developmental biology↗

bioRxiv2017

Germ layer specific regulation of cell polarity and adhesion: insight into the evolution of mesoderm

In triploblastic animals, Par-proteins regulate cell-polarity and adherens junctions of both ectodermal and endodermal epithelia. But, in embryos of the diploblastic cnidarian Nematostella vectensis, Par-proteins are degraded in all cells in the bifunctional gastrodermal epithelium. Using immunohistochemistry, CRISPR/Cas9 mutagenesis, and overexpression of specific mRNAs, we describe the functional association between Par-proteins, {beta}-catenin, and snail transcription factor genes in N. vectensis embryos. We demonstrate that the aPKC/Par complex regulates the localization of {beta}-catenin in the ectoderm by stabilizing its role in cell-adhesion, and that endomesodermal epithelial cells are organized by a different cell-adhesion system than that of overlying ectoderm. We also show that ectopic expression of snail genes, which are expressed in mesodermal derivatives in bilaterians, are sufficient to downregulate Par-proteins and translocate {beta}-catenin from the junctions to the cytoplasm in ectodermal cells. These data provide molecular insight into the evolution of epithelial structure and distinct mesodermal tissue in metazoan embryos.

developmental biology↗

bioRxiv2017

Reorientation of the primary body axis by ectopic embryonic cWnt signaling.

Gastrulation is a crucial time during embryogenesis when cells make important decisions on what larval or adult tissues (i.e. ectodermal, mesodermal, or endodermal) are going to generate. The evolution of gastrulation was a pivotal event during metazoan evolution, as it paved the way for diversification of the metazoan clade from a hollow, ciliated, radially symmetrical ancestor (1, 2). The position of the site of gastrulation (that segregates internal endomesodermal precursors from outer ectodermal tissue) has played a role in our understanding patterns of body plan evolution (e.g. deuterostomes vs protostomes) and is tightly regulated during development. In bilaterians (a large clade of bilaterally symmetrical animals that represent over 99% of all extant species), the site of gastrulation is determined by a localized molecular asymmetry resulting from a differential distribution of maternal determinants (3) along the so-called an ...

developmental biology↗

bioRxiv2017

Hox genes pattern the primary body axis of an anthozoan cnidarian prior to gastrulation

Hox gene transcription factors are important regulators of positional identity along the anterior-posterior axis in bilaterian animals. Cnidarians (e.g. sea anemones, corals and hydroids) are the sister group to the Bilateria and possess genes related to both anterior and central/posterior class Hox genes. In the absence of a conserved set of Hox genes among other early branching animal clades, cnidarians provide the best opportunity to learn about the emergence of this gene family. We report a previously unrecognized domain of Hox expression in the starlet sea anemone, Nematostella vectensis, beginning at early blastula stages. Functional perturbation reveals that two Hox genes not only regulate their respective expression domains, but interact with one another to pattern the entire oral-aboral axis mediated by Wnt signaling. This suggests an ancient link between Hox/Wnt patterning of the oral-aboral axis and suggest that these domains are likely established during blastula formation in anthozoan cnidarians.

developmental biology↗