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Bernhard M Degnan - One of the best experts on this subject based on the ideXlab platform.

  • co expression of synaptic genes in the sponge Amphimedon Queenslandica uncovers ancient neural submodules
    Scientific Reports, 2019
    Co-Authors: Eunice Wong, Jan Molter, Sandie M Degnan, Victor Anggono, Bernhard M Degnan
    Abstract:

    The synapse is a complex cellular module crucial to the functioning of neurons. It evolved largely through the exaptation of pre-existing smaller submodules, each of which are comprised of ancient sets of proteins that are conserved in modern animals and other eukaryotes. Although these ancient submodules themselves have non-neural roles, it has been hypothesized that they may mediate environmental sensing behaviors in aneural animals, such as sponges. Here we identify orthologues in the sponge Amphimedon Queenslandica of genes encoding synaptic submodules in neural animals, and analyse their cell-type specific and developmental expression to determine their potential to be co-regulated. We find that genes comprising certain synaptic submodules, including those involved in vesicle trafficking, calcium-regulation and scaffolding of postsynaptic receptor clusters, are co-expressed in adult choanocytes and during metamorphosis. Although these submodules may contribute to sensory roles in this cell type and this life cycle stage, total synaptic gene co-expression profiles do not support the existence of a functional synapse in A. Queenslandica. The lack of evidence for the co-regulation of genes necessary for pre- and post-synaptic functioning in A. Queenslandica suggests that sponges, and perhaps the last common ancestor of sponges and other extant animals, had the ability to promulgate sensory inputs without complete synapse-like functionalities. The differential co-expression of multiple synaptic submodule genes in sponge choanocytes, which have sensory and feeding roles, however, is consistent with the metazoan ancestor minimally being able to undergo exo- and endocytosis in a controlled and localized manner.

  • Sponge Long Non-Coding RNAs Are Expressed in Specific Cell Types and Conserved Networks
    Non-Coding RNA, 2018
    Co-Authors: Federico Gaiti, William L. Hatleberg, Miloš Tanurdžić, Bernhard M Degnan
    Abstract:

    Although developmental regulation by long non-coding RNAs (lncRNAs) appears to be a widespread feature amongst animals, the origin and level of evolutionary conservation of this mode of regulation remain unclear. We have previously demonstrated that the sponge Amphimedon Queenslandica—a morphologically-simple animal—developmentally expresses an array of lncRNAs in manner akin to more complex bilaterians (insects + vertebrates). Here, we first show that Amphimedon lncRNAs are expressed in specific cell types in larvae, juveniles and adults. Thus, as in bilaterians, sponge developmental regulation involves the dynamic, cell type- and context-specific regulation of specific lncRNAs. Second, by comparing gene co-expression networks between Amphimedon Queenslandica and Sycon ciliatum—a distantly-related calcisponge—we identify several putative co-expression modules that appear to be shared in sponges; these network-embedded sponge lncRNAs have no discernable sequence similarity. Together, these results suggest sponge lncRNAs are developmentally regulated and operate in conserved gene regulatory networks, as appears to be the case in more complex bilaterians.

  • lipidomics of the sea sponge Amphimedon Queenslandica and implication for biomarker geochemistry
    Geobiology, 2017
    Co-Authors: David A Gold, Shane S Oreilly, Jabin R Watson, Sandie M Degnan, Jens O Kromer, Bernhard M Degnan, Roger E Summons
    Abstract:

    Demosponges are a rich natural source of unusual lipids, some of which are of interest as geochemical biomarkers. Although demosponges are animals, they often host dense communities of microbial symbionts, and it is therefore unclear which lipids can be synthesized by the animal de novo, and which require input from the microbial community. To address this uncertainty, we analyzed the lipids of Amphimdeon Queenslandica, the only demosponge with a published genome. We correlated the genetic and lipid repertoires of A. Queenslandica to identify which biomarkers could potentially be synthesized and/or modified by the sponge. The fatty acid profile of A. Queenslandica is dominated by an unusual Δ^(5,9) fatty acid (cis-5,9-hexacosadienoic acid)—similar to what has been found in other members of the Amphimdeon genus—while the sterol profile is dominated by C_(27)-C_(29( derivatives of cholesterol. Based on our analysis of the A. Queenslandica genome, we predict that this sponge can synthesize sterols de novo, but it lacks critical genes necessary to synthesize basic saturated and unsaturated fatty acids. However, it does appear to have the genes necessary to modify simpler products into a more complex “algal-like” assemblage of unsaturated fatty acids. Ultimately, our results provide additional support for the poriferan affinity of 24-isopropylcholestanes in Neoproterozoic-age rocks (the “sponge biomarker” hypothesis) and suggest that some algal proxies in the geochemical record could also have animal contributions.

  • transcriptomic profiling of the allorecognition response to grafting in the demosponge Amphimedon Queenslandica
    Marine Drugs, 2017
    Co-Authors: Laura F. Grice, Bernhard M Degnan
    Abstract:

    Sponges, despite their simple body plan, discriminate between self and nonself with remarkable specificity. Sponge grafting experiments simulate the effects of natural self or nonself contact under laboratory conditions. Here we take a transcriptomic approach to investigate the temporal response to self and nonself grafts in the marine demosponge Amphimedon Queenslandica. Auto- and allografts were established, observed and sampled over a period of three days, over which time the grafts either rejected or accepted, depending on the identity of the paired individuals, in a replicable and predictable manner. Fourteen transcriptomes were generated that spanned the auto- and allograft responses. Self grafts fuse completely in under three days, and the process appears to be controlled by relatively few genes. In contrast, nonself grafting results in a complete lack of fusion after three days, and appears to involve a broad downregulation of normal biological processes, rather than the mounting of an intense defensive response.

  • Origin and Evolution of the Sponge Aggregation Factor Gene Family
    Molecular Biology and Evolution, 2017
    Co-Authors: Laura F. Grice, Marie Gauthier, Kathrein E. Roper, Xavier Fernàndez-busquets, Sandie M Degnan, Bernhard M Degnan
    Abstract:

    Although discriminating self from nonself is a cardinal animal trait, metazoan allorecognition genes do not appear to be homologous. Here, we characterize the Aggregation Factor (AF) gene family, which encodes putative allorecognition factors in the demosponge Amphimedon Queenslandica, and trace its evolution across 24 sponge (Porifera) species. The AF locus in Amphimedon is comprised of a cluster of five similar genes that encode Calx-beta and Von Willebrand domains and a newly defined Wreath domain, and are highly polymorphic. Further AF variance appears to be generated through individualistic patterns of RNA editing. The AF gene family varies between poriferans, with protein sequences and domains diagnostic of the AF family being present in Amphimedon and other demosponges, but absent from other sponge classes. Within the demosponges, AFs vary widely with no two species having the same AF repertoire or domain organization. The evolution of AFs suggests that their diversification occurs via high allelism, and the continual and rapid gain, loss and shuffling of domains over evolutionary time. Given the marked differences in metazoan allorecognition genes, we propose the rapid evolution of AFs in sponges provides a model for understanding the extensive diversification of self-nonself recognition systems in the animal kingdom.

Sandie M Degnan - One of the best experts on this subject based on the ideXlab platform.

  • Staining and Tracking Methods for Studying Sponge Cell Dynamics.
    Methods in molecular biology (Clifton N.J.), 2020
    Co-Authors: Carole Borchiellini, Sandie M Degnan, Emilie Le Goff, Caroline Rocher, Amélie Vernale, Stephen Baghdiguian, Nina Séjourné, Florent Marschal, André Le Bivic, Nelly Godefroy
    Abstract:

    To better understand the origin of animal cell types, body plans, and other morphological features, further biological knowledge and understanding are needed from non-bilaterian phyla, namely, Placozoa, Ctenophora, and Porifera. This chapter describes recent cell staining approaches that have been developed in three phylogenetically distinct sponge species-the homoscleromorph Oscarella lobularis, and the demosponges Amphimedon Queenslandica and Lycopodina hypogea-to enable analyses of cell death, proliferation, and migration. These methods allow for a more detailed understanding of cellular behaviors and fates, and morphogenetic processes in poriferans, building on current knowledge of sponge cell biology that relies chiefly on classical (static) histological observations.

  • bacterial symbionts in animal development arginine biosynthesis complementation enables larval settlement in a marine sponge
    bioRxiv, 2020
    Co-Authors: Hao Song, Olivia H Hewitt, Sandie M Degnan
    Abstract:

    Larval settlement and metamorphosis are regulated by nitric oxide (NO) signalling in a wide diversity of marine invertebrates (1-10). It is surprising, then, that in most invertebrates, the substrate for NO synthesis - arginine - cannot be biosynthesized but instead must be exogenously sourced (11). In the sponge Amphimedon Queenslandica, vertically-inherited proteobacterial symbionts in the larva are able to biosynthesize arginine (12,13). Here we test the hypothesis that symbionts might provide arginine to the sponge host so that nitric oxide synthase expressed in the larva can produce NO, which induces metamorphosis (8), and the byproduct citrulline (Fig. 1). First, we find support for an arginine-citrulline biosynthetic loop in this sponge larval holobiont using stable isotope tracing. In symbionts, incorporated 13C-citrulline decreases as 13C-arginine increases, consistent with the use of exogenous citrulline for arginine synthesis. In contrast, 13C-citrulline accumulates in larvae as 13C-arginine decreases, demonstrating the uptake of exogenous arginine and its conversion to NO and citrulline. Second, we show that while Amphimedon larvae can derive arginine directly from seawater, normal settlement and metamorphosis can occur in artificial sea water lacking arginine. Together, these results support holobiont complementation of the arginine-citrulline loop and NO biosynthesis in Amphimedon larvae, suggesting a critical role for bacterial symbionts in the development of this marine sponge. Given that NO regulates settlement and metamorphosis in diverse animal phyla (1-10) and arginine is procured externally in most animals (11), we propose that symbionts may play a equally critical regulatory role in this essential life cycle transition in other metazoans. O_FIG O_LINKSMALLFIG WIDTH=95 HEIGHT=200 SRC="FIGDIR/small/240770v1_fig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1625afcorg.highwire.dtl.DTLVardef@438543org.highwire.dtl.DTLVardef@e1fd20org.highwire.dtl.DTLVardef@b155de_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Amphimedon Queenslandica cannot synthesize arginine, which is required for nitric oxide-induced settlement and metamorphosis. A. In A. Queenslandica, nitric oxide (NO) is necessary for completion of larval settlement (Ueda et al.). B. Arginine, which is a necessary precursor for NO synthesis, cannot be synthesized the sponge. Its genome does not code for argininosuccinate synthase and argininosuccinate lyase, but both genes are present in its primary bacterial symbionts. Colored dots next to the enzymes comprising the arginine-citrulline synthesis loop correspond to presence in sponge and symbiont genomes. C. Fluorescence in situ hybridization (FISH) with an AqS1-specific 16S probe showing the distribution and abundance of this symbiont in the larval anterior. The outer epithelial layer (OEL), middle subepithelial layer (SEL) and inner cell mass (ICM) are shown. This symbiont is enriched in the inner cell mass (red; arrows pointing to examples); blue, DAPI-stained sponge cell nuclei. Scale bar 10 m. C_FIG

  • molecular and behavioural evidence that interdependent photo and chemosensory systems regulate larval settlement in a marine sponge
    Molecular Ecology, 2020
    Co-Authors: Tahsha E. Say, Sandie M Degnan
    Abstract:

    Marine pelagic larvae use a hierarchy of environmental cues to identify a suitable benthic habitat on which to settle and metamorphose into the adult phase of the life cycle. Most larvae are induced to settle by biochemical cues and many species have long been known to preferentially settle in the dark. Combined, these data suggest that larval responses to light and biochemical cues may be linked, but this has yet to be explored at the molecular level. Here, we track the vertical position of larvae of the sponge Amphimedon Queenslandica to show that they descend to the benthos at twilight, by which time they are competent to respond to biochemical cues, consistent with them naturally settling in the dark. We use larval settlement assays under three different light regimes, combined with transcriptomics on individual larvae, to identify candidate molecular pathways underlying larval settlement. We find that larvae do not settle in response to biochemical cues if maintained in constant light. Our transcriptome data suggest that constant light actively represses settlement via the sustained up-regulation of two putative inactivators of chemotransduction in constant light only. Our data suggest that photo- and chemosensory systems interact to regulate larval settlement via nitric oxide and cyclic guanosine monophosphate signalling in this sponge, which belongs to one of the earliest-branching animal phyla.

  • co expression of synaptic genes in the sponge Amphimedon Queenslandica uncovers ancient neural submodules
    Scientific Reports, 2019
    Co-Authors: Eunice Wong, Jan Molter, Sandie M Degnan, Victor Anggono, Bernhard M Degnan
    Abstract:

    The synapse is a complex cellular module crucial to the functioning of neurons. It evolved largely through the exaptation of pre-existing smaller submodules, each of which are comprised of ancient sets of proteins that are conserved in modern animals and other eukaryotes. Although these ancient submodules themselves have non-neural roles, it has been hypothesized that they may mediate environmental sensing behaviors in aneural animals, such as sponges. Here we identify orthologues in the sponge Amphimedon Queenslandica of genes encoding synaptic submodules in neural animals, and analyse their cell-type specific and developmental expression to determine their potential to be co-regulated. We find that genes comprising certain synaptic submodules, including those involved in vesicle trafficking, calcium-regulation and scaffolding of postsynaptic receptor clusters, are co-expressed in adult choanocytes and during metamorphosis. Although these submodules may contribute to sensory roles in this cell type and this life cycle stage, total synaptic gene co-expression profiles do not support the existence of a functional synapse in A. Queenslandica. The lack of evidence for the co-regulation of genes necessary for pre- and post-synaptic functioning in A. Queenslandica suggests that sponges, and perhaps the last common ancestor of sponges and other extant animals, had the ability to promulgate sensory inputs without complete synapse-like functionalities. The differential co-expression of multiple synaptic submodule genes in sponge choanocytes, which have sensory and feeding roles, however, is consistent with the metazoan ancestor minimally being able to undergo exo- and endocytosis in a controlled and localized manner.

  • Pluripotency and the origin of animal multicellularity
    Nature, 2019
    Co-Authors: Shunsuke Sogabe, Selene L Fernandez-valverde, William L. Hatleberg, Kathrein E. Roper, Sandie M Degnan, Kevin M. Kocot, Tahsha E. Say, Daniel Stoupin, Bernard M Degnan
    Abstract:

    Comparison of transcriptomes, cell fates and behaviour of three primary cell types from the sponge Amphimedon Queenslandica with choanoflagellates and other unicellular holozoans suggests that the first animal cells transitioned between multiple states. A widely held—but rarely tested—hypothesis for the origin of animals is that they evolved from a unicellular ancestor, with an apical cilium surrounded by a microvillar collar, that structurally resembled modern sponge choanocytes and choanoflagellates^ 1 – 4 . Here we test this view of animal origins by comparing the transcriptomes, fates and behaviours of the three primary sponge cell types—choanocytes, pluripotent mesenchymal archaeocytes and epithelial pinacocytes—with choanoflagellates and other unicellular holozoans. Unexpectedly, we find that the transcriptome of sponge choanocytes is the least similar to the transcriptomes of choanoflagellates and is significantly enriched in genes unique to either animals or sponges alone. By contrast, pluripotent archaeocytes upregulate genes that control cell proliferation and gene expression, as in other metazoan stem cells and in the proliferating stages of two unicellular holozoans, including a colonial choanoflagellate. Choanocytes in the sponge Amphimedon Queenslandica exist in a transient metastable state and readily transdifferentiate into archaeocytes, which can differentiate into a range of other cell types. These sponge cell-type conversions are similar to the temporal cell-state changes that occur in unicellular holozoans^ 5 . Together, these analyses argue against homology of sponge choanocytes and choanoflagellates, and the view that the first multicellular animals were simple balls of cells with limited capacity to differentiate. Instead, our results are consistent with the first animal cell being able to transition between multiple states in a manner similar to modern transdifferentiating and stem cells.

Bernard M Degnan - One of the best experts on this subject based on the ideXlab platform.

  • Pluripotency and the origin of animal multicellularity
    Nature, 2019
    Co-Authors: Shunsuke Sogabe, Selene L Fernandez-valverde, William L. Hatleberg, Kathrein E. Roper, Sandie M Degnan, Kevin M. Kocot, Tahsha E. Say, Daniel Stoupin, Bernard M Degnan
    Abstract:

    Comparison of transcriptomes, cell fates and behaviour of three primary cell types from the sponge Amphimedon Queenslandica with choanoflagellates and other unicellular holozoans suggests that the first animal cells transitioned between multiple states. A widely held—but rarely tested—hypothesis for the origin of animals is that they evolved from a unicellular ancestor, with an apical cilium surrounded by a microvillar collar, that structurally resembled modern sponge choanocytes and choanoflagellates^ 1 – 4 . Here we test this view of animal origins by comparing the transcriptomes, fates and behaviours of the three primary sponge cell types—choanocytes, pluripotent mesenchymal archaeocytes and epithelial pinacocytes—with choanoflagellates and other unicellular holozoans. Unexpectedly, we find that the transcriptome of sponge choanocytes is the least similar to the transcriptomes of choanoflagellates and is significantly enriched in genes unique to either animals or sponges alone. By contrast, pluripotent archaeocytes upregulate genes that control cell proliferation and gene expression, as in other metazoan stem cells and in the proliferating stages of two unicellular holozoans, including a colonial choanoflagellate. Choanocytes in the sponge Amphimedon Queenslandica exist in a transient metastable state and readily transdifferentiate into archaeocytes, which can differentiate into a range of other cell types. These sponge cell-type conversions are similar to the temporal cell-state changes that occur in unicellular holozoans^ 5 . Together, these analyses argue against homology of sponge choanocytes and choanoflagellates, and the view that the first multicellular animals were simple balls of cells with limited capacity to differentiate. Instead, our results are consistent with the first animal cell being able to transition between multiple states in a manner similar to modern transdifferentiating and stem cells.

  • Early origin and deep conservation of enhancers in animals
    2019
    Co-Authors: Emily S. W. Wong, Federico Gaiti, Siew Zhuan Tan, Victoria C. Garside, Gilles Vanwalleghem, Ethan K. Scott, Edwina Mcglinn, Mathias Francois, Bernard M Degnan
    Abstract:

    Abstract Transcription factors (TFs) bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs, the evolution of enhancers has been difficult to trace because of their rapid evolution. Here, we show enhancers from the sponge Amphimedon Queenslandica can drive cell type-specific reporter gene expression in zebrafish and mouse, despite sponge and vertebrate lineages diverging over 700 million years ago. Although sponge enhancers, which are present in both highly conserved syntenic gene regions (Islet–Scaper, Ccne1–Uri and Tdrd3–Diaph3) and sponge-specific intergenic regions, have no significant sequence identity with vertebrate genomic sequences, the type and frequency of TF binding motifs in the sponge enhancer allow for the identification of homologous enhancers in bilaterians. Islet enhancers identified in human and mouse Scaper genes drive zebrafish reporter expression patterns that are almost identical to the sponge Islet enhancer. The existence of homologous enhancers in these disparate metazoans suggests animal development is controlled by TF-enhancer DNA interactions that were present in the first multicellular animals. One-sentence summary Enhancer activity is conserved across 700 million years of trans-phyletic divergence.

  • Long non-coding regulatory RNAs in sponges and insights into the origin of animal multicellularity.
    RNA biology, 2018
    Co-Authors: Federico Gaiti, Bernard M Degnan, Miloš Tanurdžić
    Abstract:

    How animals evolved from a single-celled ancestor over 700 million years ago is poorly understood. Recent transcriptomic and chromatin analyses in the sponge Amphimedon Queenslandica, a morphologically-simple representative of one of the oldest animal phyletic lineages, have shed light on what innovations in the genome and its regulation underlie the emergence of animal multicellularity. Comparisons of the regulatory genome of this sponge with those of more complex bilaterian model species and even simpler unicellular relatives have revealed that fundamental changes in genome regulatory complexity accompanied the evolution of animal multicellularity. Here, we review and discuss the results of these recent investigations by specifically focusing on the contribution of long non-coding RNAs to the evolution of the animal regulatory genome.

  • origin of the animal circadian clock diurnal and light entrained gene expression in the sponge Amphimedon Queenslandica
    Frontiers in Marine Science, 2017
    Co-Authors: Katia Jindrich, Kathrein E. Roper, Bernard M Degnan, Sussan Lemon, Adam M Reitzel, Sandie M Degnan
    Abstract:

    The circadian clock is a molecular network that coordinates organismal behavior and physiology with daily environmental changes in the day-night cycle. In eumetazoans (bilaterians + cnidarians), this network appears to be largely conserved, yet different from other known eukaryotic circadian networks. To determine if the eumetazoan circadian network has an older origin, we ask here whether orthologues comprising this network are expressed in a manner consistent with a role in regulating circadian patterns in a representative of an earlier-branching animal lineage, the sponge Amphimedon Queenslandica. The A. Queenslandica genome encodes orthologues of many eumetazoan circadian genes, including two cryptochrome genes that encode flavoproteins, three Timeout genes, and two PAR-bZIP and seven bHLH-PAS transcription factor genes. There is no apparent Cycle orthologue, although we can identify three closely related ARNT genes. Of the putative circadian genes, only AqPARa and AqCry2 have a consistent oscillating diurnal expression profile, and the rhythmic expression of both these genes is partially lost when the animals are exposed to constant light or darkness. Expression of the other putative circadian genes, in particular AqClock, is neither diurnally-oscillating nor light-dependent. AqPARa and AqCry2 are also temporally and spatially co-expressed throughout embryonic and larval development. Transcripts of these genes are enriched first in cells comprising the larval posterior pigment ring, which is a simple photosensory organ that is responsible for the negative phototactic behaviour displayed by larvae, and subsequently in the larval epithelial and subepithelial layers. The combined findings of no clear Cycle orthologue and of PAR-bZIP and cryptochrome being the only orthologues expressed in a pattern consistent with a circadian role suggests that either (i) the ancestral metazoan circadian network was simpler than the eumetazoan network, or (ii) that this sponge has lost some components, as has occurred in some other animals such as Hydra.

  • An ancient role for nitric oxide in regulating the animal pelagobenthic life cycle: evidence from a marine sponge
    Scientific reports, 2016
    Co-Authors: Nobuo Ueda, Gemma S Richards, Maja Adamska, Bernard M Degnan, Alexandrea M. Kranz, Roger P. Croll, Sandie M Degnan
    Abstract:

    In many marine invertebrates, larval metamorphosis is induced by environmental cues that activate sensory receptors and signalling pathways. Nitric oxide (NO) is a gaseous signalling molecule that regulates metamorphosis in diverse bilaterians. In most cases NO inhibits or represses this process, although it functions as an activator in some species. Here we demonstrate that NO positively regulates metamorphosis in the poriferan Amphimedon Queenslandica. High rates of A. Queenslandica metamorphosis normally induced by a coralline alga are inhibited by an inhibitor of nitric oxide synthase (NOS) and by a NO scavenger. Consistent with this, an artificial donor of NO induces metamorphosis even in the absence of the alga. Inhibition of the ERK signalling pathway prevents metamorphosis in concert with, or downstream of, NO signalling; a NO donor cannot override the ERK inhibitor. NOS gene expression is activated late in embryogenesis and in larvae, and is enriched in specific epithelial and subepithelial cell types, including a putative sensory cell, the globular cell; DAF-FM staining supports these cells being primary sources of NO. Together, these results are consistent with NO playing an activating role in induction of A. Queenslandica metamorphosis, evidence of its highly conserved regulatory role in metamorphosis throughout the Metazoa.

Maja Adamska - One of the best experts on this subject based on the ideXlab platform.

  • An ancient role for nitric oxide in regulating the animal pelagobenthic life cycle: evidence from a marine sponge
    Scientific reports, 2016
    Co-Authors: Nobuo Ueda, Gemma S Richards, Maja Adamska, Bernard M Degnan, Alexandrea M. Kranz, Roger P. Croll, Sandie M Degnan
    Abstract:

    In many marine invertebrates, larval metamorphosis is induced by environmental cues that activate sensory receptors and signalling pathways. Nitric oxide (NO) is a gaseous signalling molecule that regulates metamorphosis in diverse bilaterians. In most cases NO inhibits or represses this process, although it functions as an activator in some species. Here we demonstrate that NO positively regulates metamorphosis in the poriferan Amphimedon Queenslandica. High rates of A. Queenslandica metamorphosis normally induced by a coralline alga are inhibited by an inhibitor of nitric oxide synthase (NOS) and by a NO scavenger. Consistent with this, an artificial donor of NO induces metamorphosis even in the absence of the alga. Inhibition of the ERK signalling pathway prevents metamorphosis in concert with, or downstream of, NO signalling; a NO donor cannot override the ERK inhibitor. NOS gene expression is activated late in embryogenesis and in larvae, and is enriched in specific epithelial and subepithelial cell types, including a putative sensory cell, the globular cell; DAF-FM staining supports these cells being primary sources of NO. Together, these results are consistent with NO playing an activating role in induction of A. Queenslandica metamorphosis, evidence of its highly conserved regulatory role in metamorphosis throughout the Metazoa.

  • Conservation and divergence of bHLH genes in the calcisponge Sycon ciliatum.
    EvoDevo, 2016
    Co-Authors: Sofia A V Fortunato, Michel Vervoort, Marcin Adamski, Maja Adamska
    Abstract:

    Basic Helix-Loop-Helix (bHLH) genes encode a large family of eukaryotic transcription factors, categorized into six high-order groups: pan-eukaryotic group B involved in regulation of cell cycle, metabolism, and development; holozoan-specific groups C and F involved in development and maintenance of homeostasis; and metazoan-specific groups A, D and E including well-studied genes, such as Atonal, Twist and Hairy, with diverse developmental roles including control of morphogenesis and specification of neurons. Current scenarios of bHLH evolution in animals are mainly based on the bHLH gene set found in the genome of demosponge Amphimedon Queenslandica. In this species, the majority of the 21 identified bHLH genes belong to group B, and the single group A gene is orthologous to several neurogenic bilaterian subfamilies, including atonal and neurogenin.

  • Surprisingly rich repertoire of Wnt genes in the demosponge Halisarca dujardini
    BMC Evolutionary Biology, 2016
    Co-Authors: Ilya Borisenko, Marcin Adamski, Alexander V. Ereskovsky, Maja Adamska
    Abstract:

    Background Wnt proteins are secreted signalling molecules found in all animal phyla. In bilaterian animals, including humans, Wnt proteins play key roles in development, maintenance of homeostasis and regeneration. While Wnt gene repertoires and roles are strongly conserved between cnidarians and bilaterians, Wnt genes from basal metazoans (sponges, ctenophores, placozoans) are difficult or impossible to assign to the bilaterian + cnidarian orthologous groups. Moreover, dramatic differences in Wnt numbers among basal metazoan exist, with only three present in the genome of Amphimedon Queenslandica, a demosponge, and 21 in the genome of Sycon ciliatum, a calcisponge. To gain insight into the ancestral Wnt repertoire and function, we have chosen to investigate Wnt genes in Halisarca dujardini, a demosponge with relatively well described development and regeneration, and a very distant phylogenetic relationship to Amphimedon.

  • Additional file 2: of Surprisingly rich repertoire of Wnt genes in the demosponge Halisarca dujardini
    2016
    Co-Authors: Ilya Borisenko, Marcin Adamski, Alexander V. Ereskovsky, Maja Adamska
    Abstract:

    wnt.tree.nwk.txt: Newick format Bayesian inference gene tree of Wnt ligands. Species: Amq, Amphimedon Queenslandica, Ate, Achaearanea (Parasteatoda) tepidariorum, Bf, Branchiostoma floridae, Cte, Capitella teleta, Hdu, Halisarca dujardini, Hs, Homo sapiens, Lgi, Lottia gigantea, Ml, Mnemiopsis leidyi, Nv, Nematostella vectensis, Oca, Oscarella carmela, Olo, Oscarella lobularis, Sci, Sycon ciliatum, Sko, Saccoglossus kowalewski, Spu, Strongylocentrotus purpuratus, Tc, Tribolium castaneum. (TXT 3 kb

  • Additional file 1: of Surprisingly rich repertoire of Wnt genes in the demosponge Halisarca dujardini
    2016
    Co-Authors: Ilya Borisenko, Marcin Adamski, Alexander V. Ereskovsky, Maja Adamska
    Abstract:

    wnt.alignment.nex.txt: trimmed alignment of Wnt protein sequences used to generate Bayesian inference trees shown in Additional file 1 and Fig. 1. Species: Amq, Amphimedon Queenslandica, Ate, Achaearanea (Parasteatoda) tepidariorum, Bf, Branchiostoma floridae, Cte, Capitella teleta, Hdu, Halisarca dujardini, Hs, Homo sapiens, Lgi, Lottia gigantea, Ml, Mnemiopsis leidyi, Nv, Nematostella vectensis, Oca, Oscarella carmela, Olo, Oscarella lobularis, Sci, Sycon ciliatum, Sko, Saccoglossus kowalewski, Spu, Strongylocentrotus purpuratus, Tc, Tribolium castaneum. (TXT 39 kb

Kenneth S Kosik - One of the best experts on this subject based on the ideXlab platform.

  • detection of prokaryotic genes in the Amphimedon Queenslandica genome
    PLOS ONE, 2016
    Co-Authors: Cecilia Conaco, Pantelis Tsoulfas, Amanda Dolan, Onur Sakarya, John H Werren, Kenneth S Kosik
    Abstract:

    Horizontal gene transfer (HGT) is common between prokaryotes and phagotrophic eukaryotes. In metazoans, the scale and significance of HGT remains largely unexplored but is usually linked to a close association with parasites and endosymbionts. Marine sponges (Porifera), which host many microorganisms in their tissues and lack an isolated germ line, are potential carriers of genes transferred from prokaryotes. In this study, we identified a number of potential horizontally transferred genes within the genome of the sponge, Amphimedon Queenslandica. We further identified homologs of some of these genes in other sponges. The transferred genes, most of which possess catalytic activity for carbohydrate or protein metabolism, have assimilated host genome characteristics and are actively expressed. The diversity of functions contributed by the horizontally transferred genes is likely an important factor in the adaptation and evolution of A. Queenslandica. These findings highlight the potential importance of HGT on the success of sponges in diverse ecological niches.

  • Transcriptome profiling of the demosponge Amphimedon Queenslandica reveals genome-wide events that accompany major life cycle transitions
    BMC Genomics, 2012
    Co-Authors: Cecilia Conaco, Sandie M Degnan, Bernard M Degnan, Pierre Neveu, Hongjun Zhou, Mary Luz Arcila, Kenneth S Kosik
    Abstract:

    Background The biphasic life cycle with pelagic larva and benthic adult stages is widely observed in the animal kingdom, including the Porifera (sponges), which are the earliest branching metazoans. The demosponge, Amphimedon Queenslandica , undergoes metamorphosis from a free-swimming larva into a sessile adult that bears no morphological resemblance to other animals. While the genome of A. Queenslandica contains an extensive repertoire of genes very similar to that of complex bilaterians, it is as yet unclear how this is drawn upon to coordinate changing morphological features and ecological demands throughout the sponge life cycle. Results To identify genome-wide events that accompany the pelagobenthic transition in A. Queenslandica , we compared global gene expression profiles at four key developmental stages by sequencing the poly(A) transcriptome using SOLiD technology. Large-scale changes in transcription were observed as sponge larvae settled on the benthos and began metamorphosis. Although previous systematics suggest that the only clear homology between Porifera and other animals is in the embryonic and larval stages, we observed extensive use of genes involved in metazoan-associated cellular processes throughout the sponge life cycle. Sponge-specific transcripts are not over-represented in the morphologically distinct adult; rather, many genes that encode typical metazoan features, such as cell adhesion and immunity, are upregulated. Our analysis further revealed gene families with candidate roles in competence, settlement, and metamorphosis in the sponge, including transcription factors, G-protein coupled receptors and other signaling molecules. Conclusions This first genome-wide study of the developmental transcriptome in an early branching metazoan highlights major transcriptional events that accompany the pelagobenthic transition and point to a network of regulatory mechanisms that coordinate changes in morphology with shifting environmental demands. Metazoan developmental and structural gene orthologs are well-integrated into the expression profiles at every stage of sponge development, including the adult. The utilization of genes involved in metazoan-associated processes throughout sponge development emphasizes the potential of the genome of the last common ancestor of animals to generate phenotypic complexity.

  • transcriptome profiling of the demosponge Amphimedon Queenslandica reveals genome wide events that accompany major life cycle transitions
    BMC Genomics, 2012
    Co-Authors: Cecilia Conaco, Sandie M Degnan, Bernard M Degnan, Pierre Neveu, Hongjun Zhou, Mary Luz Arcila, Kenneth S Kosik
    Abstract:

    The biphasic life cycle with pelagic larva and benthic adult stages is widely observed in the animal kingdom, including the Porifera (sponges), which are the earliest branching metazoans. The demosponge, Amphimedon Queenslandica, undergoes metamorphosis from a free-swimming larva into a sessile adult that bears no morphological resemblance to other animals. While the genome of A. Queenslandica contains an extensive repertoire of genes very similar to that of complex bilaterians, it is as yet unclear how this is drawn upon to coordinate changing morphological features and ecological demands throughout the sponge life cycle. To identify genome-wide events that accompany the pelagobenthic transition in A. Queenslandica, we compared global gene expression profiles at four key developmental stages by sequencing the poly(A) transcriptome using SOLiD technology. Large-scale changes in transcription were observed as sponge larvae settled on the benthos and began metamorphosis. Although previous systematics suggest that the only clear homology between Porifera and other animals is in the embryonic and larval stages, we observed extensive use of genes involved in metazoan-associated cellular processes throughout the sponge life cycle. Sponge-specific transcripts are not over-represented in the morphologically distinct adult; rather, many genes that encode typical metazoan features, such as cell adhesion and immunity, are upregulated. Our analysis further revealed gene families with candidate roles in competence, settlement, and metamorphosis in the sponge, including transcription factors, G-protein coupled receptors and other signaling molecules. This first genome-wide study of the developmental transcriptome in an early branching metazoan highlights major transcriptional events that accompany the pelagobenthic transition and point to a network of regulatory mechanisms that coordinate changes in morphology with shifting environmental demands. Metazoan developmental and structural gene orthologs are well-integrated into the expression profiles at every stage of sponge development, including the adult. The utilization of genes involved in metazoan-associated processes throughout sponge development emphasizes the potential of the genome of the last common ancestor of animals to generate phenotypic complexity.