Animal Evolution: Looking for the First Nervous System
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Basal Metazoans - Dirk Erpenbeck, Simion Paul, Michael Manuel, Paulyn Cartwright, Oliver Voigt and Gert Worheide
EVOLUTION OF PHYLOGENETIC TREE OF LIFE - Basal Metazoans - Dirk Erpenbeck, Simion Paul, Michael Manuel, Paulyn Cartwright, Oliver Voigt and Gert Worheide BASAL METAZOANS Dirk Erpenbeck Ludwig-Maximilians Universität München, Germany Simion Paul and Michaël Manuel Université Pierre et Marie Curie in Paris, France. Paulyn Cartwright University of Kansas USA. Oliver Voigt and Gert Wörheide Ludwig-Maximilians Universität München, Germany Keywords: Metazoa, Porifera, sponges, Placozoa, Cnidaria, anthozoans, jellyfishes, Ctenophora, comb jellies Contents 1. Introduction on ―Basal Metazoans‖ 2. Phylogenetic relationships among non-bilaterian Metazoa 3. Porifera (Sponges) 4. Placozoa 5. Ctenophora (Comb-jellies) 6. Cnidaria 7. Cultural impact and relevance to human welfare Glossary Bibliography Biographical Sketch Summary Basal metazoans comprise the four non-bilaterian animal phyla Porifera (sponges), Cnidaria (anthozoans and jellyfishes), Placozoa (Trichoplax) and Ctenophora (comb jellies). The phylogenetic position of these taxa in the animal tree is pivotal for our understanding of the last common metazoan ancestor and the character evolution all Metazoa,UNESCO-EOLSS but is much debated. Morphological, evolutionary, internal and external phylogenetic aspects of the four phyla are highlighted and discussed. SAMPLE CHAPTERS 1. Introduction on “Basal Metazoans” In many textbooks the term ―lower metazoans‖ still refers to an undefined assemblage of invertebrate phyla, whose phylogenetic relationships were rather undefined. This assemblage may contain both bilaterian and non-bilaterian taxa. Currently, ―Basal Metazoa‖ refers to non-bilaterian animals only, four phyla that lack obvious bilateral symmetry, Porifera, Placozoa, Cnidaria and Ctenophora. ©Encyclopedia of Life Support Systems (EOLSS) EVOLUTION OF PHYLOGENETIC TREE OF LIFE - Basal Metazoans - Dirk Erpenbeck, Simion Paul, Michael Manuel, Paulyn Cartwright, Oliver Voigt and Gert Worheide These four phyla have classically been known as ―diploblastic‖ Metazoa. -
Animal Evolution: Trichoplax, Trees, and Taxonomic Turmoil
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Dispatch R1003 Dispatches Animal Evolution: Trichoplax, Trees, and Taxonomic Turmoil The genome sequence of Trichoplax adhaerens, the founding member of the into the same major classes (C, E/F enigmatic animal phylum Placozoa, has revealed that a surprising level of and B) as do those described from genetic complexity underlies its extremely simple body plan, indicating either Amphimedon [4]. Consistent with that placozoans are secondarily simple or that there is an undiscovered a more derived position, however, morphologically complex life stage. Trichoplax has a number of Antp superclass Hox genes that are absent David J. Miller1 and Eldon E. Ball2 but no other axial differentiation, from the sponge Amphimedon. resembling an amoeba. Grell [3] who These include the ‘ParaHox’ gene With the recent or imminent release formally described these common but Trox-2 [5] and the extended Hox of the whole genome sequences of inconspicuous marine organisms as family gene Not [6] known from a number of key animal species, this belonging to a new phylum, assumed previous work. Particularly intriguing is an exciting time for the ‘evo-devo’ that their simplicity is primary, and is the discovery in Trichoplax of many community. In the last twelve months, that they therefore must represent genes associated with neuroendocrine whole genome analyses of the a key stage in animal evolution. This function across the Bilateria; in cnidarian Nematostella vectensis, view is still held by several prominent common with Amphimedon [7], many the choanoflagellate Monosiga Trichoplax biologists, but has always elements of the post-synaptic scaffold brevicollis and the cephalochordate been contentious; the view that it is are present, but so too are channel Branchiostoma floridae (commonly derived from a more complex ancestor and receptor proteins not known from known as amphioxus) have been has recently been gaining momentum sponges. -
Implications for Proteasome Nuclear Localization Revealed by the Structure of the Nuclear Proteasome Tether Protein Cut8
Implications for proteasome nuclear localization revealed by the structure of the nuclear proteasome tether protein Cut8 Kojiro Takedaa, Nam K. Tonthatb, Tiffany Gloverc, Weijun Xuc, Eugene V. Koonind, Mitsuhiro Yanagidaa, and Maria A. Schumacherb,1 aG0 Cell Unit; Okinawa Institute of Science and Technology (OIST); 1919-1 Tancha, Onna, Okinawa, Japan; bDepartment of Biochemistry, Duke University Medical Center, Room 243A Nanaline H. Duke Building, Box 3711, Durham, NC 27710; cDepartment of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Unit 1000, Houston, TX 77030; and dNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892 Edited by Axel T. Brunger, Stanford University, Stanford, CA, and approved August 29, 2011 (received for review March 7, 2011) Degradation of nuclear proteins by the 26S proteasome is essential ultimately found to be a delay in the destruction of the mitotic for cell viability. In yeast, the nuclear envelope protein Cut8 med- cyclin and securin (13). However, the polyubiquitination of these iates nuclear proteasomal sequestration by an uncharacterized proteins was normal, suggesting a role for the proteasome. Sub- mechanism. Here we describe structures of Schizosaccharomyces sequent studies showed that Cut8 is responsible for sequestering pombe Cut8, which shows that it contains a unique, modular the 26S proteasome to the nucleus (10, 11). Cut8 was found to be fold composed of an extended N-terminal, lysine-rich segment localized to the nuclear envelope and overlapping the location that when ubiquitinated binds the proteasome, a dimer domain of the proteasome (17–21). An interaction between Cut8 and followed by a six-helix bundle connected to a flexible C tail. -
Expression of Immunoproteasome Genes Is Regulated by Cell-Intrinsic
www.nature.com/scientificreports OPEN Expression of immunoproteasome genes is regulated by cell-intrinsic and –extrinsic factors in human Received: 06 April 2016 Accepted: 06 September 2016 cancers Published: 23 September 2016 Alexandre Rouette1,2,*, Assya Trofimov1,2,3,*, David Haberl1, Geneviève Boucher1, Vincent-Philippe Lavallée1,2,4,5, Giovanni D’Angelo4,5, Josée Hébert1,2,4,5, Guy Sauvageau1,2,4,5, Sébastien Lemieux1,3 & Claude Perreault1,2,4 Based on transcriptomic analyses of thousands of samples from The Cancer Genome Atlas, we report that expression of constitutive proteasome (CP) genes (PSMB5, PSMB6, PSMB7) and immunoproteasome (IP) genes (PSMB8, PSMB9, PSMB10) is increased in most cancer types. In breast cancer, expression of IP genes was determined by the abundance of tumor infiltrating lymphocytes and high expression of IP genes was associated with longer survival. In contrast, IP upregulation in acute myeloid leukemia (AML) was a cell-intrinsic feature that was not associated with longer survival. Expression of IP genes in AML was IFN-independent, correlated with the methylation status of IP genes, and was particularly high in AML with an M5 phenotype and/or MLL rearrangement. Notably, PSMB8 inhibition led to accumulation of polyubiquitinated proteins and cell death in IPhigh but not IPlow AML cells. Co-clustering analysis revealed that genes correlated with IP subunits in non-M5 AMLs were primarily implicated in immune processes. However, in M5 AML, IP genes were primarily co-regulated with genes involved in cell metabolism and proliferation, mitochondrial activity and stress responses. We conclude that M5 AML cells can upregulate IP genes in a cell-intrinsic manner in order to resist cell stress. -
The Phylogeography of the Placozoa Suggests a Taxonrich Phylum In
Molecular Ecology (2010) 19, 2315–2327 doi: 10.1111/j.1365-294X.2010.04617.x The phylogeography of the Placozoa suggests a taxon-rich phylum in tropical and subtropical waters M. EITEL* and B. SCHIERWATER*† *Tiera¨rztliche Hochschule Hannover, ITZ, Ecology and Evolution, Bu¨nteweg 17d, D-30559 Hannover, Germany, †American Museum of Natural History, New York, Division of Invertebrate Zoology, 79 St at Central Park West, New York, NY 10024, USA Abstract Placozoa has been a key phylum for understanding early metazoan evolution. Yet this phylum is officially monotypic and with respect to its general biology and ecology has remained widely unknown. Worldwide sampling and sequencing of the mitochondrial large ribosomal subunit (16S) reveals a cosmopolitan distribution in tropical and subtropical waters of genetically different clades. We sampled a total of 39 tropical and subtropical locations worldwide and found 23 positive sites for placozoans. The number of genetically characterized sites was thereby increased from 15 to 37. The new sampling identified the first genotypes from two new oceanographic regions, the Eastern Atlantic and the Indian Ocean. We found seven out of 11 previously known haplotypes as well as five new haplotypes. One haplotype resembles a new genetic clade, increasing the number of clades from six to seven. Some of these clades seem to be cosmopolitan whereas others appear to be endemic. The phylogeography also shows that different clades occupy different ecological niches and identifies several euryoecious haplotypes with a cosmopolitic distribution as well as some stenoecious haplotypes with an endemic distribution. Haplotypes of different clades differ substantially in their phylogeographic distribution according to latitude. -
Biophysical Analyses of the Oxygen Sensing Prolyl Hydroxylase from the Simplest Animal Trichoplax Adhaerens
Journal name: Hypoxia Article Designation: Original Research Year: 2018 Volume: 6 Hypoxia Dovepress Running head verso: Lippl et al Running head recto: Biophysical analyses of the oxygen sensing PHDs from the simplest animal T. adhaerens open access to scientific and medical research DOI: http://dx.doi.org/10.2147/HP.S174655 Open Access Full Text Article ORIGINAL RESEARCH Born to sense: biophysical analyses of the oxygen sensing prolyl hydroxylase from the simplest animal Trichoplax adhaerens Kerstin Lippl Background: In humans and other animals, the chronic hypoxic response is mediated by Anna Boleininger hypoxia inducible transcription factors (HIFs) which regulate the expression of genes that Michael A McDonough counteract the effects of limiting oxygen. Prolyl hydroxylases (PHDs) act as hypoxia sensors Martine I Abboud for the HIF system in organisms ranging from humans to the simplest animal Trichoplax Hanna Tarhonskaya adhaerens. We report structural and biochemical studies on the T. adhaerens HIF prolyl hydroxy- Rasheduzzaman Chowdhury Methods: lase (TaPHD) that inform about the evolution of hypoxia sensing in animals. Christoph Loenarz Results: High resolution crystal structures (≤1.3 Å) of TaPHD, with and without its HIFα Christopher J Schofield substrate, reveal remarkable conservation of key active site elements between T. adhaerens and Chemistry Research Laboratory, human PHDs, which also manifest in kinetic comparisons. University of Oxford, Oxford, UK Conclusion: Conserved structural features of TaPHD and human PHDs include those appar- ently enabling the slow binding/reaction of oxygen with the active site Fe(II), the formation of a stable 2-oxoglutarate complex, and a stereoelectronically promoted change in conformation of the hydroxylated proline-residue. -
Systema Naturae. the Classification of Living Organisms
Systema Naturae. The classification of living organisms. c Alexey B. Shipunov v. 5.601 (June 26, 2007) Preface Most of researches agree that kingdom-level classification of living things needs the special rules and principles. Two approaches are possible: (a) tree- based, Hennigian approach will look for main dichotomies inside so-called “Tree of Life”; and (b) space-based, Linnaean approach will look for the key differences inside “Natural System” multidimensional “cloud”. Despite of clear advantages of tree-like approach (easy to develop rules and algorithms; trees are self-explaining), in many cases the space-based approach is still prefer- able, because it let us to summarize any kinds of taxonomically related da- ta and to compare different classifications quite easily. This approach also lead us to four-kingdom classification, but with different groups: Monera, Protista, Vegetabilia and Animalia, which represent different steps of in- creased complexity of living things, from simple prokaryotic cell to compound Nature Precedings : doi:10.1038/npre.2007.241.2 Posted 16 Aug 2007 eukaryotic cell and further to tissue/organ cell systems. The classification Only recent taxa. Viruses are not included. Abbreviations: incertae sedis (i.s.); pro parte (p.p.); sensu lato (s.l.); sedis mutabilis (sed.m.); sedis possi- bilis (sed.poss.); sensu stricto (s.str.); status mutabilis (stat.m.); quotes for “environmental” groups; asterisk for paraphyletic* taxa. 1 Regnum Monera Superphylum Archebacteria Phylum 1. Archebacteria Classis 1(1). Euryarcheota 1 2(2). Nanoarchaeota 3(3). Crenarchaeota 2 Superphylum Bacteria 3 Phylum 2. Firmicutes 4 Classis 1(4). Thermotogae sed.m. 2(5). -
Global Diversity of the Placozoa
Review Global Diversity of the Placozoa Michael Eitel1,2*, Hans-Ju¨ rgen Osigus1, Rob DeSalle3, Bernd Schierwater1,3,4 1 Stiftung Tiera¨rztliche Hochschule Hannover, Institut fu¨r Tiero¨kologie und Zellbiologie, Ecology and Evolution, Hannover, Germany, 2 The Swire Institute of Marine Science, Faculty of Science, School of Biological Sciences, The University of Hong Kong, Hong Kong, 3 Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America, 4 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America ‘Urmetazoon’ ([7,33]; for a historical summary of placozoan Abstract: The enigmatic animal phylum Placozoa holds a research see [34–36]). More than a century after the discovery of key position in the metazoan Tree of Life. A simple Trichoplax adhaerens the phylum status of the Placozoa – as bauplan makes it appear to be the most basal metazoan envisioned by Schulze – was finally accepted. known and genetic evidence also points to a position It is important to note that animals described as Trichoplax close to the last common metazoan ancestor. Trichoplax adhaerens in Grell and colleagues’ studies might, although being adhaerens is the only formally described species in the morphologically highly similar to Schulze’s Trichoplax, actually phylum to date, making the Placozoa the only monotypic phylum in the animal kingdom. However, recent molec- belong to a different species. Given our current knowledge of ular genetic as well as morphological studies have placozoan diversity (see below) it is evident that the various studies identified a high level of diversity, and hence a potential of placozoans accomplished over the years have pooled a broad high level of taxonomic diversity, within this phylum. -
The Evolution of the Mitochondrial Genomes of Calcareous Sponges and Cnidarians Ehsan Kayal Iowa State University
Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2012 The evolution of the mitochondrial genomes of calcareous sponges and cnidarians Ehsan Kayal Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Evolution Commons, and the Molecular Biology Commons Recommended Citation Kayal, Ehsan, "The ve olution of the mitochondrial genomes of calcareous sponges and cnidarians" (2012). Graduate Theses and Dissertations. 12621. https://lib.dr.iastate.edu/etd/12621 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. The evolution of the mitochondrial genomes of calcareous sponges and cnidarians by Ehsan Kayal A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Ecology and Evolutionary Biology Program of Study Committee Dennis V. Lavrov, Major Professor Anne Bronikowski John Downing Eric Henderson Stephan Q. Schneider Jeanne M. Serb Iowa State University Ames, Iowa 2012 Copyright 2012, Ehsan Kayal ii TABLE OF CONTENTS ABSTRACT .......................................................................................................................................... -
A Self-Marker-Like Protein Governs Hemocyte Allorecognition In
Ema et al. Zoological Letters (2019) 5:34 https://doi.org/10.1186/s40851-019-0149-8 RESEARCH ARTICLE Open Access A self-marker-like protein governs hemocyte allorecognition in Halocynthia roretzi Masaki Ema1†, Taizo Okada1†, Miki Takahashi1†, Masato Uchiyama1†, Hideo Kubo2, Hideaki Moriyama3, Hitoshi Miyakawa4 and Midori Matsumoto1* Abstract Background: Self-incompatibility, fusion/non-fusion reactions, and contact reactions (CRs) have all been identified as allorecognition phenomena in ascidians. CR is a reaction characteristic of the hemocytes of Halocynthia roretzi, whereby they release phenol oxidase (PO) upon contact with non-self hemocytes. Thus, these cells may represent a primitive form of the vertebrate immune system. In the present study, we focused on the CR of H. roretzi hemocytes and sought to identify self-marker proteins that distinguish between self and non-self cells. Results: We initially generated a CR-inducing monoclonal antibody against the complete hemocyte membrane- protein complement (mAb11B16B10). This antibody was identified based on the differential induction of PO activity in individual organisms. The level of PO activity induced by this antibody in individual ascidians was consistent with the observed CR-induced PO activity. mAb11B16B10 recognized a series of 12 spots corresponding to a 100-kDa protein, with differing isoelectric points (pIs). A comparison of the 2D electrophoresis gels of samples from CR- reactive/non-reactive individuals revealed that some spots in this series in hemocytes were common to the CR- non-inducible individuals, but not to CR-inducible individuals. We cloned the corresponding gene and named it Halocynthia roretzi self-marker-like protein-1 (HrSMLP1). This gene is similar to the glycoprotein DD3–3 found in Dictyostelium, and is conserved in invertebrates. -
Lack of Activity of Recombinant HIF Prolyl Hydroxylases
RESEARCH ARTICLE Lack of activity of recombinant HIF prolyl hydroxylases (PHDs) on reported non-HIF substrates Matthew E Cockman1†*, Kerstin Lippl2†, Ya-Min Tian3†, Hamish B Pegg1, William D Figg Jnr2, Martine I Abboud2, Raphael Heilig4, Roman Fischer4, Johanna Myllyharju5‡, Christopher J Schofield2‡, Peter J Ratcliffe1,3‡* 1The Francis Crick Institute, London, United Kingdom; 2Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom; 3Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom; 4Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom; 5Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland Abstract Human and other animal cells deploy three closely related dioxygenases (PHD 1, 2 and 3) to signal oxygen levels by catalysing oxygen regulated prolyl hydroxylation of the transcription factor HIF. The discovery of the HIF prolyl-hydroxylase (PHD) enzymes as oxygen sensors raises a key question as to the existence and nature of non-HIF substrates, potentially transducing other biological responses to hypoxia. Over 20 such substrates are reported. We therefore sought to *For correspondence: characterise their reactivity with recombinant PHD enzymes. Unexpectedly, we did not detect [email protected] prolyl-hydroxylase activity on any reported non-HIF protein or peptide, using conditions supporting (MEC); robust HIF-a hydroxylation. We cannot exclude PHD-catalysed prolyl hydroxylation occurring under [email protected] (PJR) conditions other than those we have examined. However, our findings using recombinant enzymes †These authors contributed provide no support for the wide range of non-HIF PHD substrates that have been reported. -
Six Major Steps in Animal Evolution: Are We Derived Sponge Larvae?
EVOLUTION & DEVELOPMENT 10:2, 241–257 (2008) Six major steps in animal evolution: are we derived sponge larvae? Claus Nielsen Zoological Museum (The Natural History Museum of Denmark, University of Copenhagen), Universitetsparken 15, DK-2100 Copenhagen, Denmark Correspondence (email: [email protected]) SUMMARY A review of the old and new literature on animal became sexually mature, and the adult sponge-stage was morphology/embryology and molecular studies has led me to abandoned in an extreme progenesis. This eumetazoan the following scenario for the early evolution of the metazoans. ancestor, ‘‘gastraea,’’ corresponds to Haeckel’s gastraea. The metazoan ancestor, ‘‘choanoblastaea,’’ was a pelagic Trichoplax represents this stage, but with the blastopore spread sphere consisting of choanocytes. The evolution of multicellularity out so that the endoderm has become the underside of the enabled division of labor between cells, and an ‘‘advanced creeping animal. Another lineage developed a nervous system; choanoblastaea’’ consisted of choanocytes and nonfeeding cells. this ‘‘neurogastraea’’ is the ancestor of the Neuralia. Cnidarians Polarity became established, and an adult, sessile stage have retained this organization, whereas the Triploblastica developed. Choanocytes of the upper side became arranged in (Ctenophora1Bilateria), have developed the mesoderm. The a groove with the cilia pumping water along the groove. Cells bilaterians developed bilaterality in a primitive form in the overarched the groove so that a choanocyte chamber was Acoelomorpha and in an advanced form with tubular gut and formed, establishing the body plan of an adult sponge; the pelagic long Hox cluster in the Eubilateria (Protostomia1Deuterostomia). larval stage was retained but became lecithotrophic. The It is indicated that the major evolutionary steps are the result of sponges radiated into monophyletic Silicea, Calcarea, and suites of existing genes becoming co-opted into new networks Homoscleromorpha.