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Lateral Gene Transfer of Anion-Conducting Channelrhodopsins Between Green Algae and Giant Viruses
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.15.042127; this version posted April 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 5 Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses Andrey Rozenberg 1,5, Johannes Oppermann 2,5, Jonas Wietek 2,3, Rodrigo Gaston Fernandez Lahore 2, Ruth-Anne Sandaa 4, Gunnar Bratbak 4, Peter Hegemann 2,6, and Oded 10 Béjà 1,6 1Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel. 2Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, Berlin 10115, Germany. 3Present address: Department of Neurobiology, Weizmann 15 Institute of Science, Rehovot 7610001, Israel. 4Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway. 5These authors contributed equally: Andrey Rozenberg, Johannes Oppermann. 6These authors jointly supervised this work: Peter Hegemann, Oded Béjà. e-mail: [email protected] ; [email protected] 20 ABSTRACT Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity 1,2. Four ChR families are currently known. Green algal 3–5 and cryptophyte 6 cation-conducting ChRs (CCRs), cryptophyte anion-conducting ChRs (ACRs) 7, and the MerMAID ChRs 8. Here we 25 report the discovery of a new family of phylogenetically distinct ChRs encoded by marine giant viruses and acquired from their unicellular green algal prasinophyte hosts. -
Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes
G C A T T A C G G C A T genes Article Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes Yuxin Hu 1,2, Weiyue Xing 1,2, Zhengyu Hu 3 and Guoxiang Liu 1,* 1 Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; [email protected] (Y.H.); [email protected] (W.X.) 2 School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China 3 State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; [email protected] * Correspondence: [email protected]; Tel.: +86-027-6878-0576 Received: 11 December 2019; Accepted: 15 January 2020; Published: 20 January 2020 Abstract: We sequenced the mitochondrial genome of six colonial volvocine algae, namely: Pandorina morum, Pandorina colemaniae, Volvulina compacta, Colemanosphaera angeleri, Colemanosphaera charkowiensi, and Yamagishiella unicocca. Previous studies have typically reconstructed the phylogenetic relationship between colonial volvocine algae based on chloroplast or nuclear genes. Here, we explore the validity of phylogenetic analysis based on mitochondrial protein-coding genes. Wefound phylogenetic incongruence of the genera Yamagishiella and Colemanosphaera. In Yamagishiella, the stochastic error and linkage group formed by the mitochondrial protein-coding genes prevent phylogenetic analyses from reflecting the true relationship. In Colemanosphaera, a different reconstruction approach revealed a different phylogenetic relationship. This incongruence may be because of the influence of biological factors, such as incomplete lineage sorting or horizontal gene transfer. We also analyzed the substitution rates in the mitochondrial and chloroplast genomes between colonial volvocine algae. -
The Phosphatidylethanolamine-Binding Protein DTH1 Mediates Degradation of Lipid Droplets in Chlamydomonas Reinhardtii
The phosphatidylethanolamine-binding protein DTH1 mediates degradation of lipid droplets in Chlamydomonas reinhardtii Jihyeon Leea, Yasuyo Yamaokab, Fantao Kongc, Caroline Cagnond, Audrey Beyly-Adrianod, Sunghoon Jangb, Peng Gaoe, Byung-Ho Kange, Yonghua Li-Beissond,1, and Youngsook Leeb,1 aDivision of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 37673 Pohang, Korea; bDepartment of Life Sciences, Pohang University of Science and Technology, 37673 Pohang, Korea; cLaboratory of Marine Biotechnology, School of Bioengineering, Dalian University of Technology, 116024 Dalian, China; dAix-Marseille University, The Commission for Atomic Energy and Alternative Energies (CEA), CNRS, Institut de Biosciences et Biotechnologies Aix-Marseille (BIAM), CEA Cadarache, Saint Paul-Lez-Durance 13108, France; and eState Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong 999077, China Edited by Krishna K. Niyogi, University of California, Berkeley, CA, and approved August 3, 2020 (received for review March 27, 2020) Lipid droplets (LDs) are intracellular organelles found in a wide plant (17), and ∼200 in the model green microalga Chlamydo- range of organisms and play important roles in stress tolerance. monas reinhardtii (18–20). LD-associated proteins fall into sev- During nitrogen (N) starvation, Chlamydomonas reinhardtii stores eral major functional groups: 1) major structural proteins such as large amounts of triacylglycerols (TAGs) inside LDs. When N is oleosin, perilipin, and the major lipid droplet protein (MLDP) resupplied, the LDs disappear and the TAGs are degraded, presum- (2, 18, 21); 2) TAG biosynthetic enzymes, e.g., diacylglycerol ably providing carbon and energy for regrowth. The mechanism acyltransferases (DGATs) (3, 22, 23) and phospholipid:diacyl- by which cells degrade LDs is poorly understood. -
Evolution of Cytokinesis-Related Protein Localization During The
Arakaki et al. BMC Evolutionary Biology (2017) 17:243 DOI 10.1186/s12862-017-1091-z RESEARCH ARTICLE Open Access Evolution of cytokinesis-related protein localization during the emergence of multicellularity in volvocine green algae Yoko Arakaki1, Takayuki Fujiwara2, Hiroko Kawai-Toyooka1, Kaoru Kawafune1,3, Jonathan Featherston4,5, Pierre M. Durand4,6, Shin-ya Miyagishima2 and Hisayoshi Nozaki1* Abstract Background: The volvocine lineage, containing unicellular Chlamydomonas reinhardtii and differentiated multicellular Volvox carteri, is a powerful model for comparative studies aiming at understanding emergence of multicellularity. Tetrabaena socialis is the simplest multicellular volvocine alga and belongs to the family Tetrabaenaceae that is sister to more complex multicellular volvocine families, Goniaceae and Volvocaceae. Thus, T. socialis is a key species to elucidate the initial steps in the evolution of multicellularity. In the asexual life cycle of C. reinhardtii and multicellular volvocine species, reproductive cells form daughter cells/colonies by multiple fission. In embryogenesis of the multicellular species, daughter protoplasts are connected to one another by cytoplasmic bridges formed by incomplete cytokinesis during multiple fission. These bridges are important for arranging the daughter protoplasts in appropriate positions such that species-specific integrated multicellular individuals are shaped. Detailed comparative studies of cytokinesis between unicellular and simple multicellular volvocine species will help to elucidate the emergence of multicellularity from the unicellular ancestor. However, the cytokinesis-related genes between closely related unicellular and multicellular species have not been subjected to a comparative analysis. Results: Here we focused on dynamin-related protein 1 (DRP1), which is known for its role in cytokinesis in land plants. Immunofluorescence microscopy using an antibody against T. -
18S Ribosomal RNA Gene Phylogeny of a Colonial Volvocalean Lineage (Tetrabaenaceae-Goniaceae-Volvocaceae, Volvocales, Chlorophyceae) and Its Close Relatives
J. Jpn. Bot. 91 Suppl.: 345–354 (2016) 18S Ribosomal RNA Gene Phylogeny of a Colonial Volvocalean Lineage (Tetrabaenaceae-Goniaceae-Volvocaceae, Volvocales, Chlorophyceae) and Its Close Relatives a,b, a,b a,b Takashi NAKADA *, Takuro ITO and Masaru TOMITA aInstitute for Advanced Biosciences, Keio University, Kakuganji, Tsuruoka, Yamagata, 997-0052 JAPAN; bSystems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-0882 JAPAN; *Corresponding author: [email protected] (Accepted on January 19, 2016) The lineage of colonial green algae consisting of Tetrabaenaceae, Goniaceae, and Volvocaceae (TGV-clade) belongs to the clade Reinhardtinia within Volvocales (Chlorophyceae). Reinhardtinia is closely related to some species in the unicellular genera Chlamydomonas and Vitreochlamys. Although 18S rRNA gene sequences are preferred phylogenetic markers for many volvocalean species, phylogenetic relationships among the TGV-clade and its relatives have been examined mainly based on chloroplast genes and ITS2 sequences. To determine the candidate unicellular sister, 18S rRNA gene sequences of 41 species of the TGV-clade and its relatives were newly determined, and single and 6-gene phylogenetic analyses performed. No unicellular sister was determined by 18S rRNA gene analyses, but 6 unicellular clades and 11 ribospecies were recognized as candidates. Five of the candidate lineages and 27 taxa of the TGV-clade were examined by 6-gene phylogeny, revealing one clade including Chlamydomonas reinhardtii, Chlamydomonas debaryana, and Vitreochlamys ordinata to be more closely related than that containing Vitreochlamys aulata and Vitreochlamys pinguis. Key words: 18S rRNA, colonial, green algae, molecular phylogeny, unicellular, Volvocales. Tetrabaenaceae, Goniaceae, and cells) 8- to 50,000-celled genera (Pandorina, Volvocaceae constitute a colonial green Volvulina, Platydorina, Colemanosphaera, algal clade (TGV-clade) within Volvocales Yamagishiella, Eudorina, Pleodorina, and (Chlorophyceae), and include simple to Volvox). -
Jonathan Featherston*1,2, Yoko Arakaki3, Erik R. Hanschen4, Patrick J
The 4-Celled Tetrabaena socialis Nuclear Genome Reveals the Essential Components for Genetic Control of Cell Number at the Origin of Multicellularity in the Volvocine Lineage Item Type Article Authors Featherston, Jonathan; Arakaki, Yoko; Hanschen, Erik R; Ferris, Patrick J; Michod, Richard E; Olson, Bradley J S C; Nozaki, Hisayoshi; Durand, Pierre M Citation Jonathan Featherston, Yoko Arakaki, Erik R Hanschen, Patrick J Ferris, Richard E Michod, Bradley J S C Olson, Hisayoshi Nozaki, Pierre M Durand; The 4-Celled Tetrabaena socialis Nuclear Genome Reveals the Essential Components for Genetic Control of Cell Number at the Origin of Multicellularity in the Volvocine Lineage, Molecular Biology and Evolution, Volume 35, Issue 4, 1 April 2018, Pages 855–870, https://doi.org/10.1093/molbev/ msx332 DOI 10.1093/molbev/msx332 Publisher OXFORD UNIV PRESS Journal MOLECULAR BIOLOGY AND EVOLUTION Rights © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. Download date 08/10/2021 09:07:22 Item License http://rightsstatements.org/vocab/InC/1.0/ Version Final accepted manuscript Link to Item http://hdl.handle.net/10150/628254 Jonathan Featherston*1,2, Yoko Arakaki3, Erik R. Hanschen4, Patrick J. Ferris4, Richard E. Michod4, Bradley J.S.C. Olson5, Hisayoshi Nozaki3, Pierre M. Durand1 Email addresses: Jonathan Featherston [email protected] Yoko Arakaki [email protected] Erik R. Hanschen [email protected] Patrick J. Ferris [email protected] Richard E. Michod [email protected] Bradley J. S. C. Olson [email protected] Hisayoshi Nozaki [email protected] Pierre M. -
The Gonium Pectorale Genome Demonstrates Co-Option of Cell Cycle Regulation During the Evolution of Multicellularity
The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Hanschen, E. R., T. N. Marriage, P. J. Ferris, T. Hamaji, A. Toyoda, A. Fujiyama, R. Neme, et al. 2016. “The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity.” Nature Communications 7 (1): 11370. doi:10.1038/ncomms11370. http://dx.doi.org/10.1038/ncomms11370. Published Version doi:10.1038/ncomms11370 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:26859928 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA ARTICLE Received 26 Jan 2016 | Accepted 18 Mar 2016 | Published 22 Apr 2016 DOI: 10.1038/ncomms11370 OPEN The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity Erik R. Hanschen1, Tara N. Marriage2, Patrick J. Ferris1, Takashi Hamaji3, Atsushi Toyoda4,5, Asao Fujiyama4,5, Rafik Neme6, Hideki Noguchi4, Yohei Minakuchi5, Masahiro Suzuki7, Hiroko Kawai-Toyooka7, David R. Smith8, Halle Sparks2, Jaden Anderson2, Robert Bakaric´9, Victor Luria10,11, Amir Karger12, Marc W. Kirschner10, Pierre M. Durand1,13,14, Richard E. Michod1,11, Hisayoshi Nozaki7 & Bradley J.S.C. Olson2,11 The transition to multicellularity has occurred numerous times in all domains of life, yet its initial steps are poorly understood. -
Molecular Systematics of the Green Algal Order Trentepohliales (Chlorophyta)
Louisiana State University LSU Digital Commons LSU Historical Dissertations and Theses Graduate School 2000 Molecular Systematics of the Green Algal Order Trentepohliales (Chlorophyta). Juan Manuel Lopez-bautista Louisiana State University and Agricultural & Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_disstheses Recommended Citation Lopez-bautista, Juan Manuel, "Molecular Systematics of the Green Algal Order Trentepohliales (Chlorophyta)." (2000). LSU Historical Dissertations and Theses. 7209. https://digitalcommons.lsu.edu/gradschool_disstheses/7209 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Historical Dissertations and Theses by an authorized administrator of LSU Digital Commons. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm m aster UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy subm itted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bteedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. -
Volvox and Volvocine Green Algae James G
Umen EvoDevo (2020) 11:13 https://doi.org/10.1186/s13227-020-00158-7 EvoDevo REVIEW Open Access Volvox and volvocine green algae James G. Umen* Abstract The transition of life from single cells to more complex multicellular forms has occurred at least two dozen times among eukaryotes and is one of the major evolutionary transitions, but the early steps that enabled multicellular life to evolve and thrive remain poorly understood. Volvocine green algae are a taxonomic group that is uniquely suited to investigating the step-wise acquisition of multicellular organization. The multicellular volvocine species Volvox car- teri exhibits many hallmarks of complex multicellularity including complete germ–soma division of labor, asymmetric cell divisions, coordinated tissue-level morphogenesis, and dimorphic sexes—none of which have obvious analogs in its closest unicellular relative, the model alga Chlamydomonas reinhardtii. Here, I summarize some of the key questions and areas of study that are being addressed with Volvox carteri and how increasing genomic information and meth- odologies for volvocine algae are opening up the entire group as an integrated experimental system for exploring the evolution of multicellularity and more. Keywords: Volvox carteri, Chlamydomonas reinhardtii, Multicellularity, Green algae, Morphogenesis, Comparative genomics Natural habitat and lifecycle several additional multicellular genera with diferent Volvox is a polyphyletic genus of multicellular freshwater sizes, cell numbers and degrees of developmental com- green algae (Chlorophyta) that belong to a larger taxo- plexity (e.g., Tetrabaena, Gonium, Astrephomene, Pan- nomic grouping within the Order Chlamydomonadales dorina, Yamagishiella, Eudorina, Pleodorina), and a known as volvocine algae [1]. Te species Volvox carteri close unicellular outgroup species, the model alga Chla- f. -
Floristicko-Ekologická Studie Oblasti Bystřicka Se Zaměřením Na Ekologii
Jiho česká univerzita v Českých Bud ějovicích Přírodov ědecká fakulta Floristicko-ekologická studie oblasti Byst řicka se zam ěř ením na ekologii zelených volvokálních řas Bakalá řská práce David Hnátek Školitel: Mgr. Josef Jurá ň České Bud ějovice 2016 Hnátek, D. 2016. Floristicko-ekologická studie v oblasti Byst řicka se zam ěř ením na ekologii zelených volvokálních řas . [Floristic-ecological study in the Byst řice area with focus on the ecology of green volvocean algae, BSc. Thesis, in Czech] The University of South Bohemia, Faculty of Sciense, České Bud ějovice, 94 pp. Annotation: Since 1889 twenty-two different species of colonial algae from the order Volvocales have been found in the Czech Republic according to the available algological literature. In this work the morphology and ecology of these species is described in detail. Besides investigating the literature resources, I performed my own floristic research of twenty ponds near Byst řice u Benešova. Phytoplankton samples from these ponds were taken in spring, summer, and autumn of years 2014 and 2015 using phytoplankton net and at the same time the environmental characteristics such as pH, conductivity, water transparency, temperature, and degree of shading were measured. Cyanobacteria and algae in the samples were identified to the lowest possible taxonomic level and their relative abundance was assessed. The differences in species composition between ponds and between seasons were compared using basic statistical methods and relationship between environmental factors and species composition was studied. Prohlašuji, že svoji bakalá řskou práci jsem vypracoval samostatn ě pouze s použitím pramen ů a literatury uvedených v seznamu citované literatury. -
Volvocine Algae: from Simple to Complex Multicellularity
Volvocine Algae: From Simple to Complex Multicellularity Matthew D. Herron and Aurora M. Nedelcu Abstract The evolution of multicellularity provided new ways for biological systems to increase in complexity. However, although high levels of complexity have indeed been attained in several multicellular lineages, natural selection does not necessarily favor complex biological systems. Why and how, then, has complexity increased in some lineages? We argue that the volvocine green algae (Volvox and its relatives) are a uniquely valuable model system for understanding the evolution of multicellular complexity. Using a general framework for the evolution of complexity, we discuss the various levels of morphological and developmental complexity achieved in this group, and consider both the why and the how underlying the changes in complexity levels that took place in this group. Keywords Cell differentiation · Chlamydomonas · Chlorophyta · Complexity · Genetics · Multicellularity · Natural selection · Volvox The Issue of Complexity It is absurd to talk of one animal being higher than another.—C. R. Darwin (1837,p.74) Darwin famously reminded himself against using such value-laden terms as ‘higher’ and ‘lower’, but their use has continued (including in Darwin’s own writing; see Richards 1988) right up to the present. Ideas of progress have been present in the literature of evolutionary theory as long as there has been such a literature. These ideas have changed over time and differed among authors, but generally include the notion of improvement over time as either a passive or an actively (selectively) driven trend. “Improvement”, of course, implies some standard against which organisms are measured, and it is in the choice of standard that subjectivity is introduced (Ayala M. -
An Insight Into the Algal Evolution and Genomics
biomolecules Review An Insight into the Algal Evolution and Genomics Amna Komal Khan 1, Humera Kausar 1, Syyada Samra Jaferi 1, Samantha Drouet 2, Christophe Hano 2 , Bilal Haider Abbasi 3 and Sumaira Anjum 1,* 1 Department of Biotechnology, Kinnaird College for Women, Lahore 54000, Pakistan; [email protected] (A.K.K.); [email protected] (H.K.); [email protected] (S.S.J.) 2 Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRAE USC1328, Université d’Orléans, 28000 Chartres, France; [email protected] (S.D.); [email protected] (C.H.) 3 Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan; [email protected] * Correspondence: [email protected]; Tel.: +92-300-6957038 Received: 21 September 2020; Accepted: 5 November 2020; Published: 6 November 2020 Abstract: With the increase in biotechnological, environmental, and nutraceutical importance of algae, about 100 whole genomic sequences of algae have been published, and this figure is expected to double in the coming years. The phenotypic and ecological diversity among algae hints at the range of functional capabilities encoded by algal genomes. In order to explore the biodiversity of algae and fully exploit their commercial potential, understanding their evolutionary, structural, functional, and developmental aspects at genomic level is a pre-requisite. So forth, the algal genomic analysis revealed us that algae evolved through endosymbiotic gene transfer, giving rise to around eight phyla. Amongst the diverse algal species, the unicellular green algae Chlamydomonas reinhardtii has attained the status of model organism as it is an ideal organism to elucidate the biological processes critical to plants and animals, as well as commercialized to produce range of bio-products.