Coordinated Beating of Algal Flagella Is Mediated by Basal Coupling
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Palindromic Genes in the Linear Mitochondrial Genome of the Nonphotosynthetic Green Alga Polytomella Magna
GBE Palindromic Genes in the Linear Mitochondrial Genome of the Nonphotosynthetic Green Alga Polytomella magna David Roy Smith1,y,JimengHua2,3,y, John M. Archibald2, and Robert W. Lee3,* 1Department of Biology, University of Western Ontario, London, Ontario, Canada 2Department of Biochemistry and Molecular Biology, Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Dalhousie University, Halifax, Nova Scotia, Canada 3Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada *Corresponding author: E-mail: [email protected]. yThese authors contributed equally to this work. Accepted: August 8, 2013 Data deposition: Sequence data from this article have been deposited in GenBank under the accession KC733827. Abstract Organelle DNA is no stranger to palindromic repeats. But never has a mitochondrial or plastid genome been described in which every coding region is part of a distinct palindromic unit. While sequencing the mitochondrial DNA of the nonphotosynthetic green alga Polytomella magna, we uncovered precisely this type of genic arrangement. The P. magna mitochondrial genome is linear and made up entirely of palindromes, each containing 1–7 unique coding regions. Consequently, every gene in the genome is duplicated and in an inverted orientation relative to its partner. And when these palindromic genes are folded into putative stem-loops, their predicted translational start sites are often positioned in the apex of the loop. Gel electrophoresis results support the linear, 28-kb monomeric conformation of the P. magna mitochondrial genome. Analyses of other Polytomella taxa suggest that palindromic mitochondrial genes were present in the ancestor of the Polytomella lineage and lost or retained to various degrees in extant species. -
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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. -
Gc – Ms) Analysis
Academic Sciences International Journal of Pharmacy and Pharmaceutical Sciences ISSN- 0975-1491 Vol 5, Issue 3, 2013 Research Article EVALUATION OF ANTIMICROBIAL METABOLITES FROM MARINE MICROALGAE TETRASELMIS SUECICA USING GAS CHROMATOGRAPHY – MASS SPECTROMETRY (GC – MS) ANALYSIS V. DOOSLIN MERCY BAI1 AND S. KRISHNAKUMAR2* 1Department of Biomedical Engineering Rajiv Gandhi College of Enginnering and Technology.Puducherry 607402, India, 2Department of Biomedical Engineering, Sathyabama University, Chennai 600119, Tamil Nadu, India. Email: [email protected] Received: 15 Mar 2013, Revised and Accepted: 23 Apr 2013 ABSTRACT Objective: Marine natural products have been considered as one of the most promising sources of antimicrobial compounds in recent years. Marine microalgae Tetraselmis suecica (Kylin) was selected for the present antimicrobial investigation. Methods: The effects of pH, temperature and salinity were tested for the growth of microalgae. The antibacterial effect of different solvent extracts of marine microalgae Tetraselmis suecica against selected human pathogens such as Vibrio cholerae, Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Salmonella sp, Proteus sp., Streptococcus pyogens, Staphylococcus aureus, Bacillus megaterium and Bacillus subtilis were investigated. The GC-MS analysis was done with standard specification to identify the active principle of bioactive compound. Results: The highest cell density was observed when the medium adjusted with 40ppt of salinity in pH of 9.0 at 250C during 9th day of incubation period. Methanol + chloroform (1:1) crude extract of Tetraselmis suecica was confirmed considerable activity against gram negative bacteria than gram positive human pathogen. GC-MS analysis revealed the presence of unique chemical compounds like 1-ethyl butyl 3-hexyl hydroperoxide (MW: 100) and methyl heptanate (MW: 186) respectively for the crude extract of Tetraselmis suecica. -
An Unrecognized Ancient Lineage of Green Plants Persists in Deep Marine Waters
FAU Institutional Repository http://purl.fcla.edu/fau/fauir This paper was submitted by the faculty of FAU’s Harbor Branch Oceanographic Institute. Notice: ©2010 Phycological Society of America. This manuscript is an author version with the final publication available at http://www.wiley.com/WileyCDA/ and may be cited as: Zechman, F. W., Verbruggen, H., Leliaert, F., Ashworth, M., Buchheim, M. A., Fawley, M. W., Spalding, H., Pueschel, C. M., Buchheim, J. A., Verghese, B., & Hanisak, M. D. (2010). An unrecognized ancient lineage of green plants persists in deep marine waters. Journal of Phycology, 46(6), 1288‐1295. (Suppl. material). doi:10.1111/j.1529‐8817.2010.00900.x J. Phycol. 46, 1288–1295 (2010) Ó 2010 Phycological Society of America DOI: 10.1111/j.1529-8817.2010.00900.x AN UNRECOGNIZED ANCIENT LINEAGE OF GREEN PLANTS PERSISTS IN DEEP MARINE WATERS1 Frederick W. Zechman2,3 Department of Biology, California State University Fresno, 2555 East San Ramon Ave, Fresno, California 93740, USA Heroen Verbruggen,3 Frederik Leliaert Phycology Research Group, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium Matt Ashworth University Station MS A6700, 311 Biological Laboratories, University of Texas at Austin, Austin, Texas 78712, USA Mark A. Buchheim Department of Biological Science, University of Tulsa, Tulsa, Oklahoma 74104, USA Marvin W. Fawley School of Mathematical and Natural Sciences, University of Arkansas at Monticello, Monticello, Arkansas 71656, USA Department of Biological Sciences, North Dakota State University, Fargo, North Dakota 58105, USA Heather Spalding Botany Department, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA Curt M. Pueschel Department of Biological Sciences, State University of New York at Binghamton, Binghamton, New York 13901, USA Julie A. -
Nucleotide Diversity of the Colorless Green Alga Polytomella Parva (Chlorophyceae, Chlorophyta): High for the Mitochondrial Telo
The Journal of Published by the International Society of Eukaryotic Microbiology Protistologists J. Eukaryot. Microbiol., 58(5), pp. 471–473 r 2011 The Author(s) Journal of Eukaryotic Microbiology r 2011 International Society of Protistologists DOI: 10.1111/j.1550-7408.2011.00569.x Nucleotide Diversity of the Colorless Green Alga Polytomella parva (Chlorophyceae, Chlorophyta): High for the Mitochondrial Telomeres, Surprisingly Low Everywhere Elseà DAVID ROY SMITH1 and ROBERT W. LEE Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2 ABSTRACT. Silent-site nucleotide diversity data (psilent) can provide insights into the forces driving genome evolution. Here we present psilent statistics for the mitochondrial and nuclear DNAs of Polytomella parva, a nonphotosynthetic green alga with a highly reduced, linear fragmented mitochondrial genome. We show that this species harbors very little genetic diversity, with the exception of the mitochondrial telomeres, which have an excess of polymorphic sites. These data are compared with previously published psilent values from the mitochondrial and nuclear genomes of the model species Chlamydomonas reinhardtii and Volvox carteri, which are close relatives of P. parva, and are used to understand the modes and tempos of genome evolution within green algae. Key Words. Chlamydomonas, Chlorophyte, genetic diversity, mitochondrial DNA, Volvox. HE nucleotide diversity at silent sites (psilent), which include RESULTS AND DISCUSSION T noncoding positions and the synonymous sites of protein-cod- ing DNA, can provide insights into the combined contributions of For measuring nucleotide diversity we used the following Poly- genetic drift and mutation acting on a genome—parameters that are tomella SAG strains, with origins of isolation listed in brackets: SAG arguably among the key determinants driving the evolution of ge- 63-2 (Glasgow, Scotland), 63-2b (Bohemia, Czech Republic), 63-3 nomic architecture (Lynch 2007). -
The Dunaliella Salina Organelle Genomes: Large Sequences, Inflated with Intronic and Intergenic DNA BMC Plant Biology 2010, 10:83
Smith et al. BMC Plant Biology 2010, 10:83 http://www.biomedcentral.com/1471-2229/10/83 RESEARCH ARTICLE Open Access TheResearch Dunaliella article salina organelle genomes: large sequences, inflated with intronic and intergenic DNA David Roy Smith*1, Robert W Lee1, John C Cushman2, Jon K Magnuson3, Duc Tran4 and Jürgen EW Polle4 Abstract Background: Dunaliella salina Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because D. salina can produce massive amounts of β- carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of D. salina have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of D. salina and compares them with those of the model green algae Chlamydomonas reinhardtii and Volvox carteri. Results: The D. salina organelle genomes are large, circular-mapping molecules with ~60% noncoding DNA, placing them among the most inflated organelle DNAs sampled from the Chlorophyta. In fact, the D. salina plastid genome, at 269 kb, is the largest complete plastid DNA (ptDNA) sequence currently deposited in GenBank, and both the mitochondrial and plastid genomes have unprecedentedly high intron densities for organelle DNA: ~1.5 and ~0.4 introns per gene, respectively. Moreover, what appear to be the relics of genes, introns, and intronic open reading frames are found scattered throughout the intergenic ptDNA regions -- a trait without parallel in other characterized organelle genomes and one that gives insight into the mechanisms and modes of expansion of the D. -
The Puzzling Conservation and Diversification of Lipid Droplets from Bacteria to Eukaryotes Josselin Lupette, Eric Marechal
The Puzzling Conservation and Diversification of Lipid Droplets from Bacteria to Eukaryotes Josselin Lupette, Eric Marechal To cite this version: Josselin Lupette, Eric Marechal. The Puzzling Conservation and Diversification of Lipid Droplets from Bacteria to Eukaryotes. Kloc M. Symbiosis: Cellular, Molecular, Medical and Evolutionary Aspects. Results and Problems in Cell Differentiation, 69, Springer, pp.281-334, 2020, 978-3-030- 51848-6. 10.1007/978-3-030-51849-3_11. hal-03048110 HAL Id: hal-03048110 https://hal.archives-ouvertes.fr/hal-03048110 Submitted on 9 Dec 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Chapter 11 1 The Puzzling Conservation 2 and Diversification of Lipid Droplets from 3 Bacteria to Eukaryotes 4 Josselin Lupette and Eric Maréchal 5 Abstract Membrane compartments are amongst the most fascinating markers of 6 cell evolution from prokaryotes to eukaryotes, some being conserved and the others 7 having emerged via a series of primary and secondary endosymbiosis events. 8 Membrane compartments comprise the system limiting cells (one or two membranes 9 in bacteria, a unique plasma membrane in eukaryotes) and a variety of internal 10 vesicular, subspherical, tubular, or reticulated organelles. -
Saline Microalgae for Biofuels: Outdoor Culture from Small-Scale to Pilot Scale
SALINE MICROALGAE FOR BIOFUELS: OUTDOOR CULTURE FROM SMALL-SCALE TO PILOT SCALE Andreas Isdepsky DIPL.-ING. (BIOTECH) This thesis is presented for the degree of Doctor of Philosophy of Murdoch University, Western Australia 2015 DECLARATION I declare that this thesis is my own account of my research and contains as its main content work which has not previously been submitted for a degree at any tertiary education institution. Andreas Isdepsky ii “Do not go where the path may lead, go instead where there is no path and leave a trail.” Ralph Waldo Emerson iii ABSTRACT Three local isolates of the green alga Tetraselmis sp. identified as the most promising microalgae species for outdoor mass cultivation with high potential for biodiesel production due to high amounts of total lipids and high lipid productivity were employed in this study. The aim of the study was to compare three halophilic Tetraselmis strains (Tetraselmis MUR-167, MUR-230 and MUR-233) grown in open raceway ponds over long periods with respect to their specific growth rate and lipid productivity without additional CO2 and with CO2 addition regulated at pH 7.5 by using a pH-stat system. Attention also was given to the overall culture condition including contaminating organisms, biofilm development due to cell adhesion and cell clump formation. All tested Tetraselmis strains in this study were successfully grown outdoors in open raceway ponds in hypersaline fertilised medium at 7 % w/v NaCl over a period of more than two years. A marked effect of CO2 addition on growth and productivities was observed at high solar irradiance and temperatures between 15 – 33 oC. -
Chlamydomonas Reinhardtii
Published online 9 October 2017 Nucleic Acids Research, 2017, Vol. 45, No. 22 12963–12973 doi: 10.1093/nar/gkx903 Polycytidylation of mitochondrial mRNAs in Chlamydomonas reinhardtii Thalia Salinas-Giege´ 1,*, Marina Cavaiuolo2,Valerie´ Cognat1, Elodie Ubrig1, Claire Remacle3, Anne-Marie Ducheneˆ 1, Olivier Vallon2,* and Laurence Marechal-Drouard´ 1,* 1Institut de biologie moleculaire´ des plantes, CNRS, Universite´ de Strasbourg, 67084 Strasbourg, France, 2UMR 7141, CNRS, Universite´ Pierre et Marie Curie, Institut de Biologie Physico-Chimique, 75005 Paris, France and 3Gen´ etique´ et Physiologie des microalgues, Department of Life Sciences, Institute of Botany, B22, University of Liege, B-4000 Liege, Belgium Received July 21, 2017; Revised September 18, 2017; Editorial Decision September 25, 2017; Accepted September 25, 2017 ABSTRACT the respiratory chain or the adenosine triphosphate (ATP) synthase and their expression is essential. Despite the com- The unicellular photosynthetic organism, Chlamy- mon prokaryotic origin of mitochondria, mechanisms al- domonas reinhardtii, represents a powerful model to lowing mt gene expression have diverged. Studies on mt study mitochondrial gene expression. Here, we show gene expression in various organisms have highlighted the that the 5 -and3-extremities of the eight Chlamy- acquisition of a number of new features and this, in a domonas mitochondrial mRNAs present two unusual species-specific manner (1–3). In plant mitochondria, post- characteristics. First, all mRNAs start primarily at the transcriptional processes including RNA editing, splicing AUG initiation codon of the coding sequence which of introns, maturation of 5 - and 3 -ends of RNA transcripts is often marked by a cluster of small RNAs. Sec- and RNA degradation play an important role in gene ex- ond, unusual tails are added post-transcriptionally at pression (e.g. -
Acartia Tonsa Dana and Acute Testing with Copper on Different Life Cycle Stages
Faculty of Bioscience Engineering Academic Year 2014 – 2015 Culturing Acartia tonsa Dana and Acute Testing with Copper on Different Life Cycle Stages Jonathan Baetens Promotor: Prof. Dr. Eng. Karel De Schamphelaere Tutor: Msc. Olivier Berteloot Thesis Prepared for the Degree of Master of Science in Biochemical Engineering Technology Faculty of Bioscience Engineering Academic Year 2014 – 2015 Culturing Acartia tonsa Dana and Acute Testing with Copper on Different Life Cycle Stages Jonathan Baetens Promotor: Prof. Dr. Eng. Karel De Schamphelaere Tutor: Msc. Olivier Berteloot Thesis Prepared for the Degree of Master of Science in Biochemical Engineering Technology Copyright The author, the tutor and the promoter give the permission to use this thesis for consultation and to copy parts of it for personal use. Every other use is subject to the copyright laws, more specifically the source must be extensively specified when using the results from this thesis. De auteur en de promotor geven de toelating deze scriptie voor consultatie beschikbaar te stellen en delen van de scriptie te kopiëren voor persoonlijk gebruik. Elk ander gebruik valt onder de beperkingen van het auteursrecht, in het bijzonder met betrekking tot de verplichting de bron uitdrukkelijk te vermelden bij het aanhalen van resultaten uit deze scriptie. Written in Dendermonde and Ghent on 21/08/2015 Geschreven in Dendermonde en Gent op 21/08/2015 Jonathan Baetens Prof. Dr. Eng. Karel De Schamphelaere Msc. Olivier Berteloot Acknowledgements When it was time to choose a thesis subject, I was certain of two things. One, I wanted a subject that had an environmental ‘ring’ to it. Two, I wanted to work in a laboratory. -
Genome Biol Evol-2013-Smith-1661
GBE Palindromic Genes in the Linear Mitochondrial Genome of the Nonphotosynthetic Green Alga Polytomella magna David Roy Smith1,y,JimengHua2,3,y, John M. Archibald2, and Robert W. Lee3,* 1Department of Biology, University of Western Ontario, London, Ontario, Canada 2Department of Biochemistry and Molecular Biology, Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Dalhousie University, Halifax, Nova Scotia, Canada 3Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada *Corresponding author: E-mail: [email protected]. yThese authors contributed equally to this work. Accepted: August 8, 2013 Data deposition: Sequence data from this article have been deposited in GenBank under the accession KC733827. Downloaded from Abstract Organelle DNA is no stranger to palindromic repeats. But never has a mitochondrial or plastid genome been described in which every coding region is part of a distinct palindromic unit. While sequencing the mitochondrial DNA of the nonphotosynthetic green alga Polytomella magna, we uncovered precisely this type of genic arrangement. The P. magna mitochondrial genome is linear and made http://gbe.oxfordjournals.org/ up entirely of palindromes, each containing 1–7 unique coding regions. Consequently, every gene in the genome is duplicated and in an inverted orientation relative to its partner. And when these palindromic genes are folded into putative stem-loops, their predicted translational start sites are often positioned in the apex of the loop. Gel electrophoresis results support the linear, 28-kb monomeric conformation of the P. magna mitochondrial genome. Analyses of other Polytomella taxa suggest that palindromic mitochondrial genes were present in the ancestor of the Polytomella lineage and lost or retained to various degrees in extant species. -
Chlamydomonas Reinhardtii
Published online 9 October 2017 Nucleic Acids Research, 2017, Vol. 45, No. 22 12963–12973 doi: 10.1093/nar/gkx903 Polycytidylation of mitochondrial mRNAs in Chlamydomonas reinhardtii Thalia Salinas-Giege´ 1,*, Marina Cavaiuolo2,Valerie´ Cognat1, Elodie Ubrig1, Claire Remacle3, Anne-Marie Ducheneˆ 1, Olivier Vallon2,* and Laurence Marechal-Drouard´ 1,* 1Institut de biologie moleculaire´ des plantes, CNRS, Universite´ de Strasbourg, 67084 Strasbourg, France, 2UMR 7141, CNRS, Universite´ Pierre et Marie Curie, Institut de Biologie Physico-Chimique, 75005 Paris, France and 3Gen´ etique´ et Physiologie des microalgues, Department of Life Sciences, Institute of Botany, B22, University of Liege, B-4000 Liege, Belgium Received July 21, 2017; Revised September 18, 2017; Editorial Decision September 25, 2017; Accepted September 25, 2017 ABSTRACT the respiratory chain or the adenosine triphosphate (ATP) synthase and their expression is essential. Despite the com- The unicellular photosynthetic organism, Chlamy- mon prokaryotic origin of mitochondria, mechanisms al- domonas reinhardtii, represents a powerful model to lowing mt gene expression have diverged. Studies on mt study mitochondrial gene expression. Here, we show gene expression in various organisms have highlighted the that the 5 -and3-extremities of the eight Chlamy- acquisition of a number of new features and this, in a domonas mitochondrial mRNAs present two unusual species-specific manner (1–3). In plant mitochondria, post- characteristics. First, all mRNAs start primarily at the transcriptional processes including RNA editing, splicing AUG initiation codon of the coding sequence which of introns, maturation of 5 - and 3 -ends of RNA transcripts is often marked by a cluster of small RNAs. Sec- and RNA degradation play an important role in gene ex- ond, unusual tails are added post-transcriptionally at pression (e.g.