Table S1. Pigmented Compounds of Different Microorganisms and Their Biological Properties
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Regulation of Photosynthesis by a Potassium Transporter in the Diatom Phaeodactylum Tricornutum Claire Seydoux
Regulation of photosynthesis by a potassium transporter in the diatom Phaeodactylum tricornutum Claire Seydoux To cite this version: Claire Seydoux. Regulation of photosynthesis by a potassium transporter in the diatom Phaeo- dactylum tricornutum. Vegetal Biology. Université Grenoble Alpes [2020-..], 2020. English. NNT : 2020GRALV031. tel-03172222 HAL Id: tel-03172222 https://tel.archives-ouvertes.fr/tel-03172222 Submitted on 17 Mar 2021 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. THÈSE Pour obtenir le grade de DOCTEUR DE L’UNIVERSITÉ GRENOBLE ALPES Spécialité : Biologie Végétale Arrêté ministériel : 25 mai 2016 Présentée par Claire SEYDOUX Thèse dirigée par Florence COURTOIS, Maitre de conferences, Université Grenoble Alpes et codirigée par Giovanni FINAZZI, Université Grenoble Alpes préparée au sein du Laboratoire Laboratoire de Physiologie Cellulaire Végétale dans l'École Doctorale Chimie et Sciences du Vivant Régulation de la photosynthèse par un transporteur de potassium chez la diatomée Phaeodactylum tricornutum Regulation of photosynthesis -
The Genomes of Polyextremophilic Cyanidiales Contain 1% 2 Horizontally Transferred Genes with Diverse Adaptive Functions 3 4 Alessandro W
bioRxiv preprint doi: https://doi.org/10.1101/526111; this version posted January 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 4.0 International license. 1 The genomes of polyextremophilic Cyanidiales contain 1% 2 horizontally transferred genes with diverse adaptive functions 3 4 Alessandro W. Rossoni1#, Dana C. Price2, Mark Seger3, Dagmar Lyska1, Peter Lammers3, 5 Debashish Bhattacharya4 & Andreas P.M. Weber1* 6 7 1Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich 8 Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany 9 2Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA 10 3Arizona Center for Algae Technology and Innovation, Arizona State University, Mesa, AZ 11 85212, USA 12 4Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 13 08901, USA 14 15 *Corresponding author: Prof. Dr. Andreas P.M. Weber, 16 e-mail: [email protected] 17 bioRxiv preprint doi: https://doi.org/10.1101/526111; this version posted January 23, 2019. 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 4.0 International license. 18 Abstract 19 The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics 20 that impact our understanding regarding the origin of metabolic processes and the role of 21 organelles in cellular evolution. -
Anoxygenic Photosynthesis in Photolithotrophic Sulfur Bacteria and Their Role in Detoxication of Hydrogen Sulfide
antioxidants Review Anoxygenic Photosynthesis in Photolithotrophic Sulfur Bacteria and Their Role in Detoxication of Hydrogen Sulfide Ivan Kushkevych 1,* , Veronika Bosáková 1,2 , Monika Vítˇezová 1 and Simon K.-M. R. Rittmann 3,* 1 Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; [email protected] (V.B.); [email protected] (M.V.) 2 Department of Biology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic 3 Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, 1090 Vienna, Austria * Correspondence: [email protected] (I.K.); [email protected] (S.K.-M.R.R.); Tel.: +420-549-495-315 (I.K.); +431-427-776-513 (S.K.-M.R.R.) Abstract: Hydrogen sulfide is a toxic compound that can affect various groups of water microorgan- isms. Photolithotrophic sulfur bacteria including Chromatiaceae and Chlorobiaceae are able to convert inorganic substrate (hydrogen sulfide and carbon dioxide) into organic matter deriving energy from photosynthesis. This process takes place in the absence of molecular oxygen and is referred to as anoxygenic photosynthesis, in which exogenous electron donors are needed. These donors may be reduced sulfur compounds such as hydrogen sulfide. This paper deals with the description of this metabolic process, representatives of the above-mentioned families, and discusses the possibility using anoxygenic phototrophic microorganisms for the detoxification of toxic hydrogen sulfide. Moreover, their general characteristics, morphology, metabolism, and taxonomy are described as Citation: Kushkevych, I.; Bosáková, well as the conditions for isolation and cultivation of these microorganisms will be presented. V.; Vítˇezová,M.; Rittmann, S.K.-M.R. -
Bioactivity of Bacterial Strains Isolated from Marine Biofilms in Hong Kong Waters for the Induction of Larval Settlement in the Marine Polychaete Hydroides Elegans
MARINE ECOLOGY PROGRESS SERIES Vol. 226: 301–310, 2002 Published January 31 Mar Ecol Prog Ser Bioactivity of bacterial strains isolated from marine biofilms in Hong Kong waters for the induction of larval settlement in the marine polychaete Hydroides elegans Stanley C. K. Lau1,*, Karen K. W. Mak1,**, Feng Chen2, Pei-Yuan Qian1 1Department of Biology, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, PR China 2Center of Marine Biotechnology, University of Maryland, 701 East Pratt Street, Suite 236, Baltimore, Maryland 21202, USA ABSTRACT: In the present study, 38 bacterial isolates were obtained from a marine biofilm, identi- fied by the comparison of 16S rRNA gene sequences, and investigated by laboratory bioassays for their effects on larval settlement of the marine polychaete Hydroides elegans (Haswell). The bacter- ial isolates belonged to 3 phylogenetic branches: γ-Proteobacteria (26 isolates), Gram-positive (8 iso- lates) and Cytophaga-Flexibacter-Bacteroides (4 isolates). Most of the isolates were affiliated to the genera Vibrio (7 isolates), Alteromonas (8 isolates) or Pseudoalteromonas (8 isolates), which are in the γ-Proteobacteria branch. According to their efficacy to induce larval settlement of H. elegans in lab- oratory bioassays, the isolates were categorized as strongly, moderately, and non-inductive for larval settlement. About 42% of the isolates were categorized as non-inductive and the rest of the isolates contained equal numbers of highly and moderately inductive strains. The results indicated that lar- val settlement of H. elegans could be induced by bacteria in a wide range of taxa. The isolates that induced high and moderate levels of larval settlement belonged to the genus Cytophaga in the Cytophaga-Flexibacter-Bacteroides branch; the genera Bacillus, Brevibacterium, Micrococcus and Staphylococcus in the Gram-positive branch; and the genera Alteromonas, Pseudoalteromonas and Vibrio in the γ-Proteobacteria branch. -
METABOLIC EVOLUTION in GALDIERIA SULPHURARIA By
METABOLIC EVOLUTION IN GALDIERIA SULPHURARIA By CHAD M. TERNES Bachelor of Science in Botany Oklahoma State University Stillwater, Oklahoma 2009 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY May, 2015 METABOLIC EVOLUTION IN GALDIERIA SUPHURARIA Dissertation Approved: Dr. Gerald Schoenknecht Dissertation Adviser Dr. David Meinke Dr. Andrew Doust Dr. Patricia Canaan ii Name: CHAD M. TERNES Date of Degree: MAY, 2015 Title of Study: METABOLIC EVOLUTION IN GALDIERIA SULPHURARIA Major Field: PLANT SCIENCE Abstract: The thermoacidophilic, unicellular, red alga Galdieria sulphuraria possesses characteristics, including salt and heavy metal tolerance, unsurpassed by any other alga. Like most plastid bearing eukaryotes, G. sulphuraria can grow photoautotrophically. Additionally, it can also grow solely as a heterotroph, which results in the cessation of photosynthetic pigment biosynthesis. The ability to grow heterotrophically is likely correlated with G. sulphuraria ’s broad capacity for carbon metabolism, which rivals that of fungi. Annotation of the metabolic pathways encoded by the genome of G. sulphuraria revealed several pathways that are uncharacteristic for plants and algae, even red algae. Phylogenetic analyses of the enzymes underlying the metabolic pathways suggest multiple instances of horizontal gene transfer, in addition to endosymbiotic gene transfer and conservation through ancestry. Although some metabolic pathways as a whole appear to be retained through ancestry, genes encoding individual enzymes within a pathway were substituted by genes that were acquired horizontally from other domains of life. Thus, metabolic pathways in G. sulphuraria appear to be composed of a ‘metabolic patchwork’, underscored by a mosaic of genes resulting from multiple evolutionary processes. -
CUED Phd and Mphil Thesis Classes
High-throughput Experimental and Computational Studies of Bacterial Evolution Lars Barquist Queens' College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 23 August 2013 Arrakis teaches the attitude of the knife { chopping off what's incomplete and saying: \Now it's complete because it's ended here." Collected Sayings of Muad'dib Declaration High-throughput Experimental and Computational Studies of Bacterial Evolution The work presented in this dissertation was carried out at the Wellcome Trust Sanger Institute between October 2009 and August 2013. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the limit of 60,000 words as specified by the Faculty of Biology Degree Committee. This dissertation has been typeset in 12pt Computer Modern font using LATEX according to the specifications set by the Board of Graduate Studies and the Faculty of Biology Degree Committee. No part of this dissertation or anything substantially similar has been or is being submitted for any other qualification at any other university. Acknowledgements I have been tremendously fortunate to spend the past four years on the Wellcome Trust Genome Campus at the Sanger Institute and the European Bioinformatics Institute. I would like to thank foremost my main collaborators on the studies described in this thesis: Paul Gardner and Gemma Langridge. Their contributions and support have been invaluable. I would also like to thank my supervisor, Alex Bateman, for giving me the freedom to pursue a wide range of projects during my time in his group and for advice. -
Updating the Taxonomic Toolbox: Classification of Alteromonas Spp
1 Updating the taxonomic toolbox: classification of Alteromonas spp. 2 using Multilocus Phylogenetic Analysis and MALDI-TOF Mass 3 Spectrometry a a a 4 Hooi Jun Ng , Hayden K. Webb , Russell J. Crawford , François a b b c 5 Malherbe , Henry Butt , Rachel Knight , Valery V. Mikhailov and a, 6 Elena P. Ivanova * 7 aFaculty of Life and Social Sciences, Swinburne University of Technology, 8 PO Box 218, Hawthorn, Vic 3122, Australia 9 bBioscreen, Bio21 Institute, The University of Melbourne, Vic 3010, Australia 10 cG.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian 11 Academy of Sciences, Vladivostok 690022, Russian Federation 12 13 *Corresponding author: Tel: +61-3-9214-5137. Fax: +61-3-9214-5050. 14 E-mail: [email protected] 15 16 Abstract 17 Bacteria of the genus Alteromonas are Gram-negative, strictly aerobic, motile, 18 heterotrophic marine bacteria, known for their versatile metabolic activities. 19 Identification and classification of novel species belonging to the genus Alteromonas 20 generally involves DNA-DNA hybridization (DDH) as distinct species often fail to be 1 21 resolved at the 97% threshold value of the 16S rRNA gene sequence similarity. In this 22 study, the applicability of Multilocus Phylogenetic Analysis (MLPA) and Matrix- 23 Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF 24 MS) for the differentiation of Alteromonas species has been evaluated. Phylogenetic 25 analysis incorporating five house-keeping genes (dnaK, sucC, rpoB, gyrB, and rpoD) 26 revealed a threshold value of 98.9% that could be considered as the species cut-off 27 value for the delineation of Alteromonas spp. -
Diverse Biosynthetic Pathways and Protective Functions Against Environmental Stress of Antioxidants in Microalgae
plants Review Diverse Biosynthetic Pathways and Protective Functions against Environmental Stress of Antioxidants in Microalgae Shun Tamaki 1,* , Keiichi Mochida 1,2,3,4 and Kengo Suzuki 1,5 1 Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, Yokohama 230-0045, Japan; [email protected] (K.M.); [email protected] (K.S.) 2 RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan 3 Kihara Institute for Biological Research, Yokohama City University, Yokohama 230-0045, Japan 4 School of Information and Data Sciences, Nagasaki University, Nagasaki 852-8521, Japan 5 euglena Co., Ltd., Tokyo 108-0014, Japan * Correspondence: [email protected]; Tel.: +81-45-503-9576 Abstract: Eukaryotic microalgae have been classified into several biological divisions and have evo- lutionarily acquired diverse morphologies, metabolisms, and life cycles. They are naturally exposed to environmental stresses that cause oxidative damage due to reactive oxygen species accumulation. To cope with environmental stresses, microalgae contain various antioxidants, including carotenoids, ascorbate (AsA), and glutathione (GSH). Carotenoids are hydrophobic pigments required for light harvesting, photoprotection, and phototaxis. AsA constitutes the AsA-GSH cycle together with GSH and is responsible for photooxidative stress defense. GSH contributes not only to ROS scavenging, but also to heavy metal detoxification and thiol-based redox regulation. The evolutionary diversity of microalgae influences the composition and biosynthetic pathways of these antioxidants. For example, α-carotene and its derivatives are specific to Chlorophyta, whereas diadinoxanthin and fucoxanthin are found in Heterokontophyta, Haptophyta, and Dinophyta. It has been suggested that Citation: Tamaki, S.; Mochida, K.; Suzuki, K. Diverse Biosynthetic AsA is biosynthesized via the plant pathway in Chlorophyta and Rhodophyta and via the Euglena Pathways and Protective Functions pathway in Euglenophyta, Heterokontophyta, and Haptophyta. -
The Synthesis and Biological Evaluation of Potential ABA-Like Analogues: Prospective Substrates to Control Berry Ripening of Wine Grapes
The Synthesis and Biological Evaluation of Potential ABA-Like Analogues: Prospective Substrates to Control Berry Ripening of Wine Grapes. A thesis presented in fulfilment of the requirements for the degree of Doctor of Philosophy Ruyi Li BSc (Bio-Eng), MSc (Vit./Oen.) Northwest A&F University The University of Adelaide School of Agriculture, Food and Wine July 2012 Table of Contents Abstract........................................................................................................................... iii Declaration...................................................................................................................... vi Acknowledgements......................................................................................................... vii Abbreviations.................................................................................................................. ix Figures, Schemes and Tables......................................................................................... xi CHAPTER 1: INTRODUCTION................................................................................ 1 1.1 General Introduction................................................................................................... 1 1.2 Carotenoids................................................................................................................. 3 1.2.1 Definition, types and identification of carotenoids................................................. 3 1.2.2 Factors influencing the concentration of carotenoids -
Altered Xanthophyll Compositions Adversely Affect Chlorophyll Accumulation and Nonphotochemical Quenching in Arabidopsis Mutants
Proc. Natl. Acad. Sci. USA Vol. 95, pp. 13324–13329, October 1998 Plant Biology Altered xanthophyll compositions adversely affect chlorophyll accumulation and nonphotochemical quenching in Arabidopsis mutants BARRY J. POGSON*, KRISHNA K. NIYOGI†,OLLE BJO¨RKMAN‡, AND DEAN DELLAPENNA§¶ *Department of Plant Biology, Arizona State University, Tempe, AZ 85287-1601; †Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102; ‡Department of Plant Biology, Carnegie Institution of Washington, Stanford, CA 94305-4101; and §Department of Biochemistry, University of Nevada, Reno, NV 89557-0014 Contributed by Olle Bjo¨rkman, September 4, 1998 ABSTRACT Collectively, the xanthophyll class of carote- thin, are enriched in the LHCs, where they contribute to noids perform a variety of critical roles in light harvesting assembly, light harvesting, and photoprotection (2–8). antenna assembly and function. The xanthophyll composition A summary of the carotenoid biosynthetic pathway of higher of higher plant photosystems (lutein, violaxanthin, and neox- plants and relevant chemical structures is shown in Fig. 1. anthin) is remarkably conserved, suggesting important func- Lycopene is cyclized twice by the enzyme lycopene b-cyclase tional roles for each. We have taken a molecular genetic to form b-carotene. The two beta rings of b-carotene are approach in Arabidopsis toward defining the respective roles of subjected to identical hydroxylation reactions to yield zeaxan- individual xanthophylls in vivo by using a series of mutant thin, which in turn is epoxidated once to form antheraxanthin lines that selectively eliminate and substitute a range of and twice to form violaxanthin. Neoxanthin is derived from xanthophylls. The mutations, lut1 and lut2 (lut 5 lutein violaxanthin by an additional rearrangement (9). -
Myoglobin with Modified Tetrapyrrole Chromophores: Binding Specificity and Photochemistry ⁎ Stephanie Pröll A, Brigitte Wilhelm A, Bruno Robert B, Hugo Scheer A
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Biochimica et Biophysica Acta 1757 (2006) 750–763 www.elsevier.com/locate/bbabio Myoglobin with modified tetrapyrrole chromophores: Binding specificity and photochemistry ⁎ Stephanie Pröll a, Brigitte Wilhelm a, Bruno Robert b, Hugo Scheer a, a Department Biologie I-Botanik, Universität München, Menzingerstr, 67, 80638 München, Germany b Sections de Biophysique des Protéines et des Membranes, DBCM/CEA et URA CNRS 2096, C.E. Saclay, 91191 Gif (Yvette), France Received 2 August 2005; received in revised form 2 March 2006; accepted 28 March 2006 Available online 12 May 2006 Abstract Complexes were prepared of horse heart myoglobin with derivatives of (bacterio)chlorophylls and the linear tetrapyrrole, phycocyanobilin. Structural factors important for binding are (i) the presence of a central metal with open ligation site, which even induces binding of phycocyanobilin, and (ii) the absence of the hydrophobic esterifying alcohol, phytol. Binding is further modulated by the stereochemistry at the isocyclic ring. The binding pocket can act as a reaction chamber: with enolizable substrates, apo-myoglobin acts as a 132-epimerase converting, e.g., Zn-pheophorbide a' (132S) to a (132R). Light-induced reduction and oxidation of the bound pigments are accelerated as compared to solution. Some flexibility of the myoglobin is required for these reactions to occur; a nucleophile is required near the chromophores for photoreduction (Krasnovskii reaction), and oxygen for photooxidation. Oxidation of the bacteriochlorin in the complex and in aqueous solution continues in the dark. © 2006 Elsevier B.V. -
Novel Bioactive Metabolites from a Marine Derived Bacterium Nocardia Sp. ALAA 2000 Mervat M
J. Antibiot. 61(6): 379–386, 2008 THE JOURNAL OF ORIGINAL ARTICLE ANTIBIOTICS Novel Bioactive Metabolites from a Marine Derived Bacterium Nocardia sp. ALAA 2000 Mervat M. A. El-Gendy, Usama W. Hawas, Marcel Jaspars Received: November 4, 2007 / Accepted: June 10, 2008 © Japan Antibiotics Research Association Abstract Extracts of the Egyptian marine actinomycete, represent an enormous resource for the discovery of Nocardia sp. ALAA 2000, were found to be highly chemotherapeutic agents. Given the diversity of marine bioactive. It was isolated from the marine red alga organisms and habitats, marine natural products encompass Laurenica spectabilis collected off the Ras-Gharib coast of a wide variety of chemical classes such as terpenes, the Red Sea, Egypt. According to detailed identification polyketides, acetogenins, peptides and alkaloids of varying studies, the strain was classified as a member of the genus structures, representing biosynthetic schemes of stunning Nocardia. The cultivation and chemical analysis of this variety. Over the past 30 to 40 years, marine organisms species yielded four structurally related compounds have been the focus of a worldwide effort for the discovery namely, chrysophanol 8-methyl ether (1), asphodelin; 4,7Ј- of novel natural products [1]. Marine microorganisms bichrysophanol (2) and justicidin B (3), in addition to (actinobacteria) are sources of novel compounds with often a novel bioactive compound ayamycin; 1,1-dichloro-4- unique structures and potential therapeutic applications. ethyl-5-(4-nitro-phenyl)-hexan-2-one (4) which is unique The Actinomycetes are widely distributed in natural and in contain both chlorination and a rarely observed nitro manmade environments and are also well known as a rich group.