DOCSLIB.ORG

Assessing the Robustness of Genetic Codes and Genomes

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Université de Montréal Assessing the robustness of genetic codes and genomes par Miguel Sautié Castellanos Département d’informatique et de recherche opérationnelle Faculté des arts et des sciences Mémoire présenté à la Faculté des études supérieures en vue de l’obtention du grade de Maître ès sciences (M.Sc.) en informatique Juin, 2020 © Miguel Sautié Castellanos, 2020 Université de Montréal Faculté des arts et des sciences Ce mémoire intitulé: Assessing the robustness of genetic codes and genomes présenté par: Miguel Sautié Castellanos a été évalué par un jury composé des personnes suivantes: Miklós Csűrös, président-rapporteur Nadia El-Mabrouk, directeur de recherche François Major, membre du jury Mémoire accepté le: . ABSTRACT There are two main approaches to assess the robustness of genetic codes and coding sequences. The statistical approach is based on empirical estimates of probabilities computed from random samples of permutations representing assignments of amino acids to codons, whereas, the optimization-based approach relies on the optimization percentage frequently computed by using metaheuristics. We propose a method based on the first two moments of the distribution of robustness values for all possible genetic codes. Based on a polynomially solvable instance of the Quadratic Assignment Problem, we propose also an exact greedy algorithm to find the minimum value of the genome robustness. To reduce the number of operations for computing the scores and Cantelli’s upper bound, we developed methods based on the genetic code neighborhood structure and pairwise comparisons between genetic codes, among others. For assessing the robustness of natural genetic codes and genomes, we have chosen 23 natural genetic codes, 235 amino acid properties, as well as 324 thermophilic and 418 non-thermophilic prokaryotes. Among our results, we found that although the standard genetic code is more robust than most genetic codes, some mitochondrial and nuclear genetic codes are more robust than the standard code at the third and first codon positions, respectively. We also observed that the synonymous codon usage tends to be highly optimized to buffer the impact of single-base changes, mainly, in thermophilic prokaryotes. Keywords: Quadratic assignment problem, Cantelli’s upper bound, Generalized linear mixed models, Genetic code, hydrophobicity, thermophiles, codon usage bias. i RÉSUMÉ Deux approches principales existent pour évaluer la robustesse des codes génétiques et des séquences de codage. L'approche statistique est basée sur des estimations empiriques de probabilité calculées à partir d'échantillons aléatoires de permutations représentant les affectations d'acides aminés aux codons, alors que l'approche basée sur l'optimisation repose sur le pourcentage d’optimisation, généralement calculé en utilisant des métaheuristiques. Nous proposons une méthode basée sur les deux premiers moments de la distribution des valeurs de robustesse pour tous les codes génétiques possibles. En se basant sur une instance polynomiale du Problème d'Affectation Quadratique, nous proposons un algorithme vorace exact pour trouver la valeur minimale de la robustesse génomique. Pour réduire le nombre d'opérations de calcul des scores et de la borne supérieure de Cantelli, nous avons développé des méthodes basées sur la structure de voisinage du code génétique et sur la comparaison par paires des codes génétiques, entre autres. Pour calculer la robustesse des codes génétiques naturels et des génomes procaryotes, nous avons choisi 23 codes génétiques naturels, 235 propriétés d'acides aminés, ainsi que 324 procaryotes thermophiles et 418 procaryotes non thermophiles. Parmi nos résultats, nous avons constaté que bien que le code génétique standard soit plus robuste que la plupart des codes génétiques, certains codes génétiques mitochondriaux et nucléaires sont plus robustes que le code standard aux troisièmes et premières positions des codons, respectivement. Nous avons observé que l'utilisation des codons synonymes tend à être fortement optimisée pour amortir l'impact des changements d'une seule base, principalement chez les procaryotes thermophiles. Mots-clés: Problème d'Affectation Quadratique, La borne supérieure de Cantelli, Modèles linéaires Généralisés mixtes, Code génétique, hydrophobicité, thermophiles, biais d'utilisation des codons. ii CONTENTS ABSTRACT ......................................................................................................................................................i RÉSUMÉ .......................................................................................................................................................... ii CHAPTER 1 : INTRODUCTION ..................................................................................................................... 1 CHAPTER 2: ON THE ROBUSTNESS OF THE GENETIC CODES AND GENOMES .................................. 8 2.1 Early evolution of the standard genetic code ................................................................................................. 8 2.2 Recent evolution of the standard genetic code .............................................................................................. 9 2.3 Methods to quantify the genetic code robustness ....................................................................................... 11 2.3.1 Exploring different functions of weighted mean phenotypic change .................................................. 11 2.3.2 Evaluating different scenarios of genetic code evolution .................................................................... 12 2.3.3 The optimization algorithms used to assess genetic code robustness .............................................. 14 2.4 Robustness at the gene and genome level ................................................................................................... 15 CHAPTER 3: A BRIEF INTRODUCTION ON THE QUADRATIC ASSIGNMENT PROBLEM .................... 18 3.1 Solution methods ............................................................................................................................................ 18 3.2 Lower bounds .................................................................................................................................................. 19 3.3 Instances of QAP solvable in polynomial time ............................................................................................. 20 CHAPTER 4: METHODS .............................................................................................................................. 23 4.1 Research objectives and methods ................................................................................................................. 23 4.2 Two methods for assessing the relevance of the mean phenotypic change ............................................. 27 4.2.1 Load minimization problem (LMP) .......................................................................................................... 28 4.2.2 The statistical approach .......................................................................................................................... 31 4.3 Representations of the genetic codes ........................................................................................................... 33 4.3.1 The codon-based representations .......................................................................................................... 34 4.3.2 The representations based on synonymous codon blocks ................................................................. 35 4.3.3 Partial genetic code representations ...................................................................................................... 36 4.3.4 Block and codon neighborhood representations .................................................................................. 36 4.4 Weight functions .............................................................................................................................................. 38 4.4.1 Weights for genetic code robustness ..................................................................................................... 38 4.4.2 Weights for genomic robustness ............................................................................................................ 40 4.5 Methods to process stop codons ................................................................................................................... 41 4.6 The neighborhood structure of the genetic codes ....................................................................................... 43 4.7 Methods to compute the mean phenotypic change ..................................................................................... 46 4.7.1 Computing the mean phenotypic change for different genetic code representations ....................... 47 4.7.2 Considering the codon neighborhood structure for computing the genomic robustness ................ 48 4.7.3 Computing the mean phenotypic change for different genetic codes ................................................ 50 4.8 Methods to assess the relevance of genome and genetic code robustness ............................................. 51 4.8.1 Mean of the null population distribution ................................................................................................ 52 4.8.2 Variance of the null population distribution .........................................................................................
Recommended publications
  • Deinococcus Radiodurans : La Recombinaison Entre S´Equencesr´Ep´Et´Eeset La Transformation Naturelle Solenne Ithurbide

    Deinococcus Radiodurans : La Recombinaison Entre S´Equencesr´Ep´Et´Eeset La Transformation Naturelle Solenne Ithurbide

    Variabilit´eg´en´etiquechez la bact´erieradior´esistante Deinococcus radiodurans : la recombinaison entre s´equencesr´ep´et´eeset la transformation naturelle Solenne Ithurbide To cite this version: Solenne Ithurbide. Variabilit´eg´en´etiquechez la bact´erieradior´esistante Deinococcus radio- durans : la recombinaison entre s´equencesr´ep´et´eeset la transformation naturelle. Biologie mol´eculaire.Universit´eParis Sud - Paris XI, 2015. Fran¸cais. <NNT : 2015PA112193>. <tel- 01374867> HAL Id: tel-01374867 https://tel.archives-ouvertes.fr/tel-01374867 Submitted on 2 Oct 2016 HAL is a multi-disciplinary open access L'archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destin´eeau d´ep^otet `ala diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publi´esou non, lished or not. The documents may come from ´emanant des ´etablissements d'enseignement et de teaching and research institutions in France or recherche fran¸caisou ´etrangers,des laboratoires abroad, or from public or private research centers. publics ou priv´es. UNIVERSITÉ PARIS-SUD ÉCOLE DOCTORALE 426 GÈNES GÉNOMES CELLULES Institut de Biologie Intégrative de la Cellule THÈSE DE DOCTORAT SCIENCES DE LA VIE ET DE LA SANTÉ par Solenne ITHURBIDE Variabilité génétique chez la bactérie radiorésistante Deinococcus radiodurans : La recombinaison entre séquences répétées et la transformation naturelle Soutenue le 23 Septembre 2015 Composition du jury : Directeur de thèse : Suzanne SOMMER Professeur
  • The Hydrocarbon Biodegradation Potential of Faroe-Shetland Channel Bacterioplankton

    The Hydrocarbon Biodegradation Potential of Faroe-Shetland Channel Bacterioplankton

    THE HYDROCARBON BIODEGRADATION POTENTIAL OF FAROE-SHETLAND CHANNEL BACTERIOPLANKTON Angelina G. Angelova Submitted for the degree of Doctor of Philosophy Heriot Watt University School of Engineering and Physical Sciences July 2017 The copyright in this thesis is owned by the author. Any quotation from the thesis or use of any of the information contained in it must acknowledge this thesis as the source of the quotation or information. ABSTRACT The Faroe-Shetland Channel (FSC) is an important gateway for dynamic water exchange between the North Atlantic Ocean and the Nordic Seas. In recent years it has also become a frontier for deep-water oil exploration and petroleum production, which has raised the risk of oil pollution to local ecosystems and adjacent waterways. In order to better understand the factors that influence the biodegradation of spilled petroleum, a prerequisite has been recognized to elucidate the complex dynamics of microbial communities and their relationships to their ecosystem. This research project was a pioneering attempt to investigate the FSC’s microbial community composition, its response and potential to degrade crude oil hydrocarbons under the prevailing regional temperature conditions. Three strategies were used to investigate this. Firstly, high throughput sequencing and 16S rRNA gene-based community profiling techniques were utilized to explore the spatiotemporal patterns of the FSC bacterioplankton. Monitoring proceeded over a period of 2 years and interrogated the multiple water masses flowing through the region producing 2 contrasting water cores: Atlantic (surface) and Nordic (subsurface). Results revealed microbial profiles more distinguishable based on water cores (rather than individual water masses) and seasonal variability patterns within each core.
  • Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide

    Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide

    microorganisms Article Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide Kelly J. Hidalgo 1,2,* , Isabel N. Sierra-Garcia 3 , German Zafra 4 and Valéria M. de Oliveira 1 1 Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas–UNICAMP, Av. Alexandre Cazellato 999, 13148-218 Paulínia, Brazil; [email protected] 2 Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato 255, Cidade Universitária, 13083-862 Campinas, Brazil 3 Biology Department & CESAM, University of Aveiro, Aveiro, Portugal, Campus de Santiago, Avenida João Jacinto de Magalhães, 3810-193 Aveiro, Portugal; [email protected] 4 Grupo de Investigación en Bioquímica y Microbiología (GIBIM), Escuela de Microbiología, Universidad Industrial de Santander, Cra 27 calle 9, 680002 Bucaramanga, Colombia; [email protected] * Correspondence: [email protected]; Tel.: +55-19981721510 Abstract: Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to decipher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301.2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 metagenome-assembled genomes (MAGs) of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to archaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied.
  • Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations

    Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations

    fmicb-09-02879 December 1, 2018 Time: 14:0 # 1 ORIGINAL RESEARCH published: 04 December 2018 doi: 10.3389/fmicb.2018.02879 Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations Klervi Crenn, Delphine Duffieux and Christian Jeanthon* CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community- level methods and culture-based or natural diatom populations. Although bacterial assemblages attached to individual diatoms represents tight associations little is known on their makeup or interactions. Here, we examined the epibiotic bacteria of 436 Thalassiosira and 329 Chaetoceros single cells isolated from natural samples and Edited by: collection cultures, regarded here as short- and long-term associations, respectively. Matthias Wietz, Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning- Alfred Wegener Institut, Germany sequencing of 16S rRNA genes obtained from whole-genome amplification products. Reviewed by: The prevalence of epibiotic bacteria was higher in cultures and dependent of the host Lydia Jeanne Baker, Cornell University, United States species. Culture approaches demonstrated that both diatoms carry distinct bacterial Bryndan Paige Durham, communities in short- and long-term associations. Bacterial epibonts, commonly University of Washington, United States associated with phytoplankton, were repeatedly isolated from cells of diatom collection *Correspondence: cultures but were not recovered from environmental cells.
  • Geomicrobiological Processes in Extreme Environments: a Review

    Geomicrobiological Processes in Extreme Environments: a Review

    202 Articles by Hailiang Dong1, 2 and Bingsong Yu1,3 Geomicrobiological processes in extreme environments: A review 1 Geomicrobiology Laboratory, China University of Geosciences, Beijing, 100083, China. 2 Department of Geology, Miami University, Oxford, OH, 45056, USA. Email: [email protected] 3 School of Earth Sciences, China University of Geosciences, Beijing, 100083, China. The last decade has seen an extraordinary growth of and Mancinelli, 2001). These unique conditions have selected Geomicrobiology. Microorganisms have been studied in unique microorganisms and novel metabolic functions. Readers are directed to recent review papers (Kieft and Phelps, 1997; Pedersen, numerous extreme environments on Earth, ranging from 1997; Krumholz, 2000; Pedersen, 2000; Rothschild and crystalline rocks from the deep subsurface, ancient Mancinelli, 2001; Amend and Teske, 2005; Fredrickson and Balk- sedimentary rocks and hypersaline lakes, to dry deserts will, 2006). A recent study suggests the importance of pressure in the origination of life and biomolecules (Sharma et al., 2002). In and deep-ocean hydrothermal vent systems. In light of this short review and in light of some most recent developments, this recent progress, we review several currently active we focus on two specific aspects: novel metabolic functions and research frontiers: deep continental subsurface micro- energy sources. biology, microbial ecology in saline lakes, microbial Some metabolic functions of continental subsurface formation of dolomite, geomicrobiology in dry deserts, microorganisms fossil DNA and its use in recovery of paleoenviron- Because of the unique geochemical, hydrological, and geological mental conditions, and geomicrobiology of oceans. conditions of the deep subsurface, microorganisms from these envi- Throughout this article we emphasize geomicrobiological ronments are different from surface organisms in their metabolic processes in these extreme environments.
  • ( 12 ) United States Patent

    ( 12 ) United States Patent

    US010314866B2 (12 ) United States Patent (10 ) Patent No. : US 10 ,314 ,866 B2 Kovarik ( 45 ) Date of Patent: * Jun . 11, 2019 ( 54 ) METHOD OF REDUCING THE 61/ 919 , 297 , filed on Dec . 20 , 2013, provisional LIKELIHOOD OF SKIN CANCER IN AN application No . 61/ 467, 767 , filed on Mar . 25, 2011 . INDIVIDUAL HUMAN BEING (71 ) Applicant: Joseph E . Kovarik , Englewood , CO (51 ) Int. Cl. (US ) A61K 31 / 58 ( 2006 . 01 ) A61K 35 /00 (2006 . 01 ) (72 ) Inventor: Joseph E . Kovarik , Englewood , CO A61K 35 / 74 (2015 . 01 ) ( US ) A61K 38 / 17 ( 2006 .01 ) A61K 31 / 715 ( 2006 . 01 ) ( * ) Notice : Subject to any disclaimer , the term of this patent is extended or adjusted under 35 (32 ) U . S . Cl. CPC .. .. .. .. A61K 35 / 74 ( 2013 .01 ) ; A61K 31 /58 U . S . C . 154 ( b ) by 0 days . (2013 .01 ) ; A61K 31/ 715 (2013 . 01 ) ; A61K This patent is subject to a terminal dis 38 / 1709 (2013 . 01 ) ; A61K 38 / 1758 ( 2013 .01 ) ; claimer . A61K 2035 / 11 ( 2013 .01 ) (58 ) Field of Classification Search ( 21) Appl. No .: 16 / 160, 336 None (22 ) Filed : Oct . 15, 2018 See application file for complete search history . (65 ) Prior Publication Data ( 56 ) References Cited US 2019 / 0038680 A1 Feb . 7 , 2019 U . S . PATENT DOCUMENTS Related U . S . Application Data 3 , 178 , 341 A 4 / 1965 Hamill et al . 4 , 568 ,639 A 2 / 1986 Lew (63 ) Continuation of application No . 15 / 403 , 823 , filed on 4 ,687 , 841 A 8 / 1987 Spilburg et al. Jan . 11 , 2017 , now Pat. No. 10 , 111, 913 , which is a 4 , 720 ,486 A 1 / 1988 Spilburg et al .
  • Studies on the Role of the Keratinocytes in Cutaneous Immnity

    Studies on the Role of the Keratinocytes in Cutaneous Immnity

    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Repository of the Academy's Library Factors shaping the composition of the cutaneous microbiota K. Szabó1, L. Erdei2, B. Sz. Bolla2, G. Tax2, T. Bíró3, L. Kemény1,2 1. MTA-SZTE Dermatological Research Group, Szeged, Hungary 2. Department of Dermatology and Allergology, University of Szeged, Hungary 3. DE-MTA “Lendület” Cellular Physiology Research Group, Departments of Physiology and Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary Running head: Factors shaping the composition of the cutaneous microbiota Manuscript word count: Manuscript table count: none Manuscript figure count: none Corresponding author: Kornélia Szabó Tel: +36-62-545 799 Fax: +36-62-545 799 E-mail address: [email protected] Keywords: microbiota, cutaneous microbiota, Propionibacterium acnes, acne vulgaris, disappearing microbiota hypothesis What's already known about this topic: -Microbes are integral components of the human ecosystem. -The cutaneous microbiota plays an important role in the regulation of skin homeostasis. -The composition of skin microbiota is influenced by many factors. What does this study add? -The dominance of P. acnes in the postadolescent sebum-rich skin regions and its role in acne pathogenesis may be explained by the disappearing microbiota hypothesis. Funding sources: Hungarian Scientific Research Fund (OTKA NK105369), János Bolyai Research Scholarship from the Hungarian Academy of Sciences (for K. Sz). Conflict of interest: The authors declare no conflict of interest. 1 Abstract From our birth, we are constantly exposed to bacteria, fungi and viruses, some of which are capable of transiently or permanently inhabiting our different body parts as our microbiota.
  • Bacterium That Produces Antifouling Agents

    Bacterium That Produces Antifouling Agents

    International Journal of Systematic Bacteriology (1998), 48, 1205-1 21 2 Printed in Great Britain ~- Pseudoalteromonas tunicata sp. now, a bacterium that produces antifouling agents Carola Holmstromfl Sally James,’ Brett A. Neilan,’ David C. White’ and Staffan Kjellebergl Author for correspondence : Carola Holmstrom. Tel: + 61 2 9385 260 1. Fax: + 6 1 2 9385 159 1. e-mail: c.holmstrom(cx unsw.edu.au 1 School of Microbiology A dark-green-pigmented marine bacterium, previously designated D2, which and Immunology, The produces components that are inhibitory to common marine fouling organisms University of New South Wales, Sydney 2052, has been characterized and assessed for taxonomic assignment. Based on Australia direct double-stranded sequencing of the 16s rRNA gene, D2Twas found to show the highest similarity to members of the genus 2 Center for Environmental (93%) B iotechnology, Un iversity Pseudoalteromonas. The G+C content of DZT is 42 molo/o, and it is a of Tennessee, 10515 facultatively anaerobic rod and oxidase-positive. DZT is motile by a sheathed research Drive, Suite 300, Knoxville, TN 37932, USA polar flagellum, exhibited non-fermentative metabolism and required sodium ions for growth. The strain was not capable of using citrate, fructose, sucrose, sorbitol and glycerol but it utilizes mannose and maltose and hydrolyses gelatin. The molecular evidence, together with phenotypic characteristics, showed that this bacterium which produces an antifouling agent constitutes a new species of the genus Pseudoalteromonas.The name Pseudoalteromonas tunicata is proposed for this bacterium, and the type strain is DZT (= CCUG 2 6 7 5 7T). 1 Kevwords: PseudoalttJvomonas tunicata, pigment, antifouling bacterium, marine, 16s I rRNA sequence .__ , INTRODUCTION results suggested that the genus Alteromonas should be separated into two genera.
  • Isolation and Characterization of a Biosurfactant from Deinococcus Caeni PO5 Using Jackfruit Seed Powder As a Substrate

    Isolation and Characterization of a Biosurfactant from Deinococcus Caeni PO5 Using Jackfruit Seed Powder As a Substrate

    Ann Microbiol (2014) 64:1007–1020 DOI 10.1007/s13213-013-0738-2 ORIGINAL ARTICLE Isolation and characterization of a biosurfactant from Deinococcus caeni PO5 using jackfruit seed powder as a substrate Chanika Saenge Chooklin & Sirirat Petmeaun & Suppasil Maneerat & Atipan Saimmai Received: 15 April 2013 /Accepted: 18 October 2013 /Published online: 22 January 2014 # Springer-Verlag Berlin Heidelberg and the University of Milan 2014 Abstract Biosurfactant-producing bacteria were isolated Keywords Deinococcus caeni . Isolation . Jackfruit seed from various sources in the south of Thailand. Isolates were powder . Surface tension . Biosurfactant . Polyaromatic screened for biosurfactant production using jackfruit seed hydrocarbons . Microbial oil recovery powder (JSP) as a novel and promising substrate. The highest biosurfactant activity was obtained with a bacterial strain which was identified by 16S rRNA gene sequence analysis Introduction as Deinococcus caeni PO5. D. caeni PO5 was able to grow and reduce the surface tension of the culture supernatant from Biosurfactants are a diverse group of surface-active agents 67.0 to 25.0 mN/m after 87 h of cultivation when 40 g/l of JSP with both hydrophilic and hydrophobic moieties and are pro- and 1 g/l of commercial monosodium glutamate were used as duced by many living microorganisms, such as bacteria and carbon and nitrogen sources, respectively. The biosurfactant fungi (Desai and Banat 1997). Biosurfactants have many obtained by ethyl acetate extraction showed high surface advantages over synthetic surfactants. These include a lower tension reduction (47.0 mN/m), a small critical micelle con- toxicity and higher biodegradability, which makes them more centration value (8 mg/l), thermal and pH stability with re- environmentally friendly, better foaming properties, milder spect to surface tension reduction and emulsification activity, production conditions, lower critical micelle concentration, and a high level of salt tolerance.
  • Deinococcus Antarcticus Sp. Nov., Isolated from Soil

    Deinococcus Antarcticus Sp. Nov., Isolated from Soil

    International Journal of Systematic and Evolutionary Microbiology (2015), 65, 331–335 DOI 10.1099/ijs.0.066324-0 Deinococcus antarcticus sp. nov., isolated from soil Ning Dong,1,2 Hui-Rong Li,1 Meng Yuan,1,2 Xiao-Hua Zhang2 and Yong Yu1 Correspondence 1SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, Yong Yu PR China [email protected] 2College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China A pink-pigmented, non-motile, coccoid bacterial strain, designated G3-6-20T, was isolated from a soil sample collected in the Grove Mountains, East Antarctica. This strain was resistant to UV irradiation (810 J m”2) and slightly more sensitive to desiccation as compared with Deinococcus radiodurans. Phylogenetic analyses based on the 16S rRNA gene sequence of the isolate indicated that the organism belongs to the genus Deinococcus. Highest sequence similarities were with Deinococcus ficus CC-FR2-10T (93.5 %), Deinococcus xinjiangensis X-82T (92.8 %), Deinococcus indicus Wt/1aT (92.5 %), Deinococcus daejeonensis MJ27T (92.3 %), Deinococcus wulumuqiensis R-12T (92.3 %), Deinococcus aquaticus PB314T (92.2 %) and T Deinococcus radiodurans DSM 20539 (92.2 %). Major fatty acids were C18 : 1v7c, summed feature 3 (C16 : 1v7c and/or C16 : 1v6c), anteiso-C15 : 0 and C16 : 0. The G+C content of the genomic DNA of strain G3-6-20T was 63.1 mol%. Menaquinone 8 (MK-8) was the predominant respiratory quinone. Based on its phylogenetic position, and chemotaxonomic and phenotypic characteristics, strain G3-6-20T represents a novel species of the genus Deinococcus, for which the name Deinococcus antarcticus sp.
  • Differences in Lateral Gene Transfer in Hypersaline Versus Thermal Environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1

    Differences in Lateral Gene Transfer in Hypersaline Versus Thermal Environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1

    Rhodes et al. BMC Evolutionary Biology 2011, 11:199 http://www.biomedcentral.com/1471-2148/11/199 RESEARCH ARTICLE Open Access Differences in lateral gene transfer in hypersaline versus thermal environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1 Abstract Background: The role of lateral gene transfer (LGT) in the evolution of microorganisms is only beginning to be understood. While most LGT events occur between closely related individuals, inter-phylum and inter-domain LGT events are not uncommon. These distant transfer events offer potentially greater fitness advantages and it is for this reason that these “long distance” LGT events may have significantly impacted the evolution of microbes. One mechanism driving distant LGT events is microbial transformation. Theoretically, transformative events can occur between any two species provided that the DNA of one enters the habitat of the other. Two categories of microorganisms that are well-known for LGT are the thermophiles and halophiles. Results: We identified potential inter-class LGT events into both a thermophilic class of Archaea (Thermoprotei) and a halophilic class of Archaea (Halobacteria). We then categorized these LGT genes as originating in thermophiles and halophiles respectively. While more than 68% of transfer events into Thermoprotei taxa originated in other thermophiles, less than 11% of transfer events into Halobacteria taxa originated in other halophiles. Conclusions: Our results suggest that there is a fundamental difference between LGT in thermophiles and halophiles. We theorize that the difference lies in the different natures of the environments. While DNA degrades rapidly in thermal environments due to temperature-driven denaturization, hypersaline environments are adept at preserving DNA.
  • Insights Into Archaeal Evolution and Symbiosis from the Genomes of a Nanoarchaeon and Its Inferred Crenarchaeal Host from Obsidian Pool, Yellowstone National Park

    Insights Into Archaeal Evolution and Symbiosis from the Genomes of a Nanoarchaeon and Its Inferred Crenarchaeal Host from Obsidian Pool, Yellowstone National Park

    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Microbiology Publications and Other Works Microbiology 4-22-2013 Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar University of Tennessee - Knoxville, [email protected] Kira S. Makarova National Institutes of Health David E. Graham University of Tennessee - Knoxville, [email protected] Yuri I. Wolf National Institutes of Health Eugene V. Koonin National Institutes of Health See next page for additional authors Follow this and additional works at: https://trace.tennessee.edu/utk_micrpubs Part of the Microbiology Commons Recommended Citation Biology Direct 2013, 8:9 doi:10.1186/1745-6150-8-9 This Article is brought to you for free and open access by the Microbiology at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Microbiology Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Authors Mircea Podar, Kira S. Makarova, David E. Graham, Yuri I. Wolf, Eugene V. Koonin, and Anna-Louise Reysenbach This article is available at TRACE: Tennessee Research and Creative Exchange: https://trace.tennessee.edu/ utk_micrpubs/44 Podar et al. Biology Direct 2013, 8:9 http://www.biology-direct.com/content/8/1/9 RESEARCH Open Access Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar1,2*, Kira S Makarova3, David E Graham1,2, Yuri I Wolf3, Eugene V Koonin3 and Anna-Louise Reysenbach4 Abstract Background: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes.