DOCSLIB.ORG

Factors Controlling the Distribution of Archaeal Tetraethers in Terrestrial

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Factors Controlling the Distribution of Archaeal Tetraethers in Terrestrial APPLIED AND ENVIRONMENTAL MICROBIOLOGY, June 2008, p. 3523–3532 Vol. 74, No. 11 0099-2240/08/$08.00ϩ0 doi:10.1128/AEM.02450-07 Copyright © 2008, American Society for Microbiology. All Rights Reserved. Factors Controlling the Distribution of Archaeal Tetraethers in Terrestrial Hot Springsᰔ Ann Pearson,1* Yundan Pi,1,2,3 Weidong Zhao,3 WenJun Li,4 Yiliang Li,3† William Inskeep,5 Anna Perevalova,6 Christopher Romanek,3 Shuguang Li,2 and Chuanlun L. Zhang3* Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts1; School of Earth and Space Sciences, the University of Sciences and Technology of China, Hefei, China2; Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina3; Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, China4; Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana5; and Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia6 Received 30 October 2007/Accepted 10 March 2008 Glycerol dialkyl glycerol tetraethers (GDGTs) found in hot springs reflect the abundance and community structure of Archaea in these extreme environments. The relationships between GDGTs, archaeal communities, and physical or geochemical variables are underexamined to date and when reported often result in conflicting interpretations. Here, we examined profiles of GDGTs from pure cultures of Crenarchaeota and from terrestrial geothermal springs representing a wide distribution of locations, including Yellowstone National Park (United States), the Great Basin of Nevada and California (United States), Kamchatka (Russia), Tengchong thermal field (China), and Thailand. These samples had temperatures of 36.5 to 87°C and pH values of 3.0 to 9.2. GDGT abundances also were determined for three soil samples adjacent to some of the hot springs. Principal component analysis identified four factors that accounted for most of the variance among nine individual GDGTs, temperature, and pH. Significant correlations were observed between pH and the GDGTs crenar- chaeol and GDGT-4 (four cyclopentane rings, m/z 1,294); pH correlated positively with crenarchaeol and inversely with GDGT-4. Weaker correlations were observed between temperature and the four factors. Three of the four GDGTs used in the marine TEX86 paleotemperature index (GDGT-1 to -3, but not crenarchaeol isomer) were associated with a single factor. No correlation was observed for GDGT-0 (acyclic caldarchaeol): it is effectively its own variable. The biosynthetic mechanisms and exact archaeal community structures leading to these relationships remain unknown. However, the data in general show promise for the continued devel- opment of GDGT lipid-based physiochemical proxies for archaeal evolution and for paleo-ecology or paleo- climate studies. Isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs) unpublished) to be a response to increased acidity (lower pH), are widely used as taxonomic (12, 13, 27, 28) and physicochem- it is likely that multiple variables play significant roles when ical (3, 32, 45, 50, 54, 61; E. S. Boyd, A. Pearson, Y. Pi, W. Li, adjusting archaeal membranes to cope with environmental and C. L. Zhang, and G. G. Geesey, unpublished data) biomarkers energetic stresses (52, 53). to study present (1, 3, 24, 35) or ancient (30, 37, 43) commu- The cyclohexane ring-containing GDGT, crenarchaeol, is nities of Archaea. GDGTs have biphytanyl core lipids with zero widespread in the environment (e.g., see references 18, 24, 31, to as many as four cyclopentyl rings and zero or one cyclohexyl 36, 39, 41, 46, 56, and 61) and appears to be a biomarker ring on each side chain (41). Some studies of both pure cul- exclusively for Crenarchaeota (42, 46). It originally was pro- tures of Crenarchaeota (11, 16, 50, 51; Boyd et al., unpublished) posed to be specific for nonthermophilic species found in ma- and of environmental samples (39, 42, 43, 58) show that the rine systems (46). More recently, the environmental niches in number of rings increases with growth temperature, while which crenarchaeol is found have been expanded to include other studies focusing on different species or environmental lacustrine waters (39), soils (31, 56), and terrestrial geothermal settings show that this relationship is weaker or apparently environments (36, 61). The formation of a unique cyclohexane absent (6, 36, 45, 61). Because the increased number of cyclo- ring distinguishes crenarchaeol from the other GDGTs, and it pentyl rings also has been shown experimentally (14, 32; Boyd was proposed that this ring reflects physiological and evolu- et al., unpublished) and through surveys (17, 32, 57; Boyd et al., tionary adaptation to low-temperature marine environments (30, 46). Thus, the reports of crenarchaeol in geothermal springs at temperatures above 40°C were surprising (36, 61) * Corresponding author. Mailing address for A. Pearson: 20 Oxford and have been questioned (45). The recent cultivation, how- St., Cambridge, MA 02138. Phone: (617) 384-8392. Fax: (617) 496- 4387. E-mail: [email protected]. Mailing address for C. L. ever, of the hyperthermophile “Candidatus Nitrosocaldus yel- Zhang: Savannah River Ecology Laboratory, University of Georgia, lowstonii” (10) shows that synthesis of crenarchaeol can be Aiken, SC 29802. Phone: (803) 725-5299. Fax: (803) 725-3309. E-mail: abundant in organisms thriving at high temperatures. [email protected]. Multivariable control of community and lipid compositions † Present address: Department of Earth Sciences, The University of Hong Kong, Hong Kong, China. results in distributions of environmental GDGTs that can be ᰔ Published ahead of print on 4 April 2008. difficult to interpret. Examination of hot spring data using 3523 3524 PEARSON ET AL. TABLE 1. HPLC-MS data for GDGT relative abundance, hot spring temperature, and pH Locationa GDGT abundanceb c Temp GDGT- GDGT- GDGT- GDGT- GDGT- GDGT- GDGT-5‡ GDGT- GDGT- GDGT- Sample source pH GDGT-5† North West or east (°C) 0(m/z 1(m/z 2(m/z 3(m/z 4(m/z 4Ј (m/z (crenarchaeol 5Ј (m/z 6(m/z 6Ј (m/z (crenarchaeol) 1,302) 1,300) 1,298) 1,296) 1,294) 1,294) isomer) 1,292) 1,290) 1,290) Yellowstone Beowulf-ED1 44°43Ј53.4Љ 110°42Ј40.9Љ (west) 67 3.1 0.11 0.12 0.22 0.16 0.37 0.00 0.00 0.00 0.02 0.00 0.00 Beowulf-ED2 44°43Ј53.4Љ 110°42Ј 40.9Љ (west) 62 3.1 0.12 0.12 0.21 0.17 0.31 0.00 0.00 0.00 0.05 0.02 0.00 Beowulf-WD 44°43Ј53.4Љ 110°42Ј41.1Љ (west) 60 3.0 0.07 0.10 0.19 0.23 0.39 0.00 0.00 0.00 0.02 0.00 0.00 Calcite Spring-B 44°54Ј29.1Љ 110°24Ј2.42Љ (west) 74 8.2 0.35 0.19 0.13 0.09 0.10 0.00 0.00 0.00 0.06 0.08 0.00 Calcite Spring-C 44°54Ј29.1Љ 110°24Ј2.42Љ (west) 75 7.8 0.43 0.20 0.14 0.10 0.09 0.00 0.00 0.00 0.02 0.02 0.00 Cistern Spring 44°43Ј23.1Љ 110°42Ј14.5Љ (west) 82 5.3 0.24 0.18 0.14 0.18 0.22 0.00 0.00 0.00 0.02 0.02 0.0 Echinus Geyser 44°43Ј19.4Љ 110°42Ј07.6Љ (west) 75 3.4 0.02 0.04 0.10 0.23 0.52 0.00 0.00 0.00 0.07 0.02 0.00 Joseph’s Coat 44°44Ј21.4Љ 110°19Ј28.2Љ (west) 82 6.2 0.14 0.20 0.21 0.23 0.15 0.00 0.00 0.00 0.03 0.04 0.00 Monarch Geyser 44°43Ј27.5Љ 110°42Ј20.2Љ (west) 85 4.4 0.00 0.00 0.03 0.20 0.77 0.00 0.00 0.00 0.00 0.00 0.00 Porcelain Basin 44°43Ј43.9Љ 110°42Ј12.0Љ (west) 75 3.5 0.00 0.00 0.04 0.12 0.39 0.00 0.00 0.00 0.27 0.18 0.00 Perpetual Spouter-B 44°43Ј36.0Љ 110°42Ј29.8Љ (west) 82 7.0 0.07 0.10 0.13 0.22 0.43 0.02 0.00 0.00 0.03 0.00 0.00 Whirligig Geyser 44°43Ј43.3Љ 110°42Ј11.3Љ (west) 66 3.4 0.02 0.03 0.06 0.29 0.53 0.00 0.02 0.00 0.05 0.00 0.00 Kamchatka, Russia Yellow Blue 51°29Ј53.1Љ 160°00Ј52.6Љ (east) 55 6.3 0.20 0.10 0.20 0.20 0.30 0.00 0.00 0.00 0.00 0.00 0.00 Zavarzin NA NA 57 6.3 0.21 0.09 0.16 0.21 0.33 0.00 0.00 0.00 0.00 0.00 0.00 Vent 1, North (K11) 51°30Ј40.5Љ 160°00Ј19.2Љ (east) 64 5.8 0.27 0.11 0.17 0.18 0.23 0.00 0.00 0.00 0.04 0.00 0.00 Rubber Mat (CR03022) 51°29Ј56.3Љ 160°00Ј55.9Љ (east) 66 5.6 0.20 0.10 0.20 0.20 0.30 0.00 0.00 0.00 0.00 0.00 0.00 Rubber Mat (JK04078) 51°29Ј56.3Ј 160°00Ј55.9Љ (east) 66 6.1 0.16 0.10 0.18 0.22 0.34 0.00 0.00 0.00 0.00 0.00 0.00 Arkashin (K1) 51°30Ј00.0Љ 160°00Ј20.0Љ (east) 69 4.9 0.05 0.05 0.13 0.27 0.45 0.00 0.00 0.00 0.05 0.00 0.00 Bubbler (K4) 51°30Ј02.4Љ 160°00Ј27.2Љ (east) 69 5.8 0.32 0.12 0.16 0.11 0.27 0.00 0.00 0.00 0.02 0.00 0.00 Blue pool (K7) 51°30Ј39.7Љ 160°00Ј18.7Љ (east) 74 5.0 0.27 0.10 0.16 0.17 0.25 0.00 0.00 0.00 0.05 0.00 0.00 Vent 2, North 51°30Ј39.7Љ 160°00Ј18.7Љ (east) 75 5.9 0.30 0.10 0.10 0.20 0.30 0.00 0.00 0.00 0.00 0.00 0.00 Vent 2, Jen’s site (K3) 51°30Ј02.5Љ 160°00Ј27.3Љ (east) 75 5.8 0.22 0.11 0.15 0.17 0.32 0.00 0.00 0.00 0.03 0.00 0.00 Green mat (K2) 51°30Ј02.4Љ 160°00Ј27.2Љ (east) 75 5.8 0.13 0.10 0.15 0.24 0.24 0.00 0.00 0.00 0.14 0.00 0.00 Tengchong, China Tengchong-A NA NA 80 6.6 0.13 0.24 0.25 0.25 0.13 0.00 0.00 0.00 0.00 0.00 0.00 Tengchong-C NA NA 80 6.6 0.13 0.11 0.16 0.25 0.30 0.00 0.00 0.00 0.05 0.00 0.00 Pure cultures Acidilobus aceticus 1904 82 3.5 0.20 0.00 0.00 0.00 0.34 0.00 0.00 0.00 0.46 0.00 0.00 Acidilobus saccharovorans 82 3.5 0.00 0.00 0.00 0.01 0.14 0.02 0.00 0.00 0.27 0.54 0.02 345-15 Metallosphaera sedulad 75 4.5 0.07 0.15 0.23 0.25 0.26 0.00 0.00 0.00 0.04 0.00 0.00 Sulfolobus solfataricuse 85 4.5 0.00 0.01 0.04 0.14 0.31 0.08 0.00 0.00 0.27 0.15 0.00 Vulcanisaeta moutnovskia 85 4.5 0.04 0.03 0.06 0.14 0.54 0.00 0.00 0.00 0.15 0.02 0.02 768-28 Thermoproteus uzoniensis 85 5.5 0.05 0.02 0.06 0.08 0.62 0.00 0.00 0.00 0.15 0.02 0.00 Z-605 Desulfurococcus fermentans 85 6.0 0.09 0.10 0.19 0.30 0.32 0.00 0.00 0.00 0.00 0.00 0.00 1312 Desulfurococcus 85 6.5 0.08 0.06 0.11 0.20 0.55 0.00 0.00 0.00 0.00 0.00 0.00 A amylolyticus Z-533 PPL .E Nevada soils NVIRON Surprise Valley NA NA 0.38 0.07 0.10 0.03 0.02 0.00 0.37 0.03 0.00 0.00 0.00 Eagleville NA NA 0.20 0.20 0.10 0.05 0.00 0.00 0.39 0.06 0.00 0.00 0.00 Rick’s Hot Creek NA NA 0.36 0.07 0.09 0.00 0.00 0.00 0.37 0.12 0.00 0.00 0.00 .M a NA, not available.
Load more

Recommended publications
  • Diversity of Understudied Archaeal and Bacterial Populations of Yellowstone National Park: from Genes to Genomes Daniel Colman
    University of New Mexico UNM Digital Repository Biology ETDs Electronic Theses and Dissertations 7-1-2015 Diversity of understudied archaeal and bacterial populations of Yellowstone National Park: from genes to genomes Daniel Colman Follow this and additional works at: https://digitalrepository.unm.edu/biol_etds Recommended Citation Colman, Daniel. "Diversity of understudied archaeal and bacterial populations of Yellowstone National Park: from genes to genomes." (2015). https://digitalrepository.unm.edu/biol_etds/18 This Dissertation is brought to you for free and open access by the Electronic Theses and Dissertations at UNM Digital Repository. It has been accepted for inclusion in Biology ETDs by an authorized administrator of UNM Digital Repository. For more information, please contact [email protected]. Daniel Robert Colman Candidate Biology Department This dissertation is approved, and it is acceptable in quality and form for publication: Approved by the Dissertation Committee: Cristina Takacs-Vesbach , Chairperson Robert Sinsabaugh Laura Crossey Diana Northup i Diversity of understudied archaeal and bacterial populations from Yellowstone National Park: from genes to genomes by Daniel Robert Colman B.S. Biology, University of New Mexico, 2009 DISSERTATION Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Biology The University of New Mexico Albuquerque, New Mexico July 2015 ii DEDICATION I would like to dedicate this dissertation to my late grandfather, Kenneth Leo Colman, associate professor of Animal Science in the Wool laboratory at Montana State University, who even very near the end of his earthly tenure, thought it pertinent to quiz my knowledge of oxidized nitrogen compounds. He was a man of great curiosity about the natural world, and to whom I owe an acknowledgement for his legacy of intellectual (and actual) wanderlust.
    [Show full text]
  • Tivities of the Thermococcales Alhr2 DNA/RNA Helicase
    Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 18 March 2021 doi:10.20944/preprints202103.0477.v1 Article Phylogenetic diversity of Lhr proteins and biochemical ac- tivities of the Thermococcales aLhr2 DNA/RNA helicase Mirna Hajj1,2†, Petra Langendijk-Genevaux1†, Manon Batista1, Yves Quentin1, Sébastien Laurent3, Ziad Abdel Raz- zak2, Didier Flament3, Hala Chamieh2, Gwennaele Fichant1*, Béatrice Clouet-d’Orval1* and Marie Bouvier1 1 Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse and France 2 Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and its application, Leba- nese University, Tripoli, Lebanon 3 Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, Ifremer, Université de Bretagne Oc- cidentale, CNRS, F-29280 Plouzané, France † Co-first authors * Correspondence: Corresponding authors Abstract Helicase proteins are known use the energy of ATP to unwind nucleic acids and to re- model protein-nucleic acid complexes. They are involved in almost every aspect of the DNA and RNA metabolisms and participate in numerous repair mechanisms that maintain cellular integrity. The archaeal Lhr-type proteins are SF2 helicases that are mostly uncharacterized. They have been proposed to be DNA helicases that act in DNA recombination and repair processes in Sulfolobales and Methanothermobacter. In Thermococcales, a protein annotated as an Lhr2 protein was found in the network of proteins involved in RNA metabolism. To this respect, we performed in-depth phylogenomic analyses to report the classification and taxonomic distribution of Lhr-type proteins in Archaea, and to better understand their relationship with bacterial Lhr.
    [Show full text]
  • Dominio Archaea
    FILOGENIA DE LOS SERES VIVOS: DOMINIO ARCHAEA Nuria Garzón Pinto Facultad de Farmacia Universidad de Sevilla Septiembre de 2017 FILOGENIA DE LOS SERES VIVOS: DOMINIO ARCHAEA TRABAJO FIN DE GRADO Nuria Garzón Pinto Tutores: Antonio Ventosa Ucero y Cristina Sánchez-Porro Álvarez Tipología del trabajo: Revisión bibliográfica Grado en Farmacia. Facultad de Farmacia Departamento de Microbiología y Parasitología (Área de Microbiología) Universidad de Sevilla Sevilla, septiembre de 2017 RESUMEN A lo largo de la historia, la clasificación de los seres vivos ha ido variando en función de las diversas aportaciones científicas que se iban proponiendo, y la historia evolutiva de los organismos ha sido durante mucho tiempo algo que no se lograba conocer con claridad. Actualmente, gracias sobre todo a las ideas aportadas por Carl Woese y colaboradores, se sabe que los seres vivos se clasifican en 3 dominios (Bacteria, Eukarya y Archaea) y se conocen las herramientas que nos permiten realizar estudios filogenéticos, es decir, estudiar el origen de las especies. La herramienta principal, y en base a la cual se ha realizado la clasificación actual es el ARNr 16S. Sin embargo, hoy día sedispone de otros métodos que ayudan o complementan los análisis de la evolución de los seres vivos. En este trabajo se analiza cómo surgió el dominio Archaea, se describen las características y aspectos más importantes de las especies este grupo y se compara con el resto de dominios (Bacteria y Eukarya). Las arqueas han despertado un gran interés científico y han sido investigadas sobre todo por su capacidad para adaptarse y desarrollarse en ambientes extremos.
    [Show full text]
  • A Meta-Analysis of the Publicly Available Bacterial and Archaeal Sequence Diversity in Saline Soils
    World J Microbiol Biotechnol (2013) 29:2325–2334 DOI 10.1007/s11274-013-1399-9 ORIGINAL PAPER A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils Bin Ma • Jun Gong Received: 19 April 2013 / Accepted: 3 June 2013 / Published online: 12 June 2013 Ó Springer Science+Business Media Dordrecht 2013 Abstract An integrated view of bacterial and archaeal Halorubrum and Thermofilum were the dominant archaeal diversity in saline soil habitats is essential for understanding genera in saline soils. Rarefaction analysis indicated that less the biological and ecological processes and exploiting than 25 % of bacterial diversity, and approximately 50 % of potential of microbial resources from such environments. archaeal diversity, in saline soil habitats has been sampled. This study examined the collective bacterial and archaeal This analysis of the global bacterial and archaeal diversity in diversity in saline soils using a meta-analysis approach. All saline soil habitats can guide future studies to further available 16S rDNA sequences recovered from saline soils examine the microbial diversity of saline soils. were retrieved from publicly available databases and sub- jected to phylogenetic and statistical analyses. A total of Keywords Archaea Á Bacteria Á Halophilic Á Microbial 9,043 bacterial and 1,039 archaeal sequences, each longer diversity Á Saline soil than 250 bp, were examined. The bacterial sequences were assigned into 5,784 operational taxonomic units (OTUs, based on C97 % sequence identity), representing 24 known Introduction bacterial phyla, with Proteobacteria (44.9 %), Actinobacte- ria (12.3 %), Firmicutes (10.4 %), Acidobacteria (9.0 %), Saline soils are increasingly abundant as a consequence of Bacteroidetes (6.8 %), and Chloroflexi (5.9 %) being pre- irrigation and desertification processes (Rengasamy 2006).
    [Show full text]
  • 4 Metabolic and Taxonomic Diversification in Continental Magmatic Hydrothermal Systems
    Maximiliano J. Amenabar, Matthew R. Urschel, and Eric S. Boyd 4 Metabolic and taxonomic diversification in continental magmatic hydrothermal systems 4.1 Introduction Hydrothermal systems integrate geological processes from the deep crust to the Earth’s surface yielding an extensive array of spring types with an extraordinary diversity of geochemical compositions. Such geochemical diversity selects for unique metabolic properties expressed through novel enzymes and functional characteristics that are tailored to the specific conditions of their local environment. This dynamic interaction between geochemical variation and biology has played out over evolu- tionary time to engender tightly coupled and efficient biogeochemical cycles. The timescales by which these evolutionary events took place, however, are typically in- accessible for direct observation. This inaccessibility impedes experimentation aimed at understanding the causative principles of linked biological and geological change unless alternative approaches are used. A successful approach that is commonly used in geological studies involves comparative analysis of spatial variations to test ideas about temporal changes that occur over inaccessible (i.e. geological) timescales. The same approach can be used to examine the links between biology and environment with the aim of reconstructing the sequence of evolutionary events that resulted in the diversity of organisms that inhabit modern day hydrothermal environments and the mechanisms by which this sequence of events occurred. By combining molecu- lar biological and geochemical analyses with robust phylogenetic frameworks using approaches commonly referred to as phylogenetic ecology [1, 2], it is now possible to take advantage of variation within the present – the distribution of biodiversity and metabolic strategies across geochemical gradients – to recognize the extent of diversity and the reasons that it exists.
    [Show full text]
  • Research Article on the Existence of Wavelet Symmetries in Archaea DNA
    Hindawi Publishing Corporation Computational and Mathematical Methods in Medicine Volume 2012, Article ID 673934, 21 pages doi:10.1155/2012/673934 Research Article On the Existence of Wavelet Symmetries in Archaea DNA Carlo Cattani Department of Mathematics, University of Salerno, Via Ponte Don Melillo, 84084 Fisciano, Italy Correspondence should be addressed to Carlo Cattani, [email protected] Received 13 September 2011; Revised 27 October 2011; Accepted 29 October 2011 Academic Editor: Sheng-yong Chen Copyright © 2012 Carlo Cattani. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This paper deals with the complex unit roots representation of archea DNA sequences and the analysis of symmetries in the wavelet coefficients of the digitalized sequence. It is shown that even for extremophile archaea, the distribution of nucleotides has to fulfill some (mathematical) constraints in such a way that the wavelet coefficients are symmetrically distributed, with respect to the nucleotides distribution. 1. Introduction the earth under extreme conditions of life, their DNA has to fulfill the same constraints of the more evolved DNAs. In some recent papers the existence of symmetries in nu- In order to achieve this goal some fundamental steps have cleotide distribution has been studied for several living or- to be taken into consideration and discussed. ganisms [1–6] including mammals, fungi [1–4], and vir- uses [5, 6]. Thus showing that any (investigated) DNA (1) Since DNA is a sequence of symbols, a map of these sequence, when converted into a digital sequence, features symbols into numbers has to be defined.
    [Show full text]
  • DNA Polymerase B1 Binding Protein 1 Is Important for DNA Repair by Holoenzyme Polb1 in the Extremely Thermophilic Crenarchaeon Sulfolobus Acidocaldarius
    microorganisms Article DNA Polymerase B1 Binding Protein 1 Is Important for DNA Repair by Holoenzyme PolB1 in the Extremely Thermophilic Crenarchaeon Sulfolobus acidocaldarius Hiroka Miyabayashi 1, Hiroyuki D. Sakai 2 and Norio Kurosawa 1,2,* 1 Department of Environmental Engineering for Symbiosis, Graduate School of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan; [email protected] 2 Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-42-691-8175 Abstract: DNA polymerase B1 (PolB1) is a member of the B-family DNA polymerase family and is a replicative DNA polymerase in Crenarchaea. PolB1 is responsible for the DNA replication of both the leading and lagging strands in the thermophilic crenarchaeon Sulfolobus acidocaldarius. Recently, two subunits, PolB1-binding protein (PBP)1 and PBP2, were identified in Saccharolobus solfataricus. Previous in vitro studies suggested that PBP1 and PBP2 influence the core activity of apoenzyme PolB1 (apo-PolB1). PBP1 contains a C-terminal acidic tail and modulates the strand-displacement synthesis activity of PolB1 during the synthesis of Okazaki fragments. PBP2 modestly enhances the DNA polymerase activity of apo-PolB1. These subunits are present in Sulfolobales, Acidilobales, and Citation: Miyabayashi, H.; Sakai, Desulfurococcales, which belong to Crenarchaea. However, it has not been determined whether these H.D.; Kurosawa, N. DNA Polymerase subunits are essential for the activity of apo-PolB1. In this study, we constructed a pbp1 deletion B1 Binding Protein 1 Is Important for strain in S.
    [Show full text]
  • Thermofilum Uzonense Sp
    Toshchakov et al. Standards in Genomic Sciences (2015) 10:122 DOI 10.1186/s40793-015-0105-y SHORTGENOMEREPORT Open Access Complete genome sequence of and proposal of Thermofilum uzonense sp. nov. a novel hyperthermophilic crenarchaeon and emended description of the genus Thermofilum Stepan V. Toshchakov1*, Aleksei A. Korzhenkov1, Nazar I. Samarov1, Ilia O. Mazunin1, Oleg I. Mozhey1, Ilya S. Shmyr2, Ksenia S. Derbikova3, Evgeny A. Taranov3, Irina N. Dominova1, Elizaveta A. Bonch-Osmolovskaya3, Maxim V. Patrushev1, Olga A. Podosokorskaya3 and Ilya V. Kublanov3 Abstract A strain of a hyperthermophilic filamentous archaeon was isolated from a sample of Kamchatka hot spring sediment. Isolate 1807-2 grew optimally at 85 °C, pH 6.0-6.5, the parameters being close to those at the sampling site. 16S rRNA gene sequence analysis placed the novel isolate in the crenarchaeal genus Thermofilum; Thermofilum pendens was its closest valid relative (95.7 % of sequence identity). Strain 1807-2 grew organothrophically using polysaccharides (starch and glucomannan), yeast extract or peptone as substrates. The addition of other crenarchaea culture broth filtrates was obligatory required for growth and could not be replaced by the addition of these organisms’ cell wall fractions, as it was described for T. pendens. The genome of strain 1807-2 was sequenced using Illumina and PGM technologies. The average nucleotide identities between genome of strain 1807-2 and T. pendens strain HRK 5T and “T. adornatus” strain 1910b were 85 and 82 %, respectively. On the basis of 16S rRNA gene sequence phylogeny, ANI calculations and phenotypic differences we propose a novel species Thermofilum uzonense with the type strain 1807-2T (= DSM 28062T = JCM 19810T).
    [Show full text]
  • Undinarchaeota Illuminate DPANN Phylogeny and the Impact of Gene Transfer on Archaeal Evolution
    This may be the author’s version of a work that was submitted/accepted for publication in the following source: Dombrowski, Nina, Williams, Tom A., Sun, Jiarui, Woodcroft, Benjamin J., Lee, Jun-Hoe, Minh, Bui Quang, Rinke, Christian, & Spang, Anja (2020) Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution. Nature Communications, 11(1), Article number: 3939. This file was downloaded from: https://eprints.qut.edu.au/203812/ c The Author(s) This work is covered by copyright. Unless the document is being made available under a Creative Commons Licence, you must assume that re-use is limited to personal use and that permission from the copyright owner must be obtained for all other uses. If the docu- ment is available under a Creative Commons License (or other specified license) then refer to the Licence for details of permitted re-use. It is a condition of access that users recog- nise and abide by the legal requirements associated with these rights. If you believe that this work infringes copyright please provide details by email to [email protected] License: Creative Commons: Attribution 4.0 Notice: Please note that this document may not be the Version of Record (i.e. published version) of the work. Author manuscript versions (as Sub- mitted for peer review or as Accepted for publication after peer review) can be identified by an absence of publisher branding and/or typeset appear- ance. If there is any doubt, please refer to the published source. https://doi.org/10.1038/s41467-020-17408-w ARTICLE https://doi.org/10.1038/s41467-020-17408-w OPEN Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution Nina Dombrowski 1, Tom A.
    [Show full text]
  • Metagenome-Assembled Genomes Provide New Insight Into The
    www.nature.com/scientificreports Corrected: Author Correction OPEN Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal Received: 17 August 2018 Accepted: 17 January 2019 pools in Kamchatka, Russia Published online: 28 February 2019 Laetitia G. E. Wilkins1,2, Cassandra L. Ettinger 2, Guillaume Jospin2 & Jonathan A. Eisen 2,3,4 Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refned, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We assembled genomes of bacteria and archaea using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available microbial genomes. We highlight MAGs that were taxonomically assigned to groups previously underrepresented in available genome data. This includes several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study adds comprehensive information about phylogenetic diversity and functional potential within two hot springs in the caldera of Kamchatka. Terrestrial hydrothermal systems are of great interest to the general public and to scientists alike due to their unique and extreme conditions.
    [Show full text]
  • The Archaeal Ced System Imports DNA
    The archaeal Ced system imports DNA Marleen van Wolferena,1, Alexander Wagnera,1, Chris van der Doesa, and Sonja-Verena Albersa,2 aMolecular Biology of Archaea, Institute of Biology II – Microbiology, University of Freiburg, 79104 Freiburg, Germany Edited by Norman R. Pace, University of Colorado at Boulder, Boulder, CO, and approved January 12, 2016 (received for review July 13, 2015) The intercellular transfer of DNA is a phenomenon that occurs species exchange chromosomal DNA between cells connected by in all domains of life and is a major driving force of evolution. bridges (11). This transfer is thought to occur in a bidirectional Upon UV-light treatment, cells of the crenarchaeal genus Sulfo- manner via cell fusion leading to the formation of diploid cells with lobus express Ups pili, which initiate cell aggregate formation. mixed chromosomes (12). Interestingly, this type of DNA transfer Within these aggregates, chromosomal DNA, which is used for was shown to occur between different Haloferax species and in- the repair of DNA double-strand breaks, is exchanged. Because volved DNA fragments of up to 500 kbp DNA (13). Nevertheless, so far no clear homologs of bacterial DNA transporters have the mechanism of DNA transfer is so far not understood. Other been identified among the genomes of Archaea, the mechanisms described archaeal conjugative systems include self-transmissible of archaeal DNA transport have remained a puzzling and under- plasmids, which have so far only been studied for Sulfolobus spe- saci_0568 saci_0748, investigated topic. Here we identify and cies. These plasmids are grouped into the so-called pKEF and Sulfolobus acidocaldarius two genes from that are highly in- pARN plasmids (14, 15) and only a few of their genes encode duced upon UV treatment, encoding a transmembrane protein homologs of bacterial conjugation proteins, including the so-far- and a membrane-bound VirB4/HerA homolog, respectively.
    [Show full text]
  • Research Article a Novel Highly Thermostable Multifunctional Beta-Glycosidase from Crenarchaeon Acidilobus Saccharovorans
    Hindawi Publishing Corporation Archaea Volume 2015, Article ID 978632, 6 pages http://dx.doi.org/10.1155/2015/978632 Research Article A Novel Highly Thermostable Multifunctional Beta-Glycosidase from Crenarchaeon Acidilobus saccharovorans Vadim M. Gumerov, Andrey L. Rakitin, Andrey V. Mardanov, and Nikolai V. Ravin Centre “Bioengineering”, Russian Academy of Sciences, Moscow 117312, Russia Correspondence should be addressed to Nikolai V. Ravin; [email protected] Received 10 March 2015; Revised 25 June 2015; Accepted 5 July 2015 Academic Editor: Fred´ eric´ Pecorari Copyright © 2015 Vadim M. Gumerov et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. We expressed a putative -galactosidase Asac 1390 from hyperthermophilic crenarchaeon Acidilobus saccharovorans in Escherichia coli and purified the recombinant enzyme. Asac 1390 is composed of 490 amino acid residues and showed high sequence similarity ∘ to family 1 glycoside hydrolases from various thermophilic Crenarchaeota. The maximum activity was observed at pH 6.0 and 93 C. ∘ The half-life of the enzyme at90 Cwasabout7hours.Asac 1390 displayed high tolerance to glucose and exhibits hydrolytic activity towards cellobiose and various aryl glucosides. The hydrolytic activity with p-nitrophenyl (pNP) substrates followed the order −1 −1 −1 pNP--D-galactopyranoside (328 U mg ), pNP--D-glucopyranoside (246 U mg ), pNP--D-xylopyranoside (72 U mg ), and −1 pNP--D-mannopyranoside (28 U mg ). Thus the enzyme was actually a multifunctional -glycosidase. Therefore, the utilization of Asac 1390 may contribute to facilitating the efficient degradationf o lignocellulosic biomass and help enhance bioconversion processes.
    [Show full text]