DOCSLIB.ORG

1Cz4 Lichtarge Lab 2006

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
1Cz4 Lichtarge Lab 2006 Pages 1–6 1cz4 Evolutionary trace report by report maker September 11, 2008 4.3.3 DSSP 5 4.3.4 HSSP 5 4.3.5 LaTex 5 4.3.6 Muscle 5 4.3.7 Pymol 6 4.4 Note about ET Viewer 6 4.5 Citing this work 6 4.6 About report maker 6 4.7 Attachments 6 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1cz4): Title: Nmr structure of vat-n: the n-terminal domain of vat (vcp- like atpase of thermoplasma) Compound: Mol id: 1; molecule: vcp-like atpase; chain: a; frag- ment: n-terminal domain: m1 to e183 followed by a diglycine spacer; engineered: yes Organism, scientific name: Thermoplasma Acidophilum; 1cz4 contains a single unique chain 1cz4A (185 residues long). This is an NMR-determined structure – in this report the first model in the file was used. CONTENTS 1 Introduction 1 2 CHAIN 1CZ4A 2.1 O05209 overview 2 Chain 1cz4A 1 2.1 O05209 overview 1 From SwissProt, id O05209, 100% identical to 1cz4A: Description: 2.2 Multiple sequence alignment for 1cz4A 1 VCP-like ATPase. Organism, scientific name: 2.3 Residue ranking in 1cz4A 1 Thermoplasma acidophilum. Taxonomy: 2.4 Top ranking residues in 1cz4A and their position on Archaea; Euryarchaeota; Thermoplasmata; Thermoplas- the structure 2 matales; Thermoplasmataceae; Thermoplasma. Biophysicochemical properties: 2.4.1 Clustering of residues at 25% coverage. 2 2.4.2 Possible novel functional surfaces at 25% Temperature dependence: Optimum temperature is 70 degrees coverage. 2 Celsius; Subunit: Homohexamer. Forms a ring-shaped particle. 3 Notes on using trace results 4 Similarity: Belongs to the AAA ATPase family. CDC48 subfamily. 3.1 Coverage 4 About: This Swiss-Prot entry is copyright. It is produced through a 3.2 Known substitutions 4 collaboration between the Swiss Institute of Bioinformatics and the 3.3 Surface 4 EMBL outstation - the European Bioinformatics Institute. There are 3.4 Number of contacts 4 no restrictions on its use as long as its content is in no way modified 3.5 Annotation 4 and this statement is not removed. 3.6 Mutation suggestions 5 2.2 Multiple sequence alignment for 1cz4A 4 Appendix 5 For the chain 1cz4A, the alignment 1cz4A.msf (attached) with 16 4.1 File formats 5 sequences was used. The alignment was assembled through combi- 4.2 Color schemes used 5 nation of BLAST searching on the UniProt database and alignment 4.3 Credits 5 using Muscle program. It can be found in the attachment to this 4.3.1 Alistat 5 report, under the name of 1cz4A.msf. Its statistics, from the alistat 4.3.2 CE 5 program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 1-185 in 1cz4A colored by their relative importance. (See Appendix, Fig.6, for the coloring scheme.) Format: MSF Number of sequences: 16 Total number of residues: 2855 Smallest: 171 Largest: 185 Average length: 178.4 Alignment length: 185 Average identity: 44% Most related pair: 98% Fig. 2. Residues in 1cz4A, colored by their relative importance. Clockwise: Most unrelated pair: 31% front, back, top and bottom views. Most distant seq: 39% Furthermore, 9% of residues show as conserved in this alignment. The alignment consists of 12% prokaryotic, and 87% archaean sequences. The file containing the sequence descriptions can be found in the attachment, under the name 1cz4A.descr. 2.3 Residue ranking in 1cz4A The 1cz4A sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1cz4A can be found in the file called 1cz4A.ranks sorted in the attachment. 2.4 Top ranking residues in 1cz4A and their position on the structure In the following we consider residues ranking among top 25% of residues in the protein . Figure 2 shows residues in 1cz4A colored by their importance: bright red and yellow indicate more conser- ved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. 2.4.1 Clustering of residues at 25% coverage. Fig. 3 shows the top 25% of all residues, this time colored according to clusters they Fig. 3. Residues in 1cz4A, colored according to the cluster they belong to: belong to. The clusters in Fig.3 are composed of the residues listed red, followed by blue and yellow are the largest clusters (see Appendix for in Table 1. the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. Table 1. cluster size member Table 1. continued color residues cluster size member red 21 9,11,13,14,18,19,20,22,43,44 color residues 46,52,66,70,71,74,76,78,82 blue 14 95,98,100,101,102,128,132 83,85 150,152,153,155,157,162,168 continued in next column yellow 3 177,179,181 continued in next column 2 Table 1. continued Table 2. continued cluster size member res type substitutions(%) cvg color residues 27 D P(6)D(87)T(6) 0.14 green 3 39,40,54 66 I V(6)I(87)E(6) 0.14 purple 2 25,68 82 G G(93)D(6) 0.15 azure 2 184,185 46 K G(87)K(12) 0.18 132 Q G(87)Q(12) 0.18 Table 1. Clusters of top ranking residues in 1cz4A. 13 E A(6)E(87)Q(6) 0.20 71 S G(81)S(12)R(6) 0.20 78 G E(6)K(6)G(87) 0.20 2.4.2 Possible novel functional surfaces at 25% coverage. One 153 V V(87)T(12) 0.21 group of residues is conserved on the 1cz4A surface, away from (or 83 D E(18)D(81) 0.22 susbtantially larger than) other functional sites and interfaces reco- 22 S G(81)K(6)S(12) 0.23 gnizable in PDB entry 1cz4. It is shown in Fig. 4. The residues 19 P S(12)V(75)P(12) 0.24 128 P P(75)V(25) 0.25 Table 2. Residues forming surface ”patch” in 1cz4A. Table 3. res type disruptive mutations 9 L (YR)(TH)(SKECG)(FQWD) 14 A (KYER)(QHD)(N)(FTMW) 25 R (TD)(SYEVCLAPIG)(FMW)(N) 68 R (TD)(SYEVCLAPIG)(FMW)(N) 70 D (R)(FWH)(KYVCAG)(TQM) 74 R (TD)(SYEVCLAPIG)(FMW)(N) 18 D (R)(FWH)(YVCAG)(K) 20 G (K)(ER)(QM)(D) 61 D (R)(FWH)(K)(Y) 76 N (Y)(FWH)(R)(TE) 27 D (R)(H)(FW)(K) 66 I (YR)(H)(T)(K) 82 G (R)(K)(FWH)(EQM) 46 K (Y)(FW)(T)(SVAHD) 132 Q (Y)(FWH)(T)(SVAD) 13 E (H)(FW)(Y)(R) Fig. 4. A possible active surface on the chain 1cz4A. 71 S (K)(FMWR)(H)(EQ) 78 G (FW)(HR)(Y)(KE) belonging to this surface ”patch” are listed in Table 2, while Table 153 V (KR)(E)(YQH)(D) 3 suggests possible disruptive replacements for these residues (see 83 D (R)(FWH)(YVCAG)(K) Section 3.6). 22 S (FWR)(H)(K)(YM) 19 P (R)(Y)(H)(K) Table 2. 128 P (YR)(H)(TKE)(SQCDG) res type substitutions(%) cvg 9 L L(100) 0.09 Table 3. Disruptive mutations for the surface patch in 1cz4A. 14 A A(100) 0.09 25 R R(100) 0.09 68 R R(100) 0.09 Another group of surface residues is shown in Fig.5. The right panel 70 D D(100) 0.09 shows (in blue) the rest of the larger cluster this surface belongs to. 74 R R(100) 0.09 The residues belonging to this surface ”patch” are listed in Table 18 D E(6)D(93) 0.10 4, while Table 5 suggests possible disruptive replacements for these 20 G G(93)Y(6) 0.12 residues (see Section 3.6). 61 D D(93)G(6) 0.12 Table 4. 76 N N(93)S(6) 0.12 res type substitutions(%) cvg continued in next column 101 A A(100) 0.09 continued in next column 3 example if the substitutions are “RVK” and the original protein has an R at that position, it is advisable to try anything, but RVK. Conver- sely, when looking for substitutions which will not affect the protein, one may try replacing, R with K, or (perhaps more surprisingly), with V. The percentage of times the substitution appears in the alignment is given in the immediately following bracket. No percentage is given in the cases when it is smaller than 1%. This is meant to be a rough guide - due to rounding errors these percentages often do not add up to 100%. 3.3 Surface Fig. 5. Another possible active surface on the chain 1cz4A. The larger cluster To detect candidates for novel functional interfaces, first we look for residues that are solvent accessible (according to DSSP program) by it belongs to is shown in blue. 2 at least 10A˚ , which is roughly the area needed for one water mole- cule to come in the contact with the residue. Furthermore, we require Table 4. continued that these residues form a “cluster” of residues which have neighbor res type substitutions(%) cvg within 5A˚ from any of their heavy atoms. 102 P P(100) 0.09 Note, however, that, if our picture of protein evolution is correct, 179 E E(93)D(6) 0.12 the neighboring residues which are not surface accessible might be 181 L L(93)I(6) 0.15 equally important in maintaining the interaction specificity - they 150 F L(12)F(87) 0.17 should not be automatically dropped from consideration when choo- 177 A E(6)V(68)A(25) 0.22 sing the set for mutagenesis.
Load more

Recommended publications
  • Plant Life Magill’S Encyclopedia of Science
    MAGILLS ENCYCLOPEDIA OF SCIENCE PLANT LIFE MAGILLS ENCYCLOPEDIA OF SCIENCE PLANT LIFE Volume 4 Sustainable Forestry–Zygomycetes Indexes Editor Bryan D. Ness, Ph.D. Pacific Union College, Department of Biology Project Editor Christina J. Moose Salem Press, Inc. Pasadena, California Hackensack, New Jersey Editor in Chief: Dawn P. Dawson Managing Editor: Christina J. Moose Photograph Editor: Philip Bader Manuscript Editor: Elizabeth Ferry Slocum Production Editor: Joyce I. Buchea Assistant Editor: Andrea E. Miller Page Design and Graphics: James Hutson Research Supervisor: Jeffry Jensen Layout: William Zimmerman Acquisitions Editor: Mark Rehn Illustrator: Kimberly L. Dawson Kurnizki Copyright © 2003, by Salem Press, Inc. All rights in this book are reserved. No part of this work may be used or reproduced in any manner what- soever or transmitted in any form or by any means, electronic or mechanical, including photocopy,recording, or any information storage and retrieval system, without written permission from the copyright owner except in the case of brief quotations embodied in critical articles and reviews. For information address the publisher, Salem Press, Inc., P.O. Box 50062, Pasadena, California 91115. Some of the updated and revised essays in this work originally appeared in Magill’s Survey of Science: Life Science (1991), Magill’s Survey of Science: Life Science, Supplement (1998), Natural Resources (1998), Encyclopedia of Genetics (1999), Encyclopedia of Environmental Issues (2000), World Geography (2001), and Earth Science (2001). ∞ The paper used in these volumes conforms to the American National Standard for Permanence of Paper for Printed Library Materials, Z39.48-1992 (R1997). Library of Congress Cataloging-in-Publication Data Magill’s encyclopedia of science : plant life / edited by Bryan D.
    [Show full text]
  • Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma Divulgatum
    microorganisms Article Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum Rafael Bargiela 1 , Karin Lanthaler 1,2, Colin M. Potter 1,2 , Manuel Ferrer 3 , Alexander F. Yakunin 1,2, Bela Paizs 1,2, Peter N. Golyshin 1,2 and Olga V. Golyshina 1,2,* 1 School of Natural Sciences, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK; [email protected] (R.B.); [email protected] (K.L.); [email protected] (C.M.P.); [email protected] (A.F.Y.); [email protected] (B.P.); [email protected] (P.N.G.) 2 Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK 3 Systems Biotechnology Group, Department of Applied Biocatalysis, CSIC—Institute of Catalysis, Marie Curie 2, 28049 Madrid, Spain; [email protected] * Correspondence: [email protected]; Tel.: +44-1248-388607; Fax: +44-1248-382569 Received: 27 April 2020; Accepted: 15 May 2020; Published: 19 May 2020 Abstract: The archaeon Cuniculiplasma divulgatum is ubiquitous in acidic environments with low-to-moderate temperatures. However, molecular mechanisms underlying its ability to thrive at lower temperatures remain unexplored. Using mass spectrometry (MS)-based proteomics, we analysed the effect of short-term (3 h) exposure to cold. The C. divulgatum genome encodes 2016 protein-coding genes, from which 819 proteins were identified in the cells grown under optimal conditions. In line with the peptidolytic lifestyle of C. divulgatum, its intracellular proteome revealed the abundance of proteases, ABC transporters and cytochrome C oxidase. From 747 quantifiable polypeptides, the levels of 582 proteins showed no change after the cold shock, whereas 104 proteins were upregulated suggesting that they might be contributing to cold adaptation.
    [Show full text]
  • Picrophilus Oshimae and Picrophilus Tomdus Fam. Nov., Gen. Nov., Sp. Nov
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1996, p. 814-816 Vol. 46, No. 3 0020-77 13/96/$04.00+0 Copyright 0 1996, International Union of Microbiological Societies Picrophilus oshimae and Picrophilus tomdus fam. nov., gen. nov., sp. nov., Two Species of Hyperacidophilic, Thermophilic, Heterotrophic, Aerobic Archaea CHRISTA SCHLEPER, GABRIELA PUHLER, HANS- PETER KLENK, AND WOLFRAM ZILLIG* Max Plank Institut fur Biochemie, 0-82152 Martinsried, Germany We describe two species of hyperacidophilic, thermophilic, heterotrophic, aerobic archaea that were isolated from solfataric hydrothermal areas in Hokkaido, Japan. These organisms, Picrophilus oshimae and Picrophilus torridus, represent a novel genus and a novel family, the Picrophilaceae, in the kingdom Euryarchaeota and the order Thermoplasmales. Both of these bacteria are more acidophilic than the genus Thermoplasma since they are able to grow at about pH 0. The moderately thermophilic, hyperacidophilic, aerobic ar- which comprises acid-loving (i.e., hyperacidophilic) organisms. chaea (archaebacteria) (7) Picrophilus oshimae and Picrophilus Separation of these taxa is justified by their phylogenetic dis- rorridus, which have been described previously (4, 5), were tance, (9.5% difference in the 16s rRNA sequences of mem- isolated from moderately hot hydrothermal areas in solfataric bers of the Picrophilaceae and T. acidophilum), by the lack of fields in Hokkaido, Japan. One of the sources of isolation was immunochemical cross-reactions in Ouchterlony immunodif- a solfataric spring which had a temperature of 53°C and a pH fusion assays between the RNA polymerases of P. oshimae and of 2.2, and the other was a rather dry hot soil which had a pH T. acidophilum, which also do not occur between members of of <OS.
    [Show full text]
  • Archaeal Adaptation to Higher Temperatures Revealed by Genomic Sequence of Thermoplasma Volcanium
    Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium Tsuyoshi Kawashima*†, Naoki Amano*†‡, Hideaki Koike*†, Shin-ichi Makino†, Sadaharu Higuchi†, Yoshie Kawashima-Ohya†, Koji Watanabe§, Masaaki Yamazaki§, Keiichi Kanehori¶, Takeshi Kawamotoʈ, Tatsuo Nunoshiba**, Yoshihiro Yamamoto††, Hironori Aramaki‡‡, Kozo Makino§§, and Masashi Suzuki†¶¶ †National Institute of Bioscience and Human Technology, Core Research for Evolutional Science and Technology Centre of Structural Biology, 1-1 Higashi, Tsukuba 305-0046, Japan; ‡Doctoral Program in Medical Sciences, University of Tsukuba, 1-1-1 Tennohdai, Tsukuba 305-0006, Japan; §Bioscience Research Laboratory, Fujiya, 228 Soya, Hadano 257-0031, Japan; ¶DNA Analysis Department, Techno Research Laboratory, Hitachi Science Systems, 1-280 Higashi-Koigakubo, Kokubunji 185-8601, Japan; ʈDepartment of Biochemistry, Hiroshima University, School of Dentistry, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan; **Department of Molecular and Cellular Biology, Biological Institute, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan; ††Department of Genetics, Hyogo College of Medicine, Nishinomiya 663-8501, Japan; ‡‡Department of Molecular Biology, Daiichi College of Pharmaceutical Science, 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan; and §§Department of Molecular Microbiology, The Research Institute of Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan Edited by Aaron Klug, Royal Society of London, London, United Kingdom, and approved October 16, 2000 (received for review August 18, 2000) The complete genomic sequence of the archaeon Thermoplasma contigs. The remaining gaps were bridged by DNA fragments volcanium, possessing optimum growth temperature (OGT) of constructed using the PCR. The average repetition in sequencing 60°C, is reported. By systematically comparing this genomic se- the same base positions was 13-fold.
    [Show full text]
  • The Main (Glyco) Phospholipid (MPL) of Thermoplasma Acidophilum
    International Journal of Molecular Sciences Review The Main (Glyco) Phospholipid (MPL) of Thermoplasma acidophilum Hans-Joachim Freisleben 1,2 1 Goethe-Universität, Gustav-Embden-Zentrum, Laboratory of Microbiological Chemistry, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany; [email protected] 2 Universitas Indonesia, Medical Research Unit, Faculty of Medicine, Jalan Salemba Raya 6, Jakarta 10430, Indonesia Received: 19 September 2019; Accepted: 18 October 2019; Published: 21 October 2019 Abstract: The main phospholipid (MPL) of Thermoplasma acidophilum DSM 1728 was isolated, purified and physico-chemically characterized by differential scanning calorimetry (DSC)/differential thermal analysis (DTA) for its thermotropic behavior, alone and in mixtures with other lipids, cholesterol, hydrophobic peptides and pore-forming ionophores. Model membranes from MPL were investigated; black lipid membrane, Langmuir-Blodgett monolayer, and liposomes. Laboratory results were compared to computer simulation. MPL forms stable and resistant liposomes with highly proton-impermeable membrane and mixes at certain degree with common bilayer-forming lipids. Monomeric bacteriorhodopsin and ATP synthase from Micrococcus luteus were co-reconstituted and light-driven ATP synthesis measured. This review reports about almost four decades of research on Thermoplasma membrane and its MPL as well as transfer of this research to Thermoplasma species recently isolated from Indonesian volcanoes. Keywords: Thermoplasma acidophilum; Thermoplasma volcanium;
    [Show full text]
  • Different Proteins Mediate Step-Wise Chromosome Architectures in 2 Thermoplasma Acidophilum and Pyrobaculum Calidifontis
    bioRxiv preprint doi: https://doi.org/10.1101/2020.03.13.982959; this version posted May 4, 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 4.0 International license. 1 Different Proteins Mediate Step-wise Chromosome Architectures in 2 Thermoplasma acidophilum and Pyrobaculum calidifontis 3 4 5 Hugo Maruyama1†*, Eloise I. Prieto2†, Takayuki Nambu1, Chiho Mashimo1, Kosuke 6 Kashiwagi3, Toshinori Okinaga1, Haruyuki Atomi4, Kunio Takeyasu5 7 8 1 Department of Bacteriology, Osaka Dental University, Hirakata, Japan 9 2 National Institute of Molecular Biology and Biotechnology, University of the Philippines 10 Diliman, Quezon City, Philippines 11 3 Department of Fixed Prosthodontics, Osaka Dental University, Hirakata, Japan 12 4 Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, 13 Kyoto University, Kyoto, Japan 14 5 Graduate School of Biostudies, Kyoto University, Kyoto, Japan 15 † These authors have contributed equally to this work 16 17 * Correspondence: 18 Hugo Maruyama 19 [email protected]; [email protected] 20 21 Keywords: archaea, higher-order chromosome structure, nucleoid, chromatin, HTa, histone, 22 transcriptional regulator, horizontal gene transfer 23 Running Title: Step-wise chromosome architecture in Archaea 24 Manuscript length: 6955 words 25 Number of Figures: 7 26 Number of Tables: 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.13.982959; this version posted May 4, 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.
    [Show full text]
  • (Agus Kurnia)Ok
    HAYATI Journal of Biosciences September 2012 Available online at: Vol. 19 No. 3, p 150-154 http://journal.ipb.ac.id/index.php/hayati EISSN: 2086-4094 DOI: 10.4308/hjb.19.3.150 SHORT COMMUNICATION Archaeal Life on Tangkuban Perahu- Sampling and Culture Growth in Indonesian Laboratories SRI HANDAYANI1, IMAN SANTOSO1, HANS-JOACHIM FREISLEBEN2∗, HARALD HUBER3, ANDI1, FERY ARDIANSYAH1, CENMI MULYANTO1, ZESSINDA LUTHFA1, ROSARI SALEH1, SERUNI KUSUMA UDYANINGSIH FREISLEBEN1, SEPTELIA INAWATI WANANDI2, MICHAEL THOMM3 1Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Jakarta-Depok, Jakarta 10430, Indonesia 2Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya No. 6, Jakarta 10430, Indonesia 3Department of Microbiology, Archaea Centre, University of Regensburg, Germany Received May 9, 2012/Accepted September 21, 2012 The aim of the expedition to Tangkuban Perahu, West Java was to obtain archaeal samples from the solfatara fields located in Domas crater. This was one of the places, where scientists from the University of Regensburg Germany had formerly isolated Indonesian archaea, especially Thermoplasma and Sulfolobus species but not fully characterized. We collected five samples from mud holes with temperatures from 57 to 88 oC and pH of 1.5-2. A portion of each sample was grown at the University of Regensburg in modified Allen’s medium at 80 oC. From four out of five samples enrichment cultures were obtained, autotrophically on elemental sulphur and heterotrophically on sulfur and yeast extract; electron micrographs are presented. In the laboratories of Universitas Indonesia the isolates were cultured at 55-60 oC in order to grow tetraetherlipid synthesizing archaea, both Thermoplasmatales and Sulfolobales. Here, we succeeded to culture the same type of archaeal cells, which had been cultured in Regensburg, probably a Sulfolobus species and in Freundt’s medium, Thermoplasma species.
    [Show full text]
  • Phylogeny and Taxonomy of Archaea: a Comparison of the Whole-Genome-Based Cvtree Approach with 16S Rrna Sequence Analysis
    Life 2015, 5, 949-968; doi:10.3390/life5010949 OPEN ACCESS life ISSN 2075-1729 www.mdpi.com/journal/life Article Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis Guanghong Zuo 1, Zhao Xu 2 and Bailin Hao 1;* 1 T-Life Research Center and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China; E-Mail: [email protected] 2 Thermo Fisher Scientific, 200 Oyster Point Blvd, South San Francisco, CA 94080, USA; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +86-21-6565-2305. Academic Editors: Roger A. Garrett, Hans-Peter Klenk and Michael W. W. Adams Received: 9 December 2014 / Accepted: 9 March 2015 / Published: 17 March 2015 Abstract: A tripartite comparison of Archaea phylogeny and taxonomy at and above the rank order is reported: (1) the whole-genome-based and alignment-free CVTree using 179 genomes; (2) the 16S rRNA analysis exemplified by the All-Species Living Tree with 366 archaeal sequences; and (3) the Second Edition of Bergey’s Manual of Systematic Bacteriology complemented by some current literature. A high degree of agreement is reached at these ranks. From the newly proposed archaeal phyla, Korarchaeota, Thaumarchaeota, Nanoarchaeota and Aigarchaeota, to the recent suggestion to divide the class Halobacteria into three orders, all gain substantial support from CVTree. In addition, the CVTree helped to determine the taxonomic position of some newly sequenced genomes without proper lineage information. A few discrepancies between the CVTree and the 16S rRNA approaches call for further investigation.
    [Show full text]
  • (Gid ) Genes Coding for Putative Trna:M5u-54 Methyltransferases in 355 Bacterial and Archaeal Complete Genomes
    Table S1. Taxonomic distribution of the trmA and trmFO (gid ) genes coding for putative tRNA:m5U-54 methyltransferases in 355 bacterial and archaeal complete genomes. Asterisks indicate the presence and the number of putative genes found. Genomes Taxonomic position TrmA Gid Archaea Crenarchaea Aeropyrum pernix_K1 Crenarchaeota; Thermoprotei; Desulfurococcales; Desulfurococcaceae Cenarchaeum symbiosum Crenarchaeota; Thermoprotei; Cenarchaeales; Cenarchaeaceae Pyrobaculum aerophilum_str_IM2 Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae Sulfolobus acidocaldarius_DSM_639 Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus solfataricus Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus tokodaii Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Euryarchaea Archaeoglobus fulgidus Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae Haloarcula marismortui_ATCC_43049 Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Halobacterium sp Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Haloquadratum walsbyi Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloquadra Methanobacterium thermoautotrophicum Euryarchaeota; Methanobacteria; Methanobacteriales; Methanobacteriaceae Methanococcoides burtonii_DSM_6242 Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae Methanococcus jannaschii Euryarchaeota; Methanococci; Methanococcales; Methanococcaceae Methanococcus maripaludis_S2 Euryarchaeota; Methanococci;
    [Show full text]
  • Microbial Extremophiles in Aspect of Limits of Life. Elena V. ~Ikuta
    Source of Acquisition NASA Marshall Space Flight Centel Microbial extremophiles in aspect of limits of life. Elena V. ~ikuta',Richard B. ~oover*,and Jane an^.^ IT LF " '-~ationalSpace Sciences and Technology CenterINASA, VP-62, 320 Sparkman Dr., Astrobiology Laboratory, Huntsville, AL 35805, USA. 3- Noblis, 3 150 Fairview Park Drive South, Falls Church, VA 22042, USA. Introduction. During Earth's evolution accompanied by geophysical and climatic changes a number of ecosystems have been formed. These ecosystems differ by the broad variety of physicochemical and biological factors composing our environment. Traditionally, pH and salinity are considered as geochemical extremes, as opposed to the temperature, pressure and radiation that are referred to as physical extremes (Van den Burg, 2003). Life inhabits all possible places on Earth interacting with the environment and within itself (cross species relations). In nature it is very rare when an ecotope is inhabited by a single species. As a rule, most ecosystems contain the functionally related and evolutionarily adjusted communities (consortia and populations). In contrast to the multicellular structure of eukaryotes (tissues, organs, systems of organs, whole organism), the highest organized form of prokaryotic life in nature is the benthic colonization in biofilms and microbial mats. In these complex structures all microbial cells of different species are distributed in space and time according to their functions and to physicochemical gradients that allow more effective system support, self- protection, and energy distribution. In vitro, of course, the most primitive organized structure for bacterial and archaeal cultures is the colony, the size, shape, color, consistency, and other characteristics of which could carry varies specifics on species or subspecies levels.
    [Show full text]
  • Genome Sequence of Picrophilus Torridus and Its Implications for Life Around Ph 0
    Genome sequence of Picrophilus torridus and its implications for life around pH 0 O. Fu¨ tterer*, A. Angelov*, H. Liesegang*, G. Gottschalk*, C. Schleper†, B. Schepers‡, C. Dock‡, G. Antranikian‡, and W. Liebl*§ *Institut of Microbiology and Genetics, University of Goettingen, Grisebachstrasse 8, D-37075 Goettingen, Germany; †Institut of Microbiology and Genetics, Technical University Darmstadt, Schnittspahnstrasse 10, 64287 D-Darmstadt, Germany; and ‡Technical Microbiology, Technical University Hamburg–Harburg, Kasernenstrasse 12, 21073 D-Hamburg, Germany Edited by Dieter So¨ll, Yale University, New Haven, CT, and approved April 20, 2004 (received for review February 26, 2004) The euryarchaea Picrophilus torridus and Picrophilus oshimae are (4–6). After analysis of a number of archaeal and bacterial ge- able to grow around pH 0 at up to 65°C, thus they represent the nomes, it has been argued that microorganisms that live together most thermoacidophilic organisms known. Several features that swap genes at a higher frequency (7, 8). With the genome sequence may contribute to the thermoacidophilic survival strategy of P. of P. torridus, five complete genomes of thermoacidophilic organ- torridus were deduced from analysis of its 1.55-megabase genome. isms are available, which allows a more complex investigation of the P. torridus has the smallest genome among nonparasitic aerobic evolution of organisms sharing the extreme growth conditions of a microorganisms growing on organic substrates and simulta- unique niche in the light of horizontal gene transfer. neously the highest coding density among thermoacidophiles. An exceptionally high ratio of secondary over ATP-consuming primary Methods transport systems demonstrates that the high proton concentra- Sequencing Strategy.
    [Show full text]
  • Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes
    GBE Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes Dennifier Costa Brandao~ Cruz1, Lenon Lima Santana1, Alexandre Siqueira Guedes2, Jorge Teodoro de Souza3,*, and Phellippe Arthur Santos Marbach1,* 1CCAAB, Biological Sciences, Recoˆ ncavo da Bahia Federal University, Cruz das Almas, Bahia, Brazil 2Agronomy School, Federal University of Goias, Goiania,^ Goias, Brazil 3 Department of Phytopathology, Federal University of Lavras, Minas Gerais, Brazil Downloaded from https://academic.oup.com/gbe/article/11/4/1235/5345563 by guest on 27 September 2021 *Corresponding authors: E-mails: [email protected]fla.br; [email protected]. Accepted: February 16, 2019 Abstract The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH, purP, purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ, respectively. In Bacteria, these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea, these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea. Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs.
    [Show full text]