Metagenomic Sequence Assembly Via Iterative Reclassification
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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. -
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. -
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. -
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. -
Comparative Genomic Analysis of The
de Crécy-Lagard et al. Biology Direct 2012, 7:32 http://www.biology-direct.com/content/7/1/32 RESEARCH Open Access Comparative genomic analysis of the DUF71/ COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage Valérie de Crécy-Lagard1*, Farhad Forouhar2, Céline Brochier-Armanet3, Liang Tong2 and John F Hunt2 Abstract Background: The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with function by genetic or biochemical approaches, a lengthy process that often took years. Phylogenetic distribution profiles, physical clustering, gene fusion, co-expression profiles, structural information and other genomic or post-genomic derived associations can be now used to make very strong functional hypotheses. Here, we illustrate this shift with the analysis of the DUF71/COG2102 family, a subgroup of the PP-loop ATPase family. Results: The DUF71 family contains at least two subfamilies, one of which was predicted to be the missing diphthine-ammonia ligase (EC 6.3.1.14), Dph6. This enzyme catalyzes the last ATP-dependent step in the synthesis of diphthamide, a complex modification of Elongation Factor 2 that can be ADP-ribosylated by bacterial toxins. Dph6 orthologs are found in nearly all sequenced Archaea and Eucarya, as expected from the distribution of the diphthamide modification. The DUF71 family appears to have originated in the Archaea/Eucarya ancestor and to have been subsequently horizontally transferred to Bacteria. Bacterial DUF71 members likely acquired a different function because the diphthamide modification is absent in this Domain of Life. -
Symbiosis in Archaea: Functional and Phylogenetic Diversity of Marine and Terrestrial Nanoarchaeota and Their Hosts
Portland State University PDXScholar Dissertations and Theses Dissertations and Theses Winter 3-13-2019 Symbiosis in Archaea: Functional and Phylogenetic Diversity of Marine and Terrestrial Nanoarchaeota and their Hosts Emily Joyce St. John Portland State University Follow this and additional works at: https://pdxscholar.library.pdx.edu/open_access_etds Part of the Bacteriology Commons, and the Biology Commons Let us know how access to this document benefits ou.y Recommended Citation St. John, Emily Joyce, "Symbiosis in Archaea: Functional and Phylogenetic Diversity of Marine and Terrestrial Nanoarchaeota and their Hosts" (2019). Dissertations and Theses. Paper 4939. https://doi.org/10.15760/etd.6815 This Thesis is brought to you for free and open access. It has been accepted for inclusion in Dissertations and Theses by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. Symbiosis in Archaea: Functional and Phylogenetic Diversity of Marine and Terrestrial Nanoarchaeota and their Hosts by Emily Joyce St. John A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Biology Thesis Committee: Anna-Louise Reysenbach, Chair Anne W. Thompson Rahul Raghavan Portland State University 2019 © 2019 Emily Joyce St. John i Abstract The Nanoarchaeota are an enigmatic lineage of Archaea found in deep-sea hydrothermal vents and geothermal springs across the globe. These small (~100-400 nm) hyperthermophiles live ectosymbiotically with diverse hosts from the Crenarchaeota. Despite their broad distribution in high-temperature environments, very few Nanoarchaeota have been successfully isolated in co-culture with their hosts and nanoarchaeote genomes are poorly represented in public databases. -
Isolation, Characterization, and Ecology
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Oct. 2007, p. 6669–6677 Vol. 73, No. 20 0099-2240/07/$08.00ϩ0 doi:10.1128/AEM.01321-07 Copyright © 2007, American Society for Microbiology. All Rights Reserved. Isolation, Characterization, and Ecology of Sulfur-Respiring Crenarchaea Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Parkᰔ† Eric S. Boyd,1* Robert A. Jackson,1 Gem Encarnacion,1 James A. Zahn,2‡ Trevor Beard,1 William D. Leavitt,1,3 Yundan Pi,4 Chuanlun L. Zhang,4 Ann Pearson,3 and Gill G. Geesey1 Department of Microbiology, Montana State University, Bozeman, Montana 597171; DowAgro Sciences, Indianapolis, Indiana 462682; Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts 021383; and Savannah River Ecology Laboratory, Savannah River Site, Aiken, South Carolina 298024 Received 13 June 2007/Accepted 13 August 2007 Elemental sulfur (S0) is associated with many geochemically diverse hot springs, yet little is known about the phylogeny, physiology, and ecology of the organisms involved in its cycling. Here we report the isolation, characterization, and ecology of two novel, S0-reducing Crenarchaea from an acid geothermal spring referred to as Dragon Spring. Isolate 18U65 grows optimally at 70 to 72°C and at pH 2.5 to 3.0, while isolate 18D70 grows optimally at 81°C and pH 3.0. Both isolates are chemoorganotrophs, dependent on complex peptide- containing carbon sources, S0, and anaerobic conditions for respiration-dependent growth. Glycerol dialkyl glycerol tetraethers (GDGTs) containing four to six cyclopentyl rings were present in the lipid fraction of isolates 18U65 and 18D70. Physiological characterization suggests that the isolates are adapted to the phys- icochemical conditions of Dragon Spring and can utilize the natural organic matter in the spring as a carbon and energy source. -
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. -
Genomics-Informed Isolation and Characterization of a Symbiotic Nanoarchaeota System from a Terrestrial Geothermal Environment
Portland State University PDXScholar Biology Faculty Publications and Presentations Biology 7-5-2016 Genomics-Informed Isolation and Characterization of a Symbiotic Nanoarchaeota System from a Terrestrial Geothermal Environment Louie Wurch Oak Ridge National Laboratory Richard J. Giannone Oak Ridge National Laboratory Bernard S. Belisle Oak Ridge National Laboratory Carolyn Swift Oak Ridge National Laboratory Sagar Utturkar Oak Ridge National Laboratory See next page for additional authors Follow this and additional works at: https://pdxscholar.library.pdx.edu/bio_fac Part of the Biology Commons, and the Environmental Sciences Commons Let us know how access to this document benefits ou.y Citation Details Wurch, L. et al. Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment. Nat. Commun. 7:12115 doi: 10.1038/ncomms12115 (2016). This Article is brought to you for free and open access. It has been accepted for inclusion in Biology Faculty Publications and Presentations by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. Authors Louie Wurch, Richard J. Giannone, Bernard S. Belisle, Carolyn Swift, Sagar Utturkar, Robert L. Hettich, Anna-Louise Reysenbach, and Mircea Podar This article is available at PDXScholar: https://pdxscholar.library.pdx.edu/bio_fac/120 ARTICLE Received 11 Mar 2016 | Accepted 1 Jun 2016 | Published 5 Jul 2016 DOI: 10.1038/ncomms12115 OPEN Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment Louie Wurch1,2,w, Richard J. Giannone1, Bernard S. Belisle1,2, Carolyn Swift1,2, Sagar Utturkar1, Robert L. Hettich1,2, Anna-Louise Reysenbach3 & Mircea Podar1,2 Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured. -
Supplementary Material For: Undinarchaeota Illuminate The
Supplementary Material for: Undinarchaeota illuminate the evolution of DPANN archaea Nina Dombrowski1, Tom A. Williams2, Benjamin J. Woodcroft3, Jiarui Sun3, Jun-Hoe Lee4, Bui Quang MinH5, CHristian Rinke5, Anja Spang1,5,# 1NIOZ, Royal NetHerlands Institute for Sea ResearcH, Department of Marine Microbiology and BiogeocHemistry, and UtrecHt University, P.O. Box 59, NL-1790 AB Den Burg, THe NetHerlands 2 ScHool of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK 3Australian Centre for Ecogenomics, ScHool of CHemistry and Molecular Biosciences, THe University of Queensland, QLD 4072, Australia 4Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden 5ResearcH ScHool of Computer Science and ResearcH ScHool of Biology, Australian National University, ACT 2601, Australia #corresponding autHor. Postal address: Landsdiep 4, 1797 SZ 't Horntje (Texel). Email address: [email protected]. PHone number: +31 (0)222 369 526 Table of Contents Table of Contents 2 General 3 Evaluating CHeckM completeness estimates 3 Screening for contaminants 3 Phylogenetic analyses 4 Informational processing and repair systems 7 Replication and cell division 7 Transcription 7 Translation 8 DNA-repair and modification 9 Stress tolerance 9 Metabolic features 10 Central carbon and energy metabolism 10 Anabolism 13 Purine and pyrimidine biosyntHesis 13 Amino acid degradation and biosyntHesis 14 Lipid biosyntHesis 15 Vitamin and cofactor biosyntHesis 16 Host-symbiont interactions 16 Genes potentially -
Molybdate Treatment and Sulfate Starvation Decrease ATP and DNA Levels in Ferroplasma Acidarmanus
Archaea 2, 205–209 © 2008 Heron Publishing—Victoria, Canada Molybdate treatment and sulfate starvation decrease ATP and DNA levels in Ferroplasma acidarmanus DAVID J. BAUMLER,1 KAI-FOONG HUNG,2 KWANG CHEOL JEONG2 and CHARLES W. KASPAR1–3 1 Cellular and Molecular Biology, University of Wisconsin, Madison, Wisconsin, USA 2 Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA 3 Corresponding author ([email protected]) Received June 16, 2008; accepted October 13, 2008; published online October 27, 2008 Summary Sulfate is a primary source of sulfur for most mi- spp. This order has been the subject of some study, because crobes and in some prokaryotes it is used an electron acceptor. three of the four genera have at least one isolate with a com- The acidophile Ferroplasma acidarmanus (strain fer1) re- pleted genome sequence (Ruepp et al. 2000, Futterer et al. quires a minimum of 150 mM of a sulfate-containing salt for 2004, Allen et al. 2007). Moreover, Picrophilus oshimae and growth. Sulfate is assimilated by F. acidarmanus into proteins Ferroplasma acidarmanus share the unique ability to grow at and reduced to form the volatile organic sulfur compounds pH 0.0 (Schleper et al. 1995, Edwards et al. 2000). methanethiol and dimethyldisulfide. In the absence of sulfate, Growth of prokaryotes at extremely low pH generally re- cell death occurs by an unknown mechanism. In this study, cell quires at least three characteristics: (1) a unique membrane viability and genomic DNA and ATP contents of F. acidar- composition; (2) homeostatic systems for maintenance of in- manus were monitored in response to the absence of sul- ternal pH;and (3) the ability to protect and repair essential cel- fate or the presence of sulfate and the sulfate analog lular components. -
A New Candidate Phylum in the Archaea from High-Temperature Acidic Iron Mats in Yellowstone National Park
The ISME Journal (2013) 7, 622–634 & 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13 www.nature.com/ismej ORIGINAL ARTICLE Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park Mark A Kozubal1, Margaret Romine2, Ryan deM Jennings1, Zack J Jay1, Susannah G Tringe3, Doug B Rusch4, Jacob P Beam1, Lee Ann McCue2 and William P Inskeep1 1Department of Land Resources and Environmental Sciences and Thermal Biology Institute, Montana State University, Bozeman, MT, USA; 2Environmental Microbiology Group, Pacific Northwest National Laboratory, Richland, WA, USA; 3DOE Joint Genome Institute, Walnut Creek, CA, USA and 4Department of Biology, Indiana University, Bloomington, IN, USA Geothermal systems in Yellowstone National Park (YNP) provide an outstanding opportunity to understand the origin and evolution of metabolic processes necessary for life in extreme environments including low pH, high temperature, low oxygen and elevated concentrations of reduced iron. Previous phylogenetic studies of acidic ferric iron mats from YNP have revealed considerable diversity of uncultivated and undescribed archaea. The goal of this study was to obtain replicate de novo genome assemblies for a dominant archaeal population inhabiting acidic iron- oxide mats in YNP. Detailed analysis of conserved ribosomal and informational processing genes indicates that the replicate assemblies represent a new candidate phylum within the domain Archaea referred to here as ‘Geoarchaeota’ or ‘novel archaeal group 1 (NAG1)’. The NAG1 organisms contain pathways necessary for the catabolism of peptides and complex carbohydrates as well as a bacterial-like Form I carbon monoxide dehydrogenase complex likely used for energy conservation.