DOCSLIB.ORG

Fig. S1 Complete Chemosensory Class Profile of Spirochaetota. the Three

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Fig. S1 Complete Chemosensory Class Profile of Spirochaetota. the Three GB_GCA_002328585.1 GB_GCA_002407865.1 GB_GCA_001829455.1 GB_GCA_001829495.1 A B GB_GCA_002839375.1 GB_GCA_003246895.1 GB_GCA_002839285.1 GB_GCA_002418835.1 GB_GCA_002425885.1 Turneriella parva DSM 21527 Leptonema illini DSM 21528 GB_GCA_002730875.1 GB_GCA_002729885.1 GB_GCA_002717505.1 GB_GCA_002333425.1 GB_GCA_002786225.1 Leptospira sp. YH101 Leptospira sp. E30 Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' Leptospira yanagawae serovar Saopaulo str. Sao Paulo = ATCC 700523 Leptospira sp. CN6-C-A1 Leptospira sp. E18 Leptospira sp. JW2-C-A2 Leptospira meyeri serovar Hardjo str. Went 5 Leptospira sp. FH2-B-A1 Leptospira terpstrae serovar Hualin str. LT 11-33 = ATCC 700639 Leptospira vanthielii serovar Holland str. Waz Holland = ATCC 700522 Leptospira wolbachii serovar Codice str. CDC Leptospira sp. FH1-B-B1 Leptospira fainei serovar Hurstbridge str. BUT 6 Leptospira inadai serovar Lyme str. 10 Leptospira broomii serovar Hurstbridge str. 5399 Leptospira wolffii serovar Khorat str. Khorat-H2 Leptospira sp. B5-022 Leptospira licerasiae serovar Varillal str. VAR 010 Leptospira sp. MCA2-B-A3 Leptospira sp. ES4-C-A1 Leptospira sp. E8 Leptospira sp. FH4-C-A2 Leptospira venezuelensis Leptospira sp. ATI7-C-A4 Leptospira sp. FH2-B-C1 Leptospira alstonii Leptospira sp. ATI7-C-A5 Leptospira kmetyi serovar Malaysia str. Bejo-Iso9 Leptospira sp. FH4-C-A1 Leptospira alstonii serovar Sichuan str. 79601 Leptospira weilii serovar Ranarum str. ICFT Leptospira noguchii serovar Panama str. CZ214 Leptospira kirschneri serovar Cynopteri str. 3522 CT Leptospira interrogans Leptospira santarosai serovar Shermani str. LT 821 Leptospira mayottensis 200901116 Leptospira borgpetersenii Leptospira alexanderi serovar Manhao 3 str. L 60 Leptospira weilii serovar Topaz str. LT2116 GB_GCA_003497555.1 GB_GCA_000431595.1 Brachyspira pilosicoli P43/6/78 Brachyspira alvinipulli ATCC 51933 Brachyspira sp. G79 Brachyspira murdochii DSM 12563 Brachyspira innocens ATCC 29796 Brachyspira hampsonii Brachyspira hampsonii 30446 Brachyspira hampsonii Brachyspira intermedia PWS/A Brachyspira hyodysenteriae ATCC 27164 Brachyspira suanatina GB_GCA_001829155.1 GB_GCA_002450905.1 Brevinema andersonii GB_GCA_001829395.1 GB_GCA_001829415.1 GB_GCA_001829125.1 GB_GCA_001829315.1 Candidatus Borrelia tachyglossi tachyglossi Borrelia miyamotoi LB-2001 Borrelia hermsii DAH Borrelia anserina Es Borrelia turicatae 91E135 Borrelia coriaceae Co53 Borrelia persica No12 Borrelia hispanica CRI Borrelia crocidurae str. Achema Borrelia duttonii Ly GB_GCA_000808095.1 Borrelia mayonii Borreliella bissettii DN127 Borreliella burgdorferi B31 Borreliella finlandensis Borreliella valaisiana VS116 Borreliella garinii Borreliella japonica Borreliella afzelii HLJ01 Borreliella spielmanii A14S GB_GCA_003454065.1 GB_GCA_001604265.1 GB_GCA_002406055.1 GB_GCA_002452215.1 GB_GCA_002308475.1 GB_GCA_001940825.1 GB_GCA_900321635.1 GB_GCA_003456855.1 GB_GCA_001604275.1 Sphaerochaeta coccoides DSM 17374 GB_GCA_002428625.1 GB_GCA_002839335.1 GB_GCA_002839355.1 GB_GCA_900315435.1 Sphaerochaeta pleomorpha str. Grapes GB_GCA_003446545.1 GB_GCA_003247345.1 GB_GCA_001603105.1 GB_GCA_001604325.1 GB_GCA_001603115.1 GB_GCA_002432715.1 Sphaerochaeta globosa str. Buddy GB_GCA_002688185.1 GB_GCA_003233545.1 GB_GCA_002238925.1 GB_GCA_003170115.1 GB_GCA_003141795.1 GB_GCA_003154555.1 Sediminispirochaeta smaragdinae DSM 11293 Sediminispirochaeta bajacaliforniensis DSM 16054 GB_GCA_003245835.1 GB_GCA_003454605.1 Candidatus Marispirochaeta associata associata Marispirochaeta aestuarii Spirochaeta thermophila DSM 6192 Spirochaeta thermophila DSM 6578 Salinispira pacifica Spirochaeta lutea Spirochaeta africana DSM 8902 GB_GCA_002313505.1 Alkalispirochaeta alkalica DSM 8900 Alkalispirochaeta americana Spirochaeta cellobiosiphila DSM 17781 GB_GCA_003247135.1 GB_GCA_002084805.1 GB_GCA_002408085.1 GB_GCA_003249275.1 GB_GCA_003246505.1 GB_GCA_002084135.1 GB_GCA_002352375.1 GB_GCA_002748225.1 GB_GCA_001829185.1 GB_GCA_002412825.1 GB_GCA_002839245.1 GB_GCA_002839315.1 GB_GCA_003247225.1 GB_GCA_002307245.1 GB_GCA_002839205.1 GB_GCA_002428725.1 GB_GCA_001603165.1 GB_GCA_002383375.1 GB_GCA_003452735.1 GB_GCA_002427685.1 GB_GCA_002435985.1 GB_GCA_002441395.1 GB_GCA_002425765.1 GB_GCA_002307015.1 Treponema caldarium DSM 7334 GB_GCA_003527485.1 GB_GCA_003245635.1 GB_GCA_002293455.1 Treponema azotonutricium ZAS-9 Treponema primitia ZAS-2 Treponema primitia ZAS-1 GB_GCA_003246335.1 GB_GCA_001604385.1 GB_GCA_001604405.1 GB_GCA_003246765.1 GB_GCA_003245785.1 GB_GCA_003252395.1 Treponema pallidum subsp. pallidum str. Sea 81-4 Treponema phagedenis 4A Treponema vincentii F0403 Treponema medium ATCC 700293 Treponema sp. OMZ 838 GB_GCA_002749205.1 Treponema pedis str. T A4 Treponema putidum Treponema denticola ATCC 35405 Treponema denticola SP32 Treponema brennaborense DSM 12168 GB_GCA_001885315.1 Treponema maltophilum ATCC 51939 Treponema lecithinolyticum ATCC 700332 GB_GCA_001603145.1 GB_GCA_002308875.1 GB_GCA_002369025.1 Treponema saccharophilum DSM 2985 GB_GCA_002404895.1 GB_GCA_002368605.1 GB_GCA_002393835.1 GB_GCA_002394465.1 GB_GCA_003447785.1 GB_GCA_002392405.1 GB_GCA_002477955.1 Treponema berlinense GB_GCA_002394685.1 GB_GCA_003455655.1 GB_GCA_002449305.1 Treponema succinifaciens DSM 2489 GB_GCA_002393865.1 GB_GCA_002373205.1 GB_GCA_002448445.1 GB_GCA_002392275.1 GB_GCA_002373325.1 GB_GCA_002396325.1 GB_GCA_002309305.1 GB_GCA_002319875.1 GB_GCA_002309195.1 GB_GCA_900316905.1 GB_GCA_002391235.1 GB_GCA_002399405.1 GB_GCA_002314445.1 Treponema socranskii Treponema socranskii subsp. paredis ATCC 35535 Treponema porcinum GB_GCA_002437725.1 GB_GCA_900317625.1 GB_GCA_002478955.1 GB_GCA_002296965.1 GB_GCA_002315375.1 GB_GCA_900319625.1 Treponema sp. JC4 0.2 Treponema sp. C6A8 GB_GCA_002350445.1 GB_GCA_002395155.1 Treponema bryantii NK4A124 Treponema bryantii Treponema bryantii Fig. S1 Complete chemosensory class profile of Spirochaetota. The three major taxonomy classes are colored: Leptospirae (red), Brachyspirae (purple) and Spirochaetia (green). Species found in MiST3 are represented By their species and strain name. The profile shows the presence of the chemotaxis classes F1(Blue), F8(orange), F2 (green), F7(red), F5 (purple), ACF (Brown) and TFP (pink). The systems with CheW-CheRlike are marked with a Black outline. Scale Bar represents the average numBer of suBstitutions per site. An additional high-resolution figure is separately available. Fig. S2 (A) SeQuence logo of representative seQuences of the two groups of CheR-containing proteins in the F2 system. (B) SeQuence logo of representative seQuences of the three groups of CheW-containing proteins in the F2 system. Blue Boxes denote the location of variable regions identified in the Td CheW and P5 homologs. In these locations, all regions possess uniQue conserved residues with the exception of Region 2, which is not at the CheA:CheW ring interfaces. An additional high-resolution figure is separately available. 1.0 Fig. S3 Phylogenetic tree of a non-redundant set of CheW protein seQuences in genomes with at least one CheA-F2. The initial classification of CheW classes are mapped to the tree nodes: F2 (red), F5 (purple), F7 (light green), F8 (green) and ACF (Blue). The clustering of the CheW classified as class F2 suggests a last common ancestor of CheW-F2 seQuences (larger red internal node). This clustering allows us to extrapolate the conservative selection of F2 seQuences to other CheW proteins in the cluster to get a more inclusive set. Scale Bar represents the average numBer of suBstitutions per site. Fig. S4 (A) Top: The numBer of arrays and particles selected to generate suB-tomogram averages for each Td strain, and the average resolution of the suB-tomogram averages. Resolution values were calculated at FSC = 0.3 in a masked region that contains the single central receptor hexagon and CheA:CheW ring. Bottom: Example of the masked region used for resolution calculation (WT map). Scale Bar is 12 nm. (B) SuB-tomogram averages reveal the orientation of the chemotaxis arrays with respect to the cell axis. Intriguingly, the arrays have a preferred orientation in the cells and this orientation is conserved in WT and the Δ2498 and Δ2498Δ2496 deletion mutants. The small size of arrays in the ΔCheRlike strain inhiBits direct oBservation of the cell axis. Fig. S5 (A) SEC-MALS of Td CheA and CheW-Rlike. Top: CheA forms a dimer in solution. Bottom: The CheW-Rlike protein is primarily present as a monomer, But associates into a small amount of dimer. There is also a small amount of aggregates present (Black arrow). The dRI trace is a Black dashed line. The LS trace is grey. (B) The CheW-CheRlike linker is predicted to form a single alpha helix flanked By unordered regions (Jpred). (C) Native mass spectrometry (ESI-MS) experiments indicate that CheW-Rlike (left) and the Td classical CheR protein (right) Bind SAM (398.44 Da) in a 1:1 stoichiometric ratio. Example shifts in the spectra are denoted By Black dashed lines and match expectations for 1:1 Binding. The seQuence derived mass of CheW-CheRlike and CheR is 51.784 kDa and 33.802 kDa, respectively. Source data are provided as a Source Data file. Fig. S6 Capillary chemotaxis assay of T. denticola wild-type and ΔCheRlike strain using two chemoattractants: hemin (left) and glucose (right). The ΔCheRlike strain is missing only the CheRlike domain of CheW-CheRlike. For the non-gradient control, Both the capillary tuBes and Bacterial suspensions contained chemoattractants. Differences in chemoattraction of WT and ΔCheRlike strains are statistically
Load more

Recommended publications
  • 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]
  • Genomic Insights Into the Carbon and Energy Metabolism of A
    Genomic Insights into the Carbon and Energy Metabolism of a Thermophilic Deep-Sea Bacterium Deferribacter autotrophicus Revealed New Metabolic Traits in the Phylum Deferribacteres Alexander Slobodkin, Galina Slobodkina, Maxime Allioux, Karine Alain, Mohamed Jebbar, Valerian Shadrin, Ilya Kublanov, Stepan Toshchakov, Elizaveta Bonch-Osmolovskaya To cite this version: Alexander Slobodkin, Galina Slobodkina, Maxime Allioux, Karine Alain, Mohamed Jebbar, et al.. Genomic Insights into the Carbon and Energy Metabolism of a Thermophilic Deep-Sea Bacterium Deferribacter autotrophicus Revealed New Metabolic Traits in the Phylum Deferribacteres. Genes, MDPI, 2019, 10 (11), pp.849. 10.3390/genes10110849. hal-02359529 HAL Id: hal-02359529 https://hal.archives-ouvertes.fr/hal-02359529 Submitted on 16 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. G C A T T A C G G C A T genes Article Genomic Insights into the Carbon and Energy Metabolism of a Thermophilic Deep-Sea Bacterium Deferribacter autotrophicus Revealed New Metabolic Traits in the Phylum Deferribacteres
    [Show full text]
  • Novel Hydrogenosomes in the Microaerophilic Jakobid Stygiella Incarcerata Article Open Access
    Novel Hydrogenosomes in the Microaerophilic Jakobid Stygiella incarcerata Michelle M. Leger,1 Laura Eme,1 Laura A. Hug,‡,1 and Andrew J. Roger*,1 1Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada ‡Present address: Department of Biology, University of Waterloo, Waterloo, ON, Canada *Corresponding author: E-mail: [email protected]. Associate editor: Inaki~ Ruiz-Trillo Abstract Mitochondrion-related organelles (MROs) have arisen independently in a wide range of anaerobic protist lineages. Only a few of these organelles and their functions have been investigated in detail, and most of what is known about MROs comes from studies of parasitic organisms such as the parabasalid Trichomonas vaginalis. Here, we describe the MRO of a free-living anaerobic jakobid excavate, Stygiella incarcerata. We report an RNAseq-based reconstruction of S. incarcerata’s MRO proteome, with an associated biochemical map of the pathways predicted to be present in this organelle. The pyruvate metabolism and oxidative stress response pathways are strikingly similar to those found in the MROs of other anaerobic protists, such as Pygsuia and Trichomonas. This elegant example of convergent evolution is suggestive of an anaerobic biochemical ‘module’ of prokaryotic origins that has been laterally transferred among eukaryotes, enabling them to adapt rapidly to anaerobiosis. We also identified genes corresponding to a variety of mitochondrial processes not Downloaded from found in Trichomonas, including intermembrane space components of the mitochondrial protein import apparatus, and enzymes involved in amino acid metabolism and cardiolipin biosynthesis. In this respect, the MROs of S. incarcerata more closely resemble those of the much more distantly related free-living organisms Pygsuia biforma and Cantina marsupialis, likely reflecting these organisms’ shared lifestyle as free-living anaerobes.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 8,986,963 B2 Lee (45) Date of Patent: Mar
    US008986,963B2 (12) United States Patent (10) Patent No.: US 8,986,963 B2 Lee (45) Date of Patent: Mar. 24, 2015 (54) DESIGNER CALVIN-CYCLE-CHANNELED FOREIGN PATENT DOCUMENTS PRODUCTION OF BUTANOL AND RELATED WO 2005100.582 A2 10, 2005 HIGHER ALCOHOLS WO 2006119066 11, 2006 WO 2007032837 A2 3, 2007 (76) Inventor: James Weifu Lee, Cockeysville, MD WO 2007047148 4/2007 (US) WO 2007065035 6, 2007 WO 2007134340 A2 11/2007 WO 2008OO6038 A2 1, 2008 (*) Notice: Subject to any disclaimer, the term of this WO 201OO68821 A1 6, 2010 patent is extended or adjusted under 35 U.S.C. 154(b) by 714 days. OTHER PUBLICATIONS Appl. No.: 13/075,153 Chen et al., Photo. Res., 2005, 86:165-173.* (21) Raines et al., 2003, Photosynthesis Res., 75:1-10.* Filed: Mar. 29, 2011 Pickett-Heaps et al., 1999, Am. J. of Botany, 86:153-172.* (22) Shen et al., 2008, Metabolic Engineering, 10:312-320.* Prior Publication Data Sanderson, 2006, Nature, 444:673-676.* (65) Keneko Takakazu et al., Complete Genomic Sequence of the Fila US 2011/O177571 A1 Jul. 21, 2011 mentous Nitrogen-fixing Cyanobacterium Anabaena sp. Strain PCC 7120, DNA Research 8,205-213 (2001). Ramesh V. Nair et al., Regulation of the Sol Locus Genes for Butanol and Acetone Formation in Clostridium acetobutylicum ATCC824 by Related U.S. Application Data a Putative Transcriptional Repressor, Journal of Bacteriology, Jan. (63) Continuation-in-part of application No. 12/918,784, 1999, vol. 181, No. 1, pp. 319-330. filed as application No. PCT/US2009/034801 on Feb.
    [Show full text]
  • Treponema Primitia Sp
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Mar. 2004, p. 1315–1320 Vol. 70, No. 3 0099-2240/04/$08.00ϩ0 DOI: 10.1128/AEM.70.3.1315–1320.2004 Copyright © 2004, American Society for Microbiology. All Rights Reserved. Description of Treponema azotonutricium sp. nov. and Treponema primitia sp. nov., the First Spirochetes Isolated from Termite Guts Joseph R. Graber,1 Jared R. Leadbetter,2 and John A. Breznak1* Department of Microbiology and Molecular Genetics and Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824-4320,1 and Environmental Science and Engineering, California Institute of Technology, Pasadena, California 91125-78002 Received 12 August 2003/Accepted 27 November 2003 Long after their original discovery, termite gut spirochetes were recently isolated in pure culture for the first time. They revealed metabolic capabilities hitherto unknown in the Spirochaetes division of the Bacteria, i.e., H2 plus CO2 acetogenesis (J. R. Leadbetter, T. M. Schmidt, J. R. Graber, and J. A. Breznak, Science 283:686-689, 1999) and dinitrogen fixation (T. G. Lilburn, K. S. Kim, N. E. Ostrom, K. R. Byzek, J. R. Leadbetter, and J. A. Breznak, Science 292:2495-2498, 2001). However, application of specific epithets to the strains isolated (Trepo- nema strains ZAS-1, ZAS-2, and ZAS-9) was postponed pending a more complete characterization of their pheno- typic properties. Here we describe the major properties of strain ZAS-9, which is readily distinguished from strains ZAS-1 and ZAS-2 by its shorter mean cell wavelength or body pitch (1.1 versus 2.3 ␮m), by its nonhomoacetogenic fermentation of carbohydrates to acetate, ethanol, H2, and CO2, and by 7 to 8% dissimilarity between its 16S rRNA sequence and those of ZAS-1 and ZAS-2.
    [Show full text]
  • Taxonomic, Genetic and Functional Diversity of Symbionts Associated with the Coastal Bivalve Family Lucinidae
    Clemson University TigerPrints All Dissertations Dissertations December 2018 Taxonomic, Genetic and Functional Diversity of Symbionts Associated with the Coastal Bivalve Family Lucinidae Jean S. Lim Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_dissertations Recommended Citation Lim, Jean S., "Taxonomic, Genetic and Functional Diversity of Symbionts Associated with the Coastal Bivalve Family Lucinidae" (2018). All Dissertations. 2566. https://tigerprints.clemson.edu/all_dissertations/2566 This Dissertation is brought to you for free and open access by the Dissertations at TigerPrints. It has been accepted for inclusion in All Dissertations by an authorized administrator of TigerPrints. For more information, please contact [email protected]. TAXONOMIC, GENETIC AND FUNCTIONAL DIVERSITY OF SYMBIONTS ASSOCIATED WITH THE COASTAL BIVALVE FAMILY LUCINIDAE A Dissertation Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Biological Sciences by Lim Shen Jean December 2018 Accepted by: Barbara J. Campbell, Committee Chair Antonio J. Baeza Annette S. Engel Vincent P. Richards ABSTRACT Extant bivalve members from the family Lucinidae harbor chemosynthetic gammaproteobacterial gill endosymbionts capable of thioautotrophy. These endosymbionts are environmentally acquired and belong to a paraphyletic group distantly related to other marine chemosymbionts. In coastal habitats, lucinid chemosymbionts participate in facilitative interactions with their hosts and surrounding seagrass habitat that results in symbiotic sulfide detoxification, oxygen release from seagrass roots, carbon fixation, and/or symbiotic nitrogen fixation. Currently, the structural and functional complexity of whole lucinid gill microbiomes, as well as their interactions with lucinid bivalves and their surrounding environment, have not been comprehensively characterized.
    [Show full text]
  • Enzymology and Bioenergetics of the Glycolytic Pathway of Pyrococcus Furiosus
    Enzymology and bioenergetics of the glycolytic pathway of Pyrococcus furiosus Judith E. Tuininga Promotoren prof. dr. W.M. de Vos hoogleraar in de microbiologie Wageningen Universiteit prof. dr. ir. A.J.M. Stams persoonlijk hoogleraar aan het Laboratorium voor Microbiologie Wageningen Universiteit Copromotor dr. S.W.M. Kengen universitair docent aan het Laboratorium voor Microbiologie Wageningen Universiteit Promotiecommissie dr. B. Siebers Universität Duisburg-Essen, Duitsland prof. dr. A.J.M. Driessen Rijksuniversiteit Groningen prof. dr. S.C. de Vries Wageningen Universiteit dr. T. Abee Wageningen Universiteit dr. J. van der Oost Wageningen Universiteit Enzymology and bioenergetics of the glycolytic pathway of Pyrococcus furiosus Judith E. Tuininga Proefschrift ter verkrijging van de graad van doctor op gezag van de rector magnificus van Wageningen Universiteit, prof. dr. ir. L. Speelman, in het openbaar te verdedigen op vrijdag 5 december 2003 des namiddags te half twee in de Aula. Enzymology and bioenergetics of the glycolytic pathway of Pyrococcus furiosus Judith E. Tuininga Ph.D. thesis Wageningen University, Wageningen, The Netherlands 2003 151 p. - with summary in Dutch ISBN 90-5808-924-X hoe ver je gaat heeft met afstand niets te maken hoogstens met de tijd [Bløf – Omarm] Contents CHAPTER 1 Introduction 1 CHAPTER 2 Purification and characterisation of a novel 19 ADP-dependent glucokinase from the hyperthermophilic Archaeon Pyrococcus furiosus CHAPTER 3 Molecular and biochemical characterisation of the 35 ADP-dependent phosphofructokinase
    [Show full text]
  • Ixodes Scapularis Does Not Harbor a Stable Midgut Microbiome
    The ISME Journal https://doi.org/10.1038/s41396-018-0161-6 ARTICLE Ixodes scapularis does not harbor a stable midgut microbiome 1 2 1 3 4 5 5 Benjamin D. Ross ● Beth Hayes ● Matthew C. Radey ● Xia Lee ● Tanya Josek ● Jenna Bjork ● David Neitzel ● 3 2 1,6 Susan Paskewitz ● Seemay Chou ● Joseph D. Mougous Received: 9 October 2017 / Revised: 19 April 2018 / Accepted: 9 May 2018 © International Society for Microbial Ecology 2018 Abstract Hard ticks of the order Ixodidae serve as vectors for numerous human pathogens, including the causative agent of Lyme Disease Borrelia burgdorferi. Tick-associated microbes can influence pathogen colonization, offering the potential to inhibit disease transmission through engineering of the tick microbiota. Here, we investigate whether B. burgdorferi encounters abundant bacteria within the midgut of wild adult Ixodes scapularis, its primary vector. Through the use of controlled sequencing methods and confocal microscopy, we find that the majority of field-collected adult I. scapularis harbor limited internal microbial communities that are dominated by endosymbionts. A minority of I. scapularis ticks harbor abundant midgut bacteria and lack B. burgdorferi.Wefind that the lack of a stable resident midgut microbiota is not restricted to I. scapularis since extension of our studies to I. pacificus, Amblyomma maculatum, and Dermacentor spp showed similar 1234567890();,: 1234567890();,: patterns. Finally, bioinformatic examination of the B. burgdorferi genome revealed the absence of genes encoding known interbacterial interaction pathways, a feature unique to the Borrelia genus within the phylum Spirochaetes. Our results suggest that reduced selective pressure from limited microbial populations within ticks may have facilitated the evolutionary loss of genes encoding interbacterial competition pathways from Borrelia.
    [Show full text]
  • Spirochaeta Thermophila Ligand Specificity ZZ-CBM64 Binds to Crystalline Forms of Cellulose
    Storage temperature Carbohydrate Binding Module 64A, This protein is shipped at room temperature but should be (ZZ-CBM64) stored at 4 °C. Spirochaeta thermophila Ligand specificity ZZ-CBM64 binds to crystalline forms of cellulose. See the Catalogue number(s): CZ04991, 1 mg reference below for more details on the biochemical CZ04992, 3 × 1 mg properties of ZZ-CBM64. Assay conditions To recover maximal ZZ-CBM64 activity, centrifuge a required Description volume of the precipitated protein suspension (13000 xg for ZZ-CBM64 is a bacterial polypeptide displaying high affinity 5 min), remove the ammonium sulphate supernatant and to crystalline cellulose through a C-terminal Carbohydrate ressuspend the resulting pellet in the same volume of 20 mM Binding Module of Spirochaeta thermophila. Recombinant Tris-HCl, pH 7.5, 20 mM NaCl, 5 mM CaCl2. Proceed with the ZZ-CBM64, purified from Escherichia coli, is a modular assay as required. protein containing at its N-terminus the immunoglobulin G (IgG) binding ZZ domain of protein A from Staphylococcus Reference aureus fused to a family 64 Carbohydrate Binding Module Chen et al (2006). Biotechnol Appl Biochem. 45, 87-92. (CBM64) (www.cazy.org). This ZZ domain protein derivative is particularly recommended to mediate the anchorage of antibodies to cellulosic supports. The protein is provided in 3.2 M ammonium sulphate at a 1 mg/mL concentration. Bulk Quality control assay quantities of this product are available on request. Protein purity is >90% as judged by SDS-PAGE followed by BlueSafe staining (MB15201). Electrophoretic Purity ZZ-CBM64 purity was determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) followed by BlueSafe staining (MB15201) (Figure 1).
    [Show full text]
  • A Potential Source for Cellulolytic Enzyme Discovery And
    Thompson et al. AMB Express 2013, 3:65 http://www.amb-express.com/content/3/1/65 ORIGINAL ARTICLE Open Access A potential source for cellulolytic enzyme discovery and environmental aspects revealed through metagenomics of Brazilian mangroves Claudia Elizabeth Thompson1,2*†, Walter Orlando Beys-da-Silva2†, Lucélia Santi2†, Markus Berger2, Marilene Henning Vainstein2, Jorge Almeida Guima rães2* and Ana Tereza Ribeiro Vasconcelos1* Abstract The mangroves are among the most productive and biologically important environments. The possible presence of cellulolytic enzymes and microorganisms useful for biomass degradation as well as taxonomic and functional aspects of two Brazilian mangroves were evaluated using cultivation and metagenomic approaches. From a total of 296 microorganisms with visual differences in colony morphology and growth (including bacteria, yeast and filamentous fungus), 179 (60.5%) and 117 (39.5%) were isolated from the Rio de Janeiro (RJ) and Bahia (BA) samples, respectively. RJ metagenome showed the higher number of microbial isolates, which is consistent with its most conserved state and higher diversity. The metagenomic sequencing data showed similar predominant bacterial phyla in the BA and RJ mangroves with an abundance of Proteobacteria (57.8% and 44.6%), Firmicutes (11% and 12.3%) and Actinobacteria (8.4% and 7.5%). A higher number of enzymes involved in the degradation of polycyclic aromatic compounds were found in the BA mangrove. Specific sequences involved in the cellulolytic degradation, belonging to cellulases, hemicellulases, carbohydrate binding domains, dockerins and cohesins were identified, and it was possible to isolate cultivable fungi and bacteria related to biomass decomposition and with potential applications for the production of biofuels.
    [Show full text]
  • A Phylogenomic and Molecular Signature Based
    ORIGINAL RESEARCH ARTICLE published: 30 July 2013 doi: 10.3389/fmicb.2013.00217 A phylogenomic and molecular signature based approach for characterization of the phylum Spirochaetes and its major clades: proposal for a taxonomic revision of the phylum Radhey S. Gupta*, Sharmeen Mahmood and Mobolaji Adeolu Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada Edited by: The Spirochaetes species cause many important diseases including syphilis and Lyme Hiromi Nishida, Toyama Prefectural disease. Except for their containing a distinctive endoflagella, no other molecular or University, Japan biochemical characteristics are presently known that are specific for either all Spirochaetes Reviewed by: or its different families. We report detailed comparative and phylogenomic analyses Viktoria Shcherbakova, Institute of Biochemistry and Physiology of of protein sequences from Spirochaetes genomes to understand their evolutionary Microorganisms, Russian Academy relationships and to identify molecular signatures for this group. These studies have of Sciences, Russia identified 38 conserved signature indels (CSIs) that are specific for either all members David L. Bernick, University of of the phylum Spirochaetes or its different main clades. Of these CSIs, a 3 aa insert in California, Santa Cruz, USA the FlgC protein is uniquely shared by all sequenced Spirochaetes providing a molecular *Correspondence: Radhey S. Gupta, Department of marker for this phylum. Seven, six, and five CSIs in different proteins are specific Biochemistry and Biomedical for members of the families Spirochaetaceae, Brachyspiraceae, and Leptospiraceae, Sciences, McMaster University, respectively. Of the 19 other identified CSIs, 3 are uniquely shared by members of the 1280 Main Street West, Hamilton, genera Sphaerochaeta, Spirochaeta,andTreponema, whereas 16 others are specific for ON L8N 3Z5, Canada e-mail: [email protected] the genus Borrelia.
    [Show full text]
  • Destruction of Spirochete Borrelia Burgdorferi Round-Body Propagules (Rbs) by the Antibiotic Tigecycline
    Destruction of spirochete Borrelia burgdorferi round-body propagules (RBs) by the antibiotic Tigecycline Øystein Brorsona, Sverre-Henning Brorsonb, John Scythesc, James MacAllisterd, Andrew Wiere,1, and Lynn Margulisd,2 aDepartment of Microbiology, Sentralsykehuset i Vestfold HF, N-3116 Tonsberg, Norway;bDepartment of Pathology, Rikshospitalet, N-0027 Oslo, Norway; cGlad Day Bookshop, Toronto, ON, Canada M4Y 1Z3; dDepartment of Geosciences, University of Massachusetts, Amherst, MA 01003; and eDepartment of Medical Microbiology, University of Wisconsin, Madison, WI 53706 Contributed by Lynn Margulis, July 31, 2009 (sent for review May 4, 2009) Persistence of tissue spirochetes of Borrelia burgdorferi as helices different viscosity or temperature stimulates the formation of and round bodies (RBs) explains many erythema-Lyme disease RBs. Starvation, threat of desiccation, exposure to oxygen gas, symptoms. Spirochete RBs (reproductive propagules also called total anoxia and/or sulfide may induce RB formation (3–13). coccoid bodies, globular bodies, spherical bodies, granules, cysts, RBs revert to the active helical swimmers when favorable L-forms, sphaeroplasts, or vesicles) are induced by environmental conditions that support growth return (3–5). conditions unfavorable for growth. Viable, they grow, move and That RBs reversibly convertible to healthy motile helices is reversibly convert into motile helices. Reversible pleiomorphy was bolstered by the discovery of a new member of the genus recorded in at least six spirochete genera (>12 species). Penicillin Spirochaeta: S. coccoides (14) through 16S ribosomal RNA solution is one unfavorable condition that induces RBs. This anti- sequences. Related on phylogenies to Spirochaeta thermophila, biotic that inhibits bacterial cell wall synthesis cures neither the Spirochaeta bajacaliforniensis, and Spirochaeta smaragdinae, all second ‘‘Great Imitator’’ (Lyme borreliosis) nor the first: syphilis.
    [Show full text]