DOCSLIB.ORG

Study of the Respiratory Arsenate Reductase from Halorhodospira

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Study of the Respiratory Arsenate Reductase from Halorhodospira View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector e90 Abstracts S8.P24 dicyclihexylcarbodiimide (DCCD)-inhibited ATPase activity of purple bacteria Rhodobacter sphaeroides str. MDC6521 (from mineral spring Role of DsrC in the mechanism of sulfite reduction by the waters in Armenian mountains) membrane vesicles for revealing the dissimilatory sulfite reductase DsrAB regulatory pathways of bacterial redox sensing. The membrane + André A. Santosa,SofiaS.Venceslaua,FabianGreinb, Inês Cardoso Pereiraa vesicles showed pronounced H -translocating ATPase activity, aITQB-UNL, Portugal which was inhibited on ~42% by 0.1 mM DCCD. After treatment of – – bUniversity of Bonn, Germany membrane vesicles with 0.5 2 mM DTT an additional increase (~1.6 E-mail: [email protected] 1.8-folds) of DCCD-inhibited ATPase activity was observed. The increase of the ATPase activity by DTT under reducing conditions might be connected with the change of dithiol/disulfide status of this The dissimilatory sulfite reductase (DsrAB) is one of the most enzyme due to the fact that redox-sensitive thiols gain access to the important enzymes in the biogeochemical sulfur cycle [1]. It is ATPase. Therefore, the FoF1-ATPase might have an essential role in present in all sulfate reducing microorganisms, in sulfite/thiosulfate/ redox sensing of R. sphaeroides. organosulfonate reducers and in sulfur-oxidizing bacteria. This siroheme-containing enzyme catalyzes the reduction of sulfite, but References despite years of research, the mechanism and physiological products [1] L. Hakobyan, L. Gabrielyan, A. Trchounian, Proton motive force in of sulfite reduction have not been clearly identified. It is not clear Rhodobacter sphaeroides under anaerobic conditions in the dark, why in vitro DsrAB produces a mixture of products including Curr. Microbiol. 62 (2011) 415–419. thiosulfate and trithionate, while the closely-related assimilatory [2] L. Hakobyan, L. Gabrielyan, A. Trchounian, Relationship of proton enzyme reduces sulfite directly to sulfide. More recently, the motive force and the F0F1-ATPase with bio-hydrogen production reduction of sulfite by DsrAB was proposed to involve also the small activity of Rhodobacter sphaeroides: effects of diphenylene iodonium, protein DsrC, which contains two conserved redoxactive cysteines in hydrogenase inhibitor, and its solvent dimethylsulphoxide, J. Bio- a flexible C-terminal arm [2]. The crystal structure of DsrAB in energ. Biomembr. 44 (2012) 495–502. complex with DsrC showed that one of these Cys is located right next to the active site, pointing to the involvement of DsrC in the reduction mechanism [3]. Here, we report recent results from doi:10.1016/j.bbabio.2014.05.106 the investigation on the role of DsrC in the reduction of sulfite by DsrAB, using in vivo and in vitro experiments. Our results show fi that DsrC is directly involved in sul te reduction and permits the S8.P26 identification of the mechanism and physiological product of this important reaction. Study of the respiratory arsenate reductase from Halorhodospira halophila definitively clarifies the evolutionary history of this References versatile enzyme [1] Grein F, Ramos AR, Venceslau SS, Pereira IAC (2013) Unifying Barbara Schoepp-Cotheneta, Marielle Bauzanb, Anne-Lise Ducluzeauc, concepts in anaerobic respiration: Insights from dissimilatory Fabien Pierreld, Wolfgang Nitschkea sulfur metabolism. Biochim Biophys. Acta-Bioenergetics 1827, aBioénergétique et Ingénierie des Protéines, UMR 7281, CNRS, Aix 145–60. Marseille University, IMM FR3479, Marseille, France [2] Venceslau SS, Stockdreher Y, Dahl C, Pereira IAC (2014), The bInstitut de Microbiologie de la Méditerranée, FR3479, F-13402 Marseille “bacterial heterodisulfide” DsrC is a key protein in dissimilatory Cedex 20, France sulfur metabolism, Biochim. Biophys. Acta-Bioenergetics, http:// cBeadle Center, University of Nebraska-Lincoln, 1901 Vine Street, Lincoln, dx.doi.org/10.1016/j.bbabio.2014.03.007. NE 68588-0660, USA [3] Oliveira TF, Vonrheim, Matias PM, Venceslau SS, Pereira IAC, dChimie et Biologie des Métaux, UMR 5249, CEA, CNRS, JF University, Archer M (2008) The crystal structure of a dissimilatory sulfite Grenoble, France reductase bound to DsrC provides novel insights into the E-mail: [email protected] mechanism of sulfate reduction. J. Biol. Chem. 283: 34141. doi:10.1016/j.bbabio.2014.05.105 The three presently known enzymes responsible for arsenic-using bioenergetic processes are arsenite oxidase (Aio), arsenate reductase (Arr) and alternative arsenite oxidase (Arx), all of which are molybdoenzymes from the vast group referred to as the Mo/W- S8.P25 bisPGD enzyme superfamily. Since arsenite is present in substantial amounts in hydrothermal environments (frequently considered as Dithiothreitol, redox reagent, is affecting proton-translocating vestiges of primordial biochemistry), arsenite-based bioenergetics ATPase activity of Rhodobacter sphaeroides has early on been predicted to be ancient. Conflicting scenarios, a a b Harutyun Sargsyan , Lilit Gabrielyan , Armen Trchounian however, have been put forward proposing either Arr/Arx or Aio as a Department of Microbiology, Microbes and Plants Biotechnology, operating in the ancestral metabolism. Phylogenetic data argue in Faculty of Biology, Yerevan State University, Armenia favour of Aio whereas biochemical and physiological data led several b Department of Microbiology, Plants & Microbes Biotechnology, Faculty authors to propose the Arx/Arr enzyme as the most ancient of Biology, Yerevan State University, Armenia anaerobic arsenite metabolising enzyme. Here we combine phyloge- E-mail: [email protected] netic approaches with physiological and biochemical experiments to demonstrate that the Arx/Arr enzyme could not have been functional The H+-translocating FoF1-ATPase of purple bacteria, the main in the Archaean. We show that Arr reacts with menaquinones to membrane-associated enzyme of bioenergetics relevance, can gen- reduce arsenate whereas Arx reacts with ubiquinone to oxidise erate proton motive force under various conditions [1]. Its role in arsenite, in line with thermodynamic considerations. The phylogeny photo-fermentation and hydrogen production by these bacteria is of the quinone biosynthesis pathway, however, clearly indicates that suggested [2]. In the current work we have studied effects of DL- the ubiquinone pathway is recent. An updated phylogeny of Arr/Arx dithiothreitol (DTT), a redox reagent reducing disulfides, on N,N′- furthermore indicates a recent emergence of this enzyme. We Abstracts e91 therefore conclude that only the metabolism involving Aio could The nature of the carbon metabolism of the extinct primordial have performed anaerobic As redox conversion in the Archaean. organisms is a critical question to understand the origins of life [1,2]. Central to core carbon metabolism is the C1 chemistry involving doi:10.1016/j.bbabio.2014.05.107 folate and its structural analog, methanopterin. Based on the chemical properties of the vents, Lane and Martin [3] put forward a methanogenic origin of archaea, having the Wood–Ljungdahl (WL) pathway as the universal carbon fixation pathway between the two S8.P27 prokaryotic domains. Could it be that an imprint of early chemistry is preserved in the C1 metabolism of modern organisms? We won't Exploring structural/functional relationship in Type II know unless we look, and genomes harbor abundant information. By NADH dehydrogenases studying the distribution and frequency of the enzymes for a a a Filipa V. Sena , Ana P. Batista , Bruno C. Marreiros , methanopterin and folate biosynthesis within sequenced genomes b c a Margarida Bastos , Eurico J. Cabrita , Manuela M. Pereira [4,5], we found that these distinct biosynthetic routes are unrelated a Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, across the two domains, indicating that the corresponding pathways Av. Da República EAN, 2780-157 Oeiras, Portugal arose independently. This dichotomy is also observed in the b CIQ (UP) Departmento de Química, Faculdade de Ciências, Universidade structurally unrelated enzymes and different organic cofactors that do Porto, P-4169-007 Porto, Portugal methanogens (archaea) and acetogens (bacteria) use to perform c REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, methyl synthesis in their H4F- and H4MPT-dependent versions, Universidade Nova de Lisboa, Caparica, Portugal respectively, of the WL pathway. The data suggests that, in contrast E-mail: [email protected] to the ancestry of the acetyl synthesis segment, the methyl segment of the WL pathway evolved in a later stage, after the divergence of Type-II NADH:quinone oxidoreductases (NDH-II) are membrane bacteria and archaea, which independently invented genetically- proteins involved in respiratory chains. NDH-II performs the same encoded means to synthesize methyl groups via enzymatic reactions. reaction as Complex I, but does not contribute to the generation of the ion electrochemical potential. Both enzymes may be expressed References by the same organism according to its metabolic demands. Some [1] Y. Liu, L.L. Beer, W.B. Whitman, Methanogens: a window into pathogenic bacteria contain only genes encoding NDH-II and in ancient sulfur metabolism. Trends Microbiol. 20 (2012) 251–258 animal mitochondria only Complex I is expressed. The study of NDH- [2] G. Fuchs, Alternative pathways of carbon dioxide fixation: II gained a new enthusiasm after the publication
Load more

Recommended publications
  • Coupled Reductive and Oxidative Sulfur Cycling in the Phototrophic Plate of a Meromictic Lake T
    Geobiology (2014), 12, 451–468 DOI: 10.1111/gbi.12092 Coupled reductive and oxidative sulfur cycling in the phototrophic plate of a meromictic lake T. L. HAMILTON,1 R. J. BOVEE,2 V. THIEL,3 S. R. SATTIN,2 W. MOHR,2 I. SCHAPERDOTH,1 K. VOGL,3 W. P. GILHOOLY III,4 T. W. LYONS,5 L. P. TOMSHO,3 S. C. SCHUSTER,3,6 J. OVERMANN,7 D. A. BRYANT,3,6,8 A. PEARSON2 AND J. L. MACALADY1 1Department of Geosciences, Penn State Astrobiology Research Center (PSARC), The Pennsylvania State University, University Park, PA, USA 2Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA 3Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA 4Department of Earth Sciences, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA 5Department of Earth Sciences, University of California, Riverside, CA, USA 6Singapore Center for Environmental Life Sciences Engineering, Nanyang Technological University, Nanyang, Singapore 7Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany 8Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA ABSTRACT Mahoney Lake represents an extreme meromictic model system and is a valuable site for examining the organisms and processes that sustain photic zone euxinia (PZE). A single population of purple sulfur bacte- ria (PSB) living in a dense phototrophic plate in the chemocline is responsible for most of the primary pro- duction in Mahoney Lake. Here, we present metagenomic data from this phototrophic plate – including the genome of the major PSB, as obtained from both a highly enriched culture and from the metagenomic data – as well as evidence for multiple other taxa that contribute to the oxidative sulfur cycle and to sulfate reduction.
    [Show full text]
  • Menaquinone As Pool Quinone in a Purple Bacterium
    Menaquinone as pool quinone in a purple bacterium Barbara Schoepp-Cotheneta,1, Cle´ ment Lieutauda, Frauke Baymanna, Andre´ Verme´ gliob, Thorsten Friedrichc, David M. Kramerd, and Wolfgang Nitschkea aLaboratoire de Bioe´nerge´tique et Inge´nierie des Prote´ines, Unite´Propre de Recherche 9036, Institut Fe´de´ ratif de Recherche 88, Centre National de la Recherche Scientifique, F-13402 Marseille Cedex 20, France; bLaboratoire de Bioe´nerge´tique Cellulaire, Unite´Mixte de Recherche 163, Centre National de la Recherche Scientifique–Commissariat a`l’E´ nergie Atomique, Universite´ delaMe´ diterrane´e–Commissariat a`l’E´ nergie Atomique 1000, Commissariat a` l’E´ nergie Atomique Cadarache, Direction des Sciences du Vivant, De´partement d’Ecophysiologie Ve´ge´ tale et Microbiologie, F-13108 Saint Paul Lez Durance Cedex, France; cInstitut fu¨r Organische Chemie und Biochemie, Albert-Ludwigs-Universita¨t Freiburg, Albertstr. 21, D-79104 Freiburg, Germany; and dInstitute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340 Edited by Pierre A. Joliot, Institut de Biologie Physico-Chimique, Paris, France, and approved March 31, 2009 (received for review December 23, 2008) Purple bacteria have thus far been considered to operate light- types of pool-quinones, such as ubi-, plasto-, mena-, rhodo-, driven cyclic electron transfer chains containing ubiquinone (UQ) as caldariella- or sulfolobus-quinones (to cite only the best-studied liposoluble electron and proton carrier. We show that in the purple cases) have been identified so far individually in different species ␥-proteobacterium Halorhodospira halophila, menaquinone-8 or coexisting in single organisms (2–4). (MK-8) is the dominant quinone component and that it operates in Menaquinone (MK) is the most widely distributed quinone on the QB-site of the photosynthetic reaction center (RC).
    [Show full text]
  • Towards Unveiling the Photoactive Yellow Proteins: Characterization of a Halophilic Member and a Proteomic Approach to Study Light Responses
    Department of Biochemistry, Physiology and Microbiology Laboratory for Protein Biochemistry and Biomolecular Engineering Towards unveiling the Photoactive Yellow Proteins: characterization of a halophilic member and a proteomic approach to study light responses Samy Memmi Thesis submitted to fulfill the requirements for the degree of ‘Doctor in Biochemistry’ May 2008 Promotor: Prof. Dr. Jozef Van Beeumen Co-promotor: Prof. Dr. Bart Devreese Table of contents List of publications i List of abbreviations ii Abstract iv Chapter one 1 Principles in photobiology 1 1.1 Introduction 1 1.2 The nature of light 1 1.3 Fundamentals in protein photochemistry 3 1.4 References 3 Chapter two 2 Biological photosensors 4 2.1 Light as a source of energy 4 2.2 Light as a source of information 5 2.2.1 Red-/green-light photoperception 7 2.2.1.1 Sensory rhodopsins 7 2.2.1.2 (Bacterio)phytochromes 9 2.2.2 Blue-light sensing 11 2.2.2.1 Cryptochromes 11 2.2.2.2 LOV proteins 12 2.2.2.3 BLUF domain proteins 14 2.3 References 16 Chapter three 3 Photoactive Yellow Proteins 22 3.1 History 22 3.2 Photochemical reactions 23 3.3 PYP properties 26 3.3.1 Structural features 26 3.3.2 Mutational analysis 28 3.4 Phylogenetic distribution 33 3.5 Biosynthesis 38 3.6 Pyp genes as molecular scouts in search of potential TAL biocatalysts? 40 3.7 Genetic context 43 3.7.1 Rhodobacter gene context 44 3.8 References 46 Chapter four 4 Photoactive Yellow Protein from the halophilic bacterium Salinibacter ruber 53 Chapter five 5 PYP-phytochrome-related proteins 77 5.1 Introduction 77 5.2 Properties 78 5.3 Function 81 5.4 References 84 Chapter six 6 A proteomic study of Ppr-mediated photoresponses in Rhodospirillum centenum reveals a role as regulator of polyketide synthesis 86 Abstracts of other publications 111 Summary (Dutch) 114 Dankwoord 117 List of publications List of publications Memmi, S.; Kyndt, J.A.; Meyer, T.E.; Devreese, B.; Cusanovich, M.; Van Beeumen, J.
    [Show full text]
  • Genome-Based Classification of Two
    TAXONOMIC DESCRIPTION Khaleque et al., Int J Syst Evol Microbiol DOI 10.1099/ijsem.0.003313 Genome-based classification of two halotolerant extreme acidophiles, Acidihalobacter prosperus V6 (=DSM 14174 =JCM 32253) and ’Acidihalobacter ferrooxidans’ V8 (=DSM 14175 =JCM 32254) as two new species, Acidihalobacter aeolianus sp. nov. and Acidihalobacter ferrooxydans sp. nov., respectively Himel N. Khaleque,1,2† Carolina Gonzalez, 3† Anna H. Kaksonen,2 Naomi J. Boxall,2 David S. Holmes3,* and Elizabeth L. J. Watkin1,* Abstract Phylogenomic analysis of recently released high-quality draft genome sequences of the halotolerant acidophiles, Acidihalobacter prosperus V6 (=DSM 14174=JCM 32253) and ‘Acidihalobacter ferrooxidans’ V8 (=DSM 14175=JCM 32254), was undertaken in order to clarify their taxonomic relationship. Sequence based phylogenomic approaches included 16S rRNA gene phylogeny, multi-gene phylogeny from the concatenated alignment of nine selected housekeeping genes and multiprotein phylogeny using clusters of orthologous groups of proteins from ribosomal protein families as well as those from complete sets of markers based on concatenated alignments of universal protein families. Non-sequence based approaches for species circumscription were based on analyses of average nucleotide identity, which was further reinforced by the correlation indices of tetra-nucleotide signatures as well as genome-to-genome distance (digital DNA–DNA hybridization) calculations. The different approaches undertaken in this study for species tree reconstruction resulted in a tree that was phylogenetically congruent, revealing that both micro-organisms are members of separate species of the genus Acidihalobacter. In accordance, it is proposed that A. prosperus V6T (=DSM 14174 T=JCM 32253 T) be formally classified as Acidihalobacter aeolianus sp.
    [Show full text]
  • Study of the High-Potential Iron Sulfur Protein in Halorhodospira Halophila Confirms That It Is Distinct from Cytochrome C As Electron Carrier
    Study of the high-potential iron sulfur protein in Halorhodospira halophila confirms that it is distinct from cytochrome c as electron carrier Cle´ ment Lieutaud*, Jean Alric†, Marielle Bauzan‡, Wolfgang Nitschke*, and Barbara Schoepp-Cothenet*§ *Laboratoire de Bioe´nerge´tique et Inge´nierie des Prote´ines, Unite´Propre de Recherche 9036, ‡Institut de Biologie Structurale et Microbiologie, Centre National de la Recherche Scientifique, 13402 Marseille Cedex 20, France; and †Laboratoire de Ge´ne´ tique et Biophysique des Plantes, Unite´Mixte de Recherche 163, Commissariat a`l’Energie Atomique-Centre National de la Recherche Scientifique, Universite´e de la Me´diterrane´e-Commissariat a`l’Energie Atomique 1000, 13009 Marseille, France Edited by Helmut Beinert, University of Wisconsin, Madison, WI, and approved January 14, 2005 (received for review October 19, 2004) The role of high-potential iron sulfur protein (HiPIP) in donating participation of HiPIP instead of soluble cytochrome c is the rule electrons to the photosynthetic reaction center in the halophilic rather than the exception (26). For an exhaustive description of ␥-proteobacterium Halorhodospira halophila was studied by EPR electron donation to the RC in proteobacteria, therefore, de- and time-resolved optical spectroscopy. A tight complex between tailed understanding of the interaction of HiPIP with the RC is HiPIP and the reaction center was observed. The EPR spectrum of needed. HiPIP in this complex was drastically different from that of the Among the species containing HiPIPs, one stands out for its purified protein and provides an analytical tool for the detection apparent ‘‘weirdness,’’ i.e., Halorhodospira (H.) halophila. This and characterization of the complexed form in samples ranging halophilic ␥-proteobacterium has long been known to contain from whole cells to partially purified protein.
    [Show full text]
  • Functional Type 2 Photosynthetic Reaction Centers Found in the Rare Bacterial Phylum Gemmatimonadetes
    Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes Yonghui Zenga, Fuying Fengb, Hana Medováa, Jason Deana, and Michal Koblízeka,c,1 aDepartment of Phototrophic Microorganisms, Institute of Microbiology CAS, 37981 Trebon, Czech Republic; bInstitute for Applied and Environmental Microbiology, College of Life Sciences, Inner Mongolia Agricultural University, Huhhot 010018, China; and cFaculty of Science, University of South Bohemia, 37005 Ceské Budejovice, Czech Republic Edited by Robert E. Blankenship, Washington University in St. Louis, St. Louis, MO, and accepted by the Editorial Board April 15, 2014 (received for review January 8, 2014) Photosynthetic bacteria emerged on Earth more than 3 Gyr ago. Although Cyanobacteria, green sulfur bacteria, and purple To date, despite a long evolutionary history, species containing bacteria were discovered more than 100 y ago (8), green nonsulfur (bacterio)chlorophyll-based reaction centers have been reported in bacteria and heliobacteria were not described until the second half only 6 out of more than 30 formally described bacterial phyla: Cya- of the 20th century (9, 10). The most recently identified organism nobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, and representing a novel phylum containing chlorophototrophs is Acidobacteria. Here we describe a bacteriochlorophyll a-producing Candidatus Chloracidobacterium thermophilum, described in isolate AP64 that belongs to the poorly characterized phylum Gem- 2007 (11). These six phyla
    [Show full text]
  • Study of the High-Potential Iron Sulfur Protein in Halorhodospira Halophila Confirms That It Is Distinct from Cytochrome C As Electron Carrier
    Study of the high-potential iron sulfur protein in Halorhodospira halophila confirms that it is distinct from cytochrome c as electron carrier Cle´ ment Lieutaud*, Jean Alric†, Marielle Bauzan‡, Wolfgang Nitschke*, and Barbara Schoepp-Cothenet*§ *Laboratoire de Bioe´nerge´tique et Inge´nierie des Prote´ines, Unite´Propre de Recherche 9036, ‡Institut de Biologie Structurale et Microbiologie, Centre National de la Recherche Scientifique, 13402 Marseille Cedex 20, France; and †Laboratoire de Ge´ne´ tique et Biophysique des Plantes, Unite´Mixte de Recherche 163, Commissariat a`l’Energie Atomique-Centre National de la Recherche Scientifique, Universite´e de la Me´diterrane´e-Commissariat a`l’Energie Atomique 1000, 13009 Marseille, France Edited by Helmut Beinert, University of Wisconsin, Madison, WI, and approved January 14, 2005 (received for review October 19, 2004) The role of high-potential iron sulfur protein (HiPIP) in donating participation of HiPIP instead of soluble cytochrome c is the rule electrons to the photosynthetic reaction center in the halophilic rather than the exception (26). For an exhaustive description of ␥-proteobacterium Halorhodospira halophila was studied by EPR electron donation to the RC in proteobacteria, therefore, de- and time-resolved optical spectroscopy. A tight complex between tailed understanding of the interaction of HiPIP with the RC is HiPIP and the reaction center was observed. The EPR spectrum of needed. HiPIP in this complex was drastically different from that of the Among the species containing HiPIPs, one stands out for its purified protein and provides an analytical tool for the detection apparent ‘‘weirdness,’’ i.e., Halorhodospira (H.) halophila. This and characterization of the complexed form in samples ranging halophilic ␥-proteobacterium has long been known to contain from whole cells to partially purified protein.
    [Show full text]
  • Chemosynthetic Symbionts of Marine Invertebrate Animals Are Capable of Nitrogen fixation Jillian M
    ARTICLES PUBLISHED: 24 OCTOBER 2016 | VOLUME: 2 | ARTICLE NUMBER: 16195 OPEN Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation Jillian M. Petersen1,2*, Anna Kemper2, Harald Gruber-Vodicka2,UlisseCardini1, Matthijs van der Geest3,4, Manuel Kleiner5, Silvia Bulgheresi6, Marc Mußmann1,CraigHerbold1, Brandon K.B. Seah2, Chakkiath Paul Antony2, Dan Liu5, Alexandra Belitz1 and Miriam Weber7 Chemosynthetic symbioses are partnerships between invertebrate animals and chemosynthetic bacteria. The latter are the primary producers, providing most of the organic carbon needed for the animal host’s nutrition. We sequenced genomes of the chemosynthetic symbionts from the lucinid bivalve Loripes lucinalis and the stilbonematid nematode Laxus oneistus. The symbionts of both host species encoded nitrogen fixation genes. This is remarkable as no marine chemosynthetic symbiont was previously known to be capable of nitrogen fixation. We detected nitrogenase expression by the symbionts of lucinid clams at the transcriptomic and proteomic level. Mean stable nitrogen isotope values of Loripes lucinalis were within the range expected for fixed atmospheric nitrogen, further suggesting active nitrogen fixation by the symbionts. The ability to fix nitrogen may be widespread among chemosynthetic symbioses in oligotrophic habitats, where nitrogen availability often limits primary productivity. ymbioses between animals and chemosynthetic bacteria are 400 living species, occupying a range of habitats including mangrove widespread in
    [Show full text]
  • Variability of Photosynthesis Genes in Purple Bacteria and Molecular Determinants of Their Spectral Properties
    Variability of photosynthesis genes in purple bacteria and molecular determinants of their spectral properties Von der Fakultät für Mathematik und Naturwissenschaften der Carl von Ossietzky Universität Oldenburg zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften angenommene Dissertation von Christian Tuschak geboren am 12. Dezember 1969 in Recklinghausen Oldenburg, September 2003 Erstreferent: Prof. Dr. Heribert Cypionka Korreferent: Prof. Dr. Jörg Overmann Tag der Disputation: 17.12.2003 Für meine Eltern Für Judit List of Abbreviations [32P]dCTP deoxy cytidine triphosphate, labled with radioactive phosphor 32P aa amino acids ATCC American type culture collection ATP adenosine triphosphate bp base pairs bch bacteriochlorophyll biosynthesis genes BChl bacteriochlorophyll crt carontenoid biosynthesis genes DSM / DSMZ Deutsche Sammlung für Mikroorganismen und Zellkulturen EDTA ethylendiamine tetraacetic acid iPCR inverse polymerase chain reaction LH1 light harvesting complex 1 (core antenna) LH2, LH3 light harvesting complexes 2 and 3 (peripheral antennae) MOPS 3-(N-morpholino)propanesulfonic acid NIR near infrared nt nucleotides orf open reading frame PCR polymerase chain reaction PDB protein database PS I, PS II photosystem I and II puc structural and regulatory genes for the peripheral antenna puf photosynthetic unit forming genes (reaction center + light harvesting core antenna) puh structural gene for the reaction center H subunit (photosynthetic unit H protein) QA, QB acceptor quinones A and B in the purple bacterial reaction center Qy long wavelength transition of bacteriochlorophylls RC reaction center SDS sodium dodecyl sulfate SSC sodium chloride-sodium citrate TBE Tris-boric acid-EDTA TE Tris-EDTA Tris Tris(hydroxymethyl)aminomethane i Abbreviations of genus names Acp. Acidiphilium Alc. Allochromatium Amb. Amoebobacter Blc.
    [Show full text]
  • Porin from the Halophilic Species Ectothiorhodospira Vacuolata: Cloning, Structure of the Gene and Comparison with Other Porins
    Gene 191 (1997) 225–232 Porin from the halophilic species Ectothiorhodospira vacuolata: cloning, structure of the gene and comparison with other porins Eduard Wolf a,*, Gernot Achatz b, Johannes F. Imhoff c, Emile Schiltz d,Ju¨rgen Weckesser a, Marinus C. Lamers b a Institut fu¨r Biologie II – Mikrobiologie, Albert-Ludwigs-Universita¨t, Scha¨nzlestraße 1, D-79104 Freiburg, Germany b Max-Planck-Institut fu¨r Immunbiologie, Stu¨beweg 51, D-79108 Freiburg, Germany c Abteilung Marine Mikrobiologie, Institut fu¨r Meereskunde an der Universita¨t Kiel, Du¨sternbrooker Weg 20, D-24105 Kiel, Germany d Institut fu¨r Organische Chemie und Biochemie, Albertstraße 21, D-79104 Freiburg, Germany View metadata, citation and similar papersReceived at core.ac.uk 16 September 1996; received in revised form 16 December 1996; accepted 18 December 1996; Received by A.M. Campbell brought to you by CORE provided by OceanRep Abstract The gene coding for the anion-specific porin of the halophilic eubacterium Ectothiorhodospira (Ect.) vacuolata was cloned and sequenced, the first such gene so analyzed from a purple sulfur bacterium. It encodes a precursor protein consisting of 374 amino acid (aa)-residues including a signal peptide of 22-aa residues. Comparison with aa sequences of porins from several other members of the Proteobacteria revealed little homology. Only two regions showed local homology with the previously sequenced porins of Neisseria species, Comamonas acidovorans, Bordetella pertussis, Alcaligenes eutrophus, and Burkholderia cepacia. Genomic Southern blot hybridization studies were carried out with a probe derived from the 5∞ end of the gene coding for the porin of Ect.
    [Show full text]
  • Complete Genome Sequence of Thioalkalivibrio Sp. K90mix
    Standards in Genomic Sciences (2011) 5:341-355 DOI:10.4056/sigs.2315092 Complete genome sequence of Thioalkalivibrio sp. K90mix Gerard Muyzer1,2*, Dimitry Y. Sorokin1,3, Konstantinos Mavromatis4, Alla Lapidus4, Brian Foster4, Hui Sun4, Natalia Ivanova4, Amrita Pati4, Patrik D'haeseleer5, Tanja Woyke4, Nikos C. Kyrpides4 1Department of Biotechnology, Delft University of Technology, Delft, The Netherlands 2Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands 3Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia 4Joint Genome Institute, Walnut Creek, California, USA 5Joint Bioenergy Institute, California, USA *Corresponding author: Gerard Muyzer ([email protected]) Keywords: natronophilic, sulfide, thiosulfate, sulfur-oxidizing bacteria, soda lakes Thioalkalivibrio sp. K90mix is an obligately chemolithoautotrophic, natronophilic sulfur- oxidizing bacterium (SOxB) belonging to the family Ectothiorhodospiraceae within the Gammaproteobacteria. The strain was isolated from a mixture of sediment samples obtained from different soda lakes located in the Kulunda Steppe (Altai, Russia) based on its extreme potassium carbonate tolerance as an enrichment method. Here we report the complete ge- nome sequence of strain K90mix and its annotation. The genome was sequenced within the Joint Genome Institute Community Sequencing Program, because of its relevance to the sus- tainable removal of sulfide from wastewater and gas streams. Introduction Thioalkalivibrio sp. K90mix is an obligately chemo- sulfur compounds [1,2], denitrification [5,6] and lithoautotrophic SOxB using CO2 as a carbon thiocyanate utilization [7,8]. source and reduced inorganic sulfur compounds Apart from playing an important role in the sulfur as an energy source. It belongs to the genus cycle of soda lakes, Thioalkalivibrio species also Thioalkalivibrio.
    [Show full text]
  • Thiorhodospira Sibirica Gen. Nov., Sp. Nov., a New Alkaliphilic Purple Sulfur Bacterium from a Siberian Soda Lake
    International Journal of Systematic Bacteriology (1 999),49, 697-703 Printed in Great Britain Thiorhodospira sibirica gen. nov., sp. nov., a new alkaliphilic purple sulfur bacterium from a Siberian soda lake kina Bryantseva,’ Vladimir M. Gorlenko,’ Elena 1. Kompantseva,’ Johannes F. Imhoff,2 Jdrg Suling’ and Lubov’ Mityushina’ Author for correspondence : Johannes F. Imhoff. Tel : + 49 43 1 697 3850. Fax : + 49 43 1 565 876. e-mail : [email protected] 1 Institute of Microbiology, A new purple sulfur bacterium was isolated from microbial films on decaying Russian Academy of plant mass in the near-shore area of the soda lake Malyi Kasytui (pH 95,02% Sciences, pr. 60-letiya Oktyabrya 7 k. 2, Moscow salinity) located in the steppe of the Chita region of south-east Siberia. Single 11781 1, Russia cells were vibrioid- or spiral-shaped (34 pm wide and 7-20 pm long) and motile * lnstitut fur Meereskunde, by means of a polar tuft of flagella. Internal photosynthetic membranes were Abt. Marine of the lamellar type. Lamellae almost filled the whole cell, forming strands Mikro biolog ie, and coils. Photosynthetic pigments were bacteriochlorophyll a and carotenoids Dusternbrooker Weg 20, 24105 Kiel, Germany of the spirilloxanthin group. The new bacterium was strictly anaerobic. Under anoxic conditions, hydrogen sulfide and elemental sulfur were used as photosynthetic electron donors. During growth on sulfide, sulfur globules were formed as intermediate oxidation products. They were deposited outside the cytoplasm of the cells, in the peripheral periplasmic space and extracellularly. Thiosulfate was not used. Carbon dioxide, acetate, pyruvate, propionate, succinate, f umarate and malate were utilized as carbon sources.
    [Show full text]