DOCSLIB.ORG

Archaeal-Like Chaperonins in Bacteria

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Archaeal-Like Chaperonins in Bacteria Archaeal-like chaperonins in bacteria Stephen M. Techtmann1 and Frank T. Robb2 aInstitute of Marine and Environmental Technology, Program in the Biology of Model Systems, 701 East Pratt Street, Baltimore, MD 21202 and Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 West Baltimore Street, Baltimore, MD 21201 Edited by Arthur L. Horwich, Yale University School of Medicine, New Haven, CT, and approved September 14, 2010 (received for review April 16, 2010) Chaperonins (CPN) are ubiquitous oligomeric protein machines that by preventing aggregation of the misfolded substrates (16–18). mediate the ATP-dependent folding of polypeptide chains. These Additionally, the active Iterative Annealing Model proposes that chaperones have not only been assigned stress response and nor- the misfolded protein is refolded by several rounds of binding, mal housekeeping functions but also have a role in certain human release and reengagement (19–21). disease states. A longstanding convention divides CPNs into two While both groups of chaperonins catalyze protein folding via groups that share many conserved sequence motifs but differ in encapsulation, there are key structural and mechanistic differ- both structure and distribution. Group I complexes are the well ences between the two groups. The Group II chaperonins (also known GroEL/ES heat-shock proteins in bacteria, that also occur known as the thermosome or TCP1) are structurally different in some species of mesophilic archaea and in the endosymbiotic from Group I, the GroEL/GroES complexes. Both Group I organelles of eukaryotes. Group II CPNs are found only in the and Group II complexes are composed of two stacked rings. cytosol of archaea and eukaryotes. Here we report a third, diver- The Group II CPNs are octo- or nonomeric rings (10), whereas gent group of CPNs found in several species of bacteria. We the GroEL is a homotetradecamer. Group II CPNs are often het- propose to name these Group III CPNs because of their distant erooligomers comprised of a combination of multiple subunits relatedness to both Group I and II CPNs as well as their unique (10). For example many Group II chaperonins from eukaryotes genomic context, within the hsp70 operon. The prototype Group III are heterohexadecamers composed of eight different subunits. CPN, Carboxydothermus hydrogenoformans chaperonin (Ch-CPN), Additionally, the function of the Group I cochaperone, GroES, is able to refold denatured proteins in an ATP-dependent manner is replaced in Group II CPNs by a helical protrusion in the apical and is structurally similar to the Group II CPNs, forming a 16-mer domain of each subunit. These flexible domains combine to form with each subunit contributing to a flexible lid domain. The Group a “built-in lid” that is essential for encapsulation of the denatured BIOCHEMISTRY III CPN represent a divergent group of bacterial CPNs distinct from protein (22–24). The opening and closing of this lid is ATP- the GroEL/ES CPN found in all bacteria. The Group III lineage may responsive and is allosterically regulated (24, 25). Recent work represent an ancient horizontal gene transfer from an archaeon has also indicated that, while certain CPN domains share striking into an early Firmicute lineage. An analysis of their functional similarity between Group I and Group II, the extent and types and structural characteristics may provide important insights into of structural rearrangements that occur during the CPN folding the early history of this ubiquitous family of proteins. cycle vary greatly (8, 10, 22, 25, 26). evolution ∣ protein-folding ∣ thermophilic Results Phylogeny of Group III Chaperonins. Recently, we annotated a diver- olecular chaperones have an essential role in ensuring gent class of chaperonin genes in the genomes of two carboxydo- Mproper folding of cellular proteins. Two primary protein- trophic bacteria, as encoding TCP1-like chaperonins. As shown in folding machines, Hsp70 (DnaK) and the chaperonin (CPN) are Fig. 1, these CPNs are conserved in the genomes of 11 bacteria present in the majority of living organisms (1–6). These two and are monophyletic and distant from all known Group I and systems constitute the ATP-dependent folding functions of both Group II chaperonins. Phylogenetic analysis using multiple algo- nascent polypeptides as well as the salvage of stress-denatured rithms revealed that these proteins form a deeply rooted clade, proteins (7–10). and are highly divergent from the other known chaperonins with Chaperonins are able to positively influence refolding through robust bootstrap support (Fig. 1; individual trees, Fig. S1). Trends sequestration of nonnative proteins. The general mechanism in the divergence of these proteins mirror those seen in the phy- whereby chaperonin affect refolding is through the encapsulation logenetic trees (Table S1 and Fig. S2). There are several deletions of denatured protein within a hydrophilic cavity. While the exact in Group III CPN relative to the other groups of CPNs (Fig. S3). mechanism of CPN-mediated protein folding is still unclear, These indels account for the some of the sequence divergence much is known about key steps in the CPN reaction cycle. The and may influence localized structural elements. This clade repre- most well studied chaperonin homolog is the Escherichia coli sents a previously unknown and unique group of CPNs whose GroEL (8). GroEL forms a barrel structure composed of two physiological role has yet to be determined and which we propose seven-membered rings, with each ring containing a folding cavity. to name as Group III CPNs. The significant divergence from Controversy still prevails over the exact mechanism by which the two known classes of CPNs leads us to suggest that this group GroEL catalyzes proteins folding. According to one model, is a monophyletic subfamily of the Group II CPNs, which may partially folded proteins bind to hydrophobic residues that line represent the remnant of an ancestral chaperonin group. the GroEL cavity (11). ATP binding causes large conformational changes that simultaneously draw the nonnative protein into the Author contributions: S.M.T. and F.T.R. designed research; S.M.T. performed research; cavity, increase the number of polar residues within the cavity, S.M.T. and F.T.R. analyzed data; and S.M.T. and F.T.R. wrote the paper. and trigger rapid binding of the Cochaperone GroES (12). This The authors declare no conflict of interest. sequestration in a hydrophilic cavity forces the protein to refold This article is a PNAS Direct Submission. through forcing the internalization of the hydrophobic residues of 1Present address: Department of Biochemistry and Molecular Biology, Uniformed Services the nonnative protein (13, 14). ATP hydrolysis in the GroES- University for the Health Science, 4301 Jones Bridge Road, Bethesda, MD 20814. bound ring, followed by ATP binding to the opposite ring triggers 2To whom correspondence should be addressed. E-mail: Frobb@som. the release of GroES followed by the encapsulated protein. There umaryland.edu. are several alternative models for GroEL activity (15), including This article contains supporting information online at www.pnas.org/lookup/suppl/ the passive model whereby GroEL assists in refolding simply doi:10.1073/pnas.1004783107/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1004783107 PNAS Early Edition ∣ 1of6 Downloaded by guest on September 25, 2021 Fig. 1. Phylogenetic analysis of Group III chaperonin: Un- rooted minimum evolution phylogenetic tree representing Group I, Group II, and the new Group III chaperonins, indi- cating the great phylogenetic distance between the Group III clade and the conserved Group I and Group II clusters. The same alignment was used to construct trees using multiple algorithms (minimum evolution, maximum parsimony, and neighbor-joining). Nodes present in trees created by different alogorithms and with high bootstrap values are denoted as described. The clade representing Group III CPN contains the following organisms: Carboxydothermus hydrogenoformans, Geobacillus spY412MC, Syntrophomo- nas. wolfei wolfei Goettingen, Desulforudis audaxviator, Ammonifex degensii, Heliobacterium modesticaldum, Ther- mosinus carboxydivorans, Desulfotomaculum acetoxidans, Desulfotomaculum reducens, Pelotomaculum thermopro- pionicum, and Gloeobacter violaceus. Genomic Context of Group III Chaperonins. All of the currently unique group of chaperonins we cloned, expressed, and charac- identified Group III chaperonins, with one exception, are found terized a prototype Group III CPN from the extreme thermophile internal to the Hsp70 molecular chaperone operon (Fig. 2A). Carboxydothermus hydrogenoformans (Ch-CPN). C. hydrogenofor- These species all have conventional Group I CPNs encoded in mans is a member of the phylum Firmicutes and is known for its separate operons with their GroES cochaperone. The Group ability to grow on carbon monoxide as its sole carbon and energy III chaperonins are the only CPNs found near or in association source, linking the oxidation of carbon monoxide to hydrogen with the Hsp70 operon. This unique operon structure and the unprecedented association with Hsp70 provide evidence for a functional distinction between Group II and Group III CPNs. Group III CPNs are found between hrcA, the heat-shock responsive transcriptional repressor, and the Hsp70 operon (grpE, dnaK, dnaJ). The location of the Group III chaperonin downstream of the hrcA suggested that Group III CPNs could be HrcA
Load more

Recommended publications
  • New Opportunities Revealed by Biotechnological Explorations of Extremophiles - Mircea Podar and Anna-Louise Reysenbach
    BIOTECHNOLOGY – Vol .III – New Opportunities Revealed by Biotechnological Explorations of Extremophiles - Mircea Podar and Anna-Louise Reysenbach NEW OPPORTUNITIES REVEALED BY BIOTECHNOLOGICAL EXPLORATIONS OF EXTREMOPHILES Mircea Podar and Anna-Louise Reysenbach Department of Biology, Portland State University, Portland, OR 97201, USA. Keywords: extremophiles, genomics, biotechnology, enzymes, metagenomics. Contents 1. Introduction 2. Extremophiles and Biomolecules 3. Extremophile Genomics Exposing the Biotechnological Potential 4. Tapping into the Hidden Biotechnological Potential through Metagenomics 5. Unexplored Frontiers and Future Prospects Acknowledgements Glossary Bibliography Biographical Sketches Summary Over the past few decades the extremes at which life thrives has continued to challenge our understanding of biochemistry, biology and evolution. As more new extremophiles are brought into laboratory culture, they have provided a multitude of new potential applications for biotechnology. Furthermore, more recently, innovative culturing approaches, environmental genome sequencing and whole genome sequencing have provided new opportunities for biotechnological exploration of extremophiles. 1. Introduction Organisms that live at the extremes of pH (>pH 8.5,< pH 5.0), temperature (>45°C, <15°C), pressure (>500 atm), salinity (>1.0M NaCl) and in high concentrations of recalcitrant substances or heavy metals (extremophiles) represent one of the last frontiers for biotechnological and industrial discovery. As we learn more about the
    [Show full text]
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens
    microorganisms Article Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens Maryam Rezadehbashi and Susan A. Baldwin * Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, BC V6T 1Z3, Canada; [email protected] * Correspondence: [email protected]; Tel.: +1-604-822-1973 Received: 2 January 2018; Accepted: 17 February 2018; Published: 23 February 2018 Abstract: Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations.
    [Show full text]
  • Thermophilic Carboxydotrophs and Their Applications in Biotechnology Springerbriefs in Microbiology
    SPRINGER BRIEFS IN MICROBIOLOGY EXTREMOPHILIC BACTERIA Sonia M. Tiquia-Arashiro Thermophilic Carboxydotrophs and their Applications in Biotechnology SpringerBriefs in Microbiology Extremophilic Bacteria Series editors Sonia M. Tiquia-Arashiro, Dearborn, MI, USA Melanie Mormile, Rolla, MO, USA More information about this series at http://www.springer.com/series/11917 Sonia M. Tiquia-Arashiro Thermophilic Carboxydotrophs and their Applications in Biotechnology 123 Sonia M. Tiquia-Arashiro Department of Natural Sciences University of Michigan Dearborn, MI USA ISSN 2191-5385 ISSN 2191-5393 (electronic) ISBN 978-3-319-11872-7 ISBN 978-3-319-11873-4 (eBook) DOI 10.1007/978-3-319-11873-4 Library of Congress Control Number: 2014951696 Springer Cham Heidelberg New York Dordrecht London © The Author(s) 2014 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer.
    [Show full text]
  • Dehalobacter Restrictus PER-K23T
    Standards in Genomic Sciences (2013) 8:375-388 DOI:10.4056/sigs.3787426 Complete genome sequence of Dehalobacter restrictus T PER-K23 Thomas Kruse1*, Julien Maillard2, Lynne Goodwin3,4, Tanja Woyke3, Hazuki Teshima3,4, David Bruce3,4, Chris Detter3,4, Roxanne Tapia3,4, Cliff Han3,4, Marcel Huntemann3, Chia-Lin Wei3, James Han3, Amy Chen3, Nikos Kyrpides3, Ernest Szeto3, Victor Markowitz3, Natalia Ivanova3, Ioanna Pagani3, Amrita Pati3, Sam Pitluck3, Matt Nolan3, Christof Holliger2, and Hauke Smidt1 1 Wageningen University, Agrotechnology and Food Sciences, Laboratory of Microbiology, Dreijenplein 10, NL-6703 HB Wageningen, The Netherlands. 2 Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Laboratory for Environmental Biotechnology, Station 6, CH- 1015 Lausanne, Switzerland. 3 DOE Joint Genome Institute, Walnut Creek, California, USA 4 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA *Corresponding author: Thomas Kruse ([email protected]) Keywords: Dehalobacter restrictus type strain, anaerobe, organohalide respiration, PCE, TCE, reductive dehalogenases Dehalobacter restrictus strain PER-K23 (DSM 9455) is the type strain of the species Dehalobacter restrictus. D. restrictus strain PER-K23 grows by organohalide respiration, cou- pling the oxidation of H2 to the reductive dechlorination of tetra- or trichloroethene. Growth has not been observed with any other electron donor or acceptor, nor has fermentative growth been shown. Here we introduce the first full genome of a pure culture within the ge- nus Dehalobacter. The 2,943,336 bp long genome contains 2,826 protein coding and 82 RNA genes, including 5 16S rRNA genes. Interestingly, the genome contains 25 predicted re- ductive dehalogenase genes, the majority of which appear to be full length.
    [Show full text]
  • EXPERIMENTAL STUDIES on FERMENTATIVE FIRMICUTES from ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, and THEIR GEOCHEMICAL IMPACTS By
    EXPERIMENTAL STUDIES ON FERMENTATIVE FIRMICUTES FROM ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, AND THEIR GEOCHEMICAL IMPACTS By JESSICA KEE EUN CHOI A dissertation submitted to the School of Graduate Studies Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Microbial Biology Written under the direction of Nathan Yee And approved by _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ New Brunswick, New Jersey October 2017 ABSTRACT OF THE DISSERTATION Experimental studies on fermentative Firmicutes from anoxic environments: isolation, evolution and their geochemical impacts by JESSICA KEE EUN CHOI Dissertation director: Nathan Yee Fermentative microorganisms from the bacterial phylum Firmicutes are quite ubiquitous in subsurface environments and play an important biogeochemical role. For instance, fermenters have the ability to take complex molecules and break them into simpler compounds that serve as growth substrates for other organisms. The research presented here focuses on two groups of fermentative Firmicutes, one from the genus Clostridium and the other from the class Negativicutes. Clostridium species are well-known fermenters. Laboratory studies done so far have also displayed the capability to reduce Fe(III), yet the mechanism of this activity has not been investigated
    [Show full text]
  • Syntrophic Butyrate and Propionate Oxidation Processes 491
    Environmental Microbiology Reports (2010) 2(4), 489–499 doi:10.1111/j.1758-2229.2010.00147.x Minireview Syntrophic butyrate and propionate oxidation processes: from genomes to reaction mechanismsemi4_147 489..499 Nicolai Müller,1† Petra Worm,2† Bernhard Schink,1* a cytoplasmic fumarate reductase to drive energy- Alfons J. M. Stams2 and Caroline M. Plugge2 dependent succinate oxidation. Furthermore, we 1Faculty for Biology, University of Konstanz, D-78457 propose that homologues of the Thermotoga mar- Konstanz, Germany. itima bifurcating [FeFe]-hydrogenase are involved 2Laboratory of Microbiology, Wageningen University, in NADH oxidation by S. wolfei and S. fumaroxidans Dreijenplein 10, 6703 HB Wageningen, the Netherlands. to form hydrogen. Summary Introduction In anoxic environments such as swamps, rice fields In anoxic environments such as swamps, rice paddy fields and sludge digestors, syntrophic microbial communi- and intestines of higher animals, methanogenic commu- ties are important for decomposition of organic nities are important for decomposition of organic matter to matter to CO2 and CH4. The most difficult step is the CO2 and CH4 (Schink and Stams, 2006; Mcinerney et al., fermentative degradation of short-chain fatty acids 2008; Stams and Plugge, 2009). Moreover, they are the such as propionate and butyrate. Conversion of these key biocatalysts in anaerobic bioreactors that are used metabolites to acetate, CO2, formate and hydrogen is worldwide to treat industrial wastewaters and solid endergonic under standard conditions and occurs wastes. Different types of anaerobes have specified only if methanogens keep the concentrations of these metabolic functions in the degradation pathway and intermediate products low. Butyrate and propionate depend on metabolite transfer which is called syntrophy degradation pathways include oxidation steps of (Schink and Stams, 2006).
    [Show full text]
  • Journal of Molecular Microbiology and Biotechnology "Special Issue
    1 Journal of Molecular Microbiology and Biotechnology "Special Issue - Anaerobic Hydrocarbon 2 Degradation" 3 Review article 4 5 Stable isotope probing approaches to study anaerobic hydrocarbon degradation and 6 degraders 7 8 Carsten Vogt1, Tillmann Lueders2, Hans H. Richnow1, Martin Krüger3, Martin von Bergen4,5,6, 9 Jana Seifert7* 10 11 1 UFZ - Helmholtz Centre for Environmental Research, Department of Isotope 12 Biogeochemistry, Leipzig, Germany 13 2 Helmholtz Zentrum München—German Research Center for Environmental Health, Institute 14 for Groundwater Ecology, Neuherberg, Germany 15 3 Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany 16 4 UFZ - Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, 17 Germany 18 5 UFZ - Helmholtz Centre for Environmental Research, Department of Metabolomics, Leipzig, 19 Germany 20 6 Aalborg University, Department of Biotechnology, Chemistry and Environmental 21 Engineering, Aalborg University, Aalborg, Denmark 22 7 University of Hohenheim, Institute of Animal Science, Stuttgart, Germany 23 24 *corresponding author: 25 University of Hohenheim 26 Institute of Animal Science 27 Emil-Wolff-Str. 6-10 28 70599 Stuttgart, Germany 29 [email protected] 30 31 32 Abstract 33 Stable isotope probing (SIP) techniques have become state-of-the-art in microbial ecology 34 over the last ten years, allowing for the targeted detection and identification of organisms, 35 metabolic pathways, and elemental fluxes active in specific processes within complex 36 microbial communities. For studying anaerobic hydrocarbon degrading microbial communities, 37 four stable isotope techniques have been used so far: DNA/RNA-SIP, PFLA-SIP, protein-SIP, 38 and single cell-SIP by nanoSIMS or confocal Raman microscopy.
    [Show full text]
  • Genome Diversity of Spore-Forming Firmicutes MICHAEL Y
    Genome Diversity of Spore-Forming Firmicutes MICHAEL Y. GALPERIN National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 ABSTRACT Formation of heat-resistant endospores is a specific Vibrio subtilis (and also Vibrio bacillus), Ferdinand Cohn property of the members of the phylum Firmicutes (low-G+C assigned it to the genus Bacillus and family Bacillaceae, Gram-positive bacteria). It is found in representatives of four specifically noting the existence of heat-sensitive vegeta- different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, tive cells and heat-resistant endospores (see reference 1). and Negativicutes, which all encode similar sets of core sporulation fi proteins. Each of these classes also includes non-spore-forming Soon after that, Robert Koch identi ed Bacillus anthracis organisms that sometimes belong to the same genus or even as the causative agent of anthrax in cattle and the species as their spore-forming relatives. This chapter reviews the endospores as a means of the propagation of this orga- diversity of the members of phylum Firmicutes, its current taxon- nism among its hosts. In subsequent studies, the ability to omy, and the status of genome-sequencing projects for various form endospores, the specific purple staining by crystal subgroups within the phylum. It also discusses the evolution of the violet-iodine (Gram-positive staining, reflecting the pres- Firmicutes from their apparently spore-forming common ancestor ence of a thick peptidoglycan layer and the absence of and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, an outer membrane), and the relatively low (typically ruminococci) in the course of their adaptation to the saprophytic less than 50%) molar fraction of guanine and cytosine lifestyle in a nutrient-rich environment.
    [Show full text]
  • Desulfotomaculum Acetoxidans Type Strain (5575)
    Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575). Permalink https://escholarship.org/uc/item/53z4r149 Journal Standards in genomic sciences, 1(3) ISSN 1944-3277 Authors Spring, Stefan Lapidus, Alla Schröder, Maren et al. Publication Date 2009-11-22 DOI 10.4056/sigs.39508 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2009) 1: 242-253 DOI:10.4056/sigs.39508 Complete genome sequence of Desulfotomaculum acetox- idans type strain (5575T) Stefan Spring1, Alla Lapidus2, Maren Schröder1, Dorothea Gleim1, David Sims3, Linda Meincke3, Tijana Glavina Del Rio2, Hope Tice2, Alex Copeland2, Jan-Fang Cheng2, Susan Lucas2, Feng Chen2, Matt Nolan2, David Bruce2,3, Lynne Goodwin2,3, Sam Pitluck2, Natalia Ivanova2, Konstantinos Mavromatis2, Natalia Mikhailova2, Amrita Pati2, Amy Chen4, Krish- na Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Patrick Chain2,6, Elizabeth Saunders2,3, Thomas Brettin2,3, John C. Detter2,3, Markus Göker1, Jim Bristow2, Jonathan A. Eisen2,7, Victor Markowitz4, Philip Hugenholtz2, Nikos C Kyr- pides2, Hans-Peter Klenk1*, and Cliff Han2,3 1 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Labora- tory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 Lawrence Livermore National Laboratory, Livermore, California, USA 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: sulfate-reducer, hydrogen sulfide, piggery waste, mesophile, motile, sporulating, obligate anaerobic, Peptococcaceae, Clostridiales, Firmicutes.
    [Show full text]
  • Title Genetic Engineering Studies of Ni-Carbon Monoxide Dehydrogenase
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Kyoto University Research Information Repository Genetic engineering studies of Ni-carbon monoxide Title dehydrogenase from a thermophilic carboxydotrophic bacterium( Dissertation_全文 ) Author(s) Inoue, Takahiro Citation Kyoto University (京都大学) Issue Date 2014-03-24 URL http://dx.doi.org/10.14989/doctor.k18339 Right Type Thesis or Dissertation Textversion ETD Kyoto University Genetic engineering studies of Ni-carbon monoxide dehydrogenase from a thermophilic carboxydotrophic bacterium Takahiro INOUE 2014 Table of contents Chapter 1 General introduction 1 Chapter 2 Over-expression systems for carbon monoxide dehydrogenases (CODHs) 11 2-1 A simple and large scale over-expression method for carbon monoxide dehydrogenase II from thermophilic bacterium Carboxydothermus hydrogenoformans 14 2-2 Over-expression of carbon monoxide dehydrogenase-I with an accessory protein co-expression: a key enzyme for carbon dioxide reduction 24 Chapter 3 Cysteine 295 indirectly affects Ni coordination of carbon monoxide dehydrogenase-II C-cluster 45 Chapter 4 Integration and outlook 66 Acknowledgements 68 References 69 Publication list 86 1. General Introduction Chapter 1 General introduction Carbon monoxide utilizing microbes and carbon monoxide dehydrogenases Carbon monoxide (CO) is well known as a toxic gas, especially, CO is toxic for human being, binding strongly and almost irreversibly to hemoglobin (100). Despite the potent toxicity, many recent researches have suggested CO is key metabolic function and signal transduction in eukaryote, archea and bacteria. For example, in human CO is important molecule in neural signaling and human circadian rhythms are regulated by CO-responsive transcriptional regulators (19, 36, 78).
    [Show full text]
  • D. Nigrificans and D. Carboxydivorans Are Gram- “Clostridium Nigrificans” by Werkman and Weaver Positive, Sulfate-Reducing, Rod Shaped Bacteria (1927) [2]
    Standards in Genomic Sciences (2014) 9:655-675 DOI:10.4056/sig s.4718645 Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans Michael Visser1, Sofiya N. Parshina2, Joana I. Alves3, Diana Z. Sousa1,3, Inês A. C. Pereira4, Gerard Muyzer5, Jan Kuever6, Alexander V. Lebedinsky2, Jasper J. Koehorst7, Petra Worm1, Caroline M. Plugge1, Peter J. Schaap7, Lynne A. Goodwin8,9, Alla Lapidus10,11, Nikos C. Kyrpides8, Janine C. Detter9, Tanja Woyke8, Patrick Chain 8,9, Karen W. Davenport8, 9, Stefan Spring 12, Manfred Rohde13, Hans Peter Klenk12, Alfons J.M. Stams1,3 1Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands 2Wingradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia 3Centre of Biological Engineering, University of Minho, Braga, Portugal 4Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal 5Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands 6Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany 7Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands 8DOE Joint Genome Institute, Walnut Creek, California, USA 9Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 10Theodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia 11 Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia 12Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany 13HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany Correspondence: Michael Visser ([email protected]) Keywords: Thermophilic spore-forming anaerobes, sulfate reduction, carboxydotrophic, Peptococcaceae, Clostr idiales.
    [Show full text]