archaea

Summary

Summary: One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.

Top Publications

  1. ncbi RNA-guided genetic silencing systems in bacteria and archaea
    Blake Wiedenheft
    Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland 20815 6789, USA
    Nature 482:331-8. 2012
  2. pmc An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    Daniel McDonald
    Department of Chemistry and Biochemistry and Biofrontiers Institute, University of Colorado, Boulder, CO, USA
    ISME J 6:610-8. 2012
  3. ncbi CRISPR/Cas, the immune system of bacteria and archaea
    Philippe Horvath
    Danisco France SAS, BP10, F 86220 Dangé Saint Romain, France
    Science 327:167-70. 2010
  4. ncbi CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation
    Devaki Bhaya
    Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305, USA
    Annu Rev Genet 45:273-97. 2011
  5. pmc A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
    Dongying Wu
    DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 462:1056-60. 2009
  6. ncbi Toxin-antitoxin systems in bacteria and archaea
    Yoshihiro Yamaguchi
    Department of Biochemistry, Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
    Annu Rev Genet 45:61-79. 2011
  7. pmc CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea
    Luciano A Marraffini
    Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois 60208, USA
    Nat Rev Genet 11:181-90. 2010
  8. ncbi Archaea predominate among ammonia-oxidizing prokaryotes in soils
    S Leininger
    Department of Biology, University of Bergen, Jahnebakken 5, N 5020 Bergen, Norway
    Nature 442:806-9. 2006
  9. ncbi Community genomics among stratified microbial assemblages in the ocean's interior
    Edward F DeLong
    Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 311:496-503. 2006
  10. ncbi Environmental genome shotgun sequencing of the Sargasso Sea
    J Craig Venter
    Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA
    Science 304:66-74. 2004

Detail Information

Publications281 found, 100 shown here

  1. ncbi RNA-guided genetic silencing systems in bacteria and archaea
    Blake Wiedenheft
    Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland 20815 6789, USA
    Nature 482:331-8. 2012
    ..are essential components of nucleic-acid-based adaptive immune systems that are widespread in bacteria and archaea. Similar to RNA interference (RNAi) pathways in eukaryotes, CRISPR-mediated immune systems rely on small RNAs for ..
  2. pmc An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    Daniel McDonald
    Department of Chemistry and Biochemistry and Biofrontiers Institute, University of Colorado, Boulder, CO, USA
    ISME J 6:610-8. 2012
    ..The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/...
  3. ncbi CRISPR/Cas, the immune system of bacteria and archaea
    Philippe Horvath
    Danisco France SAS, BP10, F 86220 Dangé Saint Romain, France
    Science 327:167-70. 2010
    ..In many Bacteria and most Archaea, clustered regularly interspaced short palindromic repeats (CRISPR) form peculiar genetic loci, which provide ..
  4. ncbi CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation
    Devaki Bhaya
    Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305, USA
    Annu Rev Genet 45:273-97. 2011
    Bacteria and archaea have evolved defense and regulatory mechanisms to cope with various environmental stressors, including virus attack...
  5. pmc A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
    Dongying Wu
    DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 462:1056-60. 2009
    ..evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage...
  6. ncbi Toxin-antitoxin systems in bacteria and archaea
    Yoshihiro Yamaguchi
    Department of Biochemistry, Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
    Annu Rev Genet 45:61-79. 2011
    Almost all bacteria and many archaea contain genes whose expression inhibits cell growth and may lead to cell death when overproduced, reminiscent of apoptotic genes in higher systems...
  7. pmc CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea
    Luciano A Marraffini
    Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois 60208, USA
    Nat Rev Genet 11:181-90. 2010
    ..In many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (CRISPRs) are involved in a more recently discovered ..
  8. ncbi Archaea predominate among ammonia-oxidizing prokaryotes in soils
    S Leininger
    Department of Biology, University of Bergen, Jahnebakken 5, N 5020 Bergen, Norway
    Nature 442:806-9. 2006
    ..amoA gene copies of Crenarchaeota (Archaea) were up to 3,000-fold more abundant than bacterial amoA genes...
  9. ncbi Community genomics among stratified microbial assemblages in the ocean's interior
    Edward F DeLong
    Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 311:496-503. 2006
    ..Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics...
  10. ncbi Environmental genome shotgun sequencing of the Sargasso Sea
    J Craig Venter
    Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA
    Science 304:66-74. 2004
    ..2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity...
  11. pmc Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE)
    Nathanael G Lintner
    Thermal Biology Institute, Montana State University, Bozeman, Montana 59717, USA
    J Biol Chem 286:21643-56. 2011
    ..Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea.
  12. pmc Pyrosequencing enumerates and contrasts soil microbial diversity
    Luiz F W Roesch
    Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611 0700, USA
    ISME J 1:283-90. 2007
    ..The forest site also showed far less diversity of the Archaea with only 0...
  13. ncbi CRISPR-mediated adaptive immune systems in bacteria and archaea
    Rotem Sorek
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Annu Rev Biochem 82:237-66. 2013
    ..on small RNAs for sequence-specific targeting of foreign nucleic acids was recently discovered in bacteria and archaea. Molecular vaccination in prokaryotes is achieved by integrating short fragments of foreign nucleic acids into a ..
  14. pmc CRISPR-based adaptive immune systems
    Michael P Terns
    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
    Curr Opin Microbiol 14:321-7. 2011
    ..systems are recently discovered, RNA-based immune systems that control invasions of viruses and plasmids in archaea and bacteria...
  15. ncbi Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota
    Celine Brochier-Armanet
    Universite de Provence, Aix Marseille I, CNRS, UPR 9043, Laboratoire de Chimie Bacterienne, Institut de Biologie Structurale et de Microbiologie, 13402 Marseille, France
    Nat Rev Microbiol 6:245-52. 2008
    ..During the past few years, diverse groups of uncultivated mesophilic archaea have been discovered and affiliated with the Crenarchaeota...
  16. pmc Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil
    Maria Tourna
    Department of Genetics in Ecology, University of Vienna, A 1090 Vienna, Austria
    Proc Natl Acad Sci U S A 108:8420-5. 2011
    Genes of archaea encoding homologues of ammonia monooxygenases have been found on a widespread basis and in large amounts in almost all terrestrial and marine environments, indicating that ammonia oxidizing archaea (AOA) might play a ..
  17. ncbi Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota
    Anja Spang
    University of Vienna, Department of Genetics in Ecology, Althanstrasse 14, A 1090 Vienna, Austria
    Trends Microbiol 18:331-40. 2010
    Globally distributed archaea comprising ammonia oxidizers of moderate terrestrial and marine environments are considered the most abundant archaeal organisms on Earth...
  18. ncbi A molecular view of microbial diversity and the biosphere
    N R Pace
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Science 276:734-40. 1997
    ..that the main diversity of life is microbial, distributed among three primary relatedness groups or domains: Archaea, Bacteria, and Eucarya...
  19. pmc Comparative genomics of defense systems in archaea and bacteria
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 41:4360-77. 2013
    ..The genes encoding defense system components in bacterial and archaea typically cluster in defense islands...
  20. ncbi Microbial biogeography: putting microorganisms on the map
    Jennifer B Hughes Martiny
    Department of Ecology and Evolutionary Biology, 80 Waterman Street, Box G W, Brown University, Providence, Rhode Island 02912, USA
    Nat Rev Microbiol 4:102-12. 2006
    ..However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world...
  21. pmc The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology
    Michael Pester
    Department of Microbial Ecology, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    Curr Opin Microbiol 14:300-6. 2011
    Thaumarchaeota range among the most abundant archaea on Earth. Initially classified as 'mesophilic Crenarchaeota', comparative genomics has recently revealed that they form a separate and deep-branching phylum within the Archaea...
  22. ncbi A comparison of homologous recombination rates in bacteria and archaea
    Michiel Vos
    Department of Zoology, University of Oxford, Oxford, UK
    ISME J 3:199-208. 2009
    ..Here, Multi Locus Sequence Typing (MLST) datasets from a wide variety of bacteria and archaea are analyzed using the ClonalFrame method...
  23. pmc Human gut microbiota in obesity and after gastric bypass
    Husen Zhang
    Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
    Proc Natl Acad Sci U S A 106:2365-70. 2009
    ..Unlike the highly diverse Bacteria, the Archaea comprised mainly members of the order Methanobacteriales, which are H(2)-oxidizing methanogens...
  24. pmc Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea
    Roland Hatzenpichler
    Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
    Appl Environ Microbiol 78:7501-10. 2012
    ..The cultivation of several ammonia-oxidizing archaea (AOA) as well as the discovery that archaeal ammonia monooxygenase (amo)-like gene sequences are nearly ..
  25. pmc Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil
    Laura E Lehtovirta-Morley
    Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, United Kingdom
    Proc Natl Acad Sci U S A 108:15892-7. 2011
    ..Paradoxically, autotrophic ammonia oxidizing bacteria and archaea, which perform the first stage in nitrification, demonstrate little or no growth in suspended liquid culture ..
  26. pmc Evolutionary conservation of sequence and secondary structures in CRISPR repeats
    Victor Kunin
    DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Genome Biol 8:R61. 2007
    ..It has been recently shown that CRISPR provides acquired resistance against viruses in prokaryotes...
  27. pmc The CRISPR system: small RNA-guided defense in bacteria and archaea
    Fedor V Karginov
    Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Mol Cell 37:7-19. 2010
    All cellular systems evolve ways to combat predators and genomic parasites. In bacteria and archaea, numerous resistance mechanisms have developed against phage...
  28. ncbi Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote
    Gerald Schönknecht
    Department of Botany, Oklahoma State University, Stillwater, OK 74078, USA
    Science 339:1207-10. 2013
    ..Environmental adaptation seems to have been facilitated by horizontal gene transfer from various bacteria and archaea, often followed by gene family expansion. At least 5% of protein-coding genes of G...
  29. ncbi The dynamic roles of intracellular lipid droplets: from archaea to mammals
    Denis J Murphy
    Division of Biological Sciences, University of Glamorgan, Cardiff, CF37 4AT, UK
    Protoplasma 249:541-85. 2012
    ..takes a comparative approach by examining recent work on LDs across the whole range of biological organisms from archaea and bacteria, through yeast and Drosophila to mammals, including humans...
  30. ncbi Toward automatic reconstruction of a highly resolved tree of life
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Science 311:1283-7. 2006
    ..For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor...
  31. ncbi Phylogeny and evolution of the Archaea: one hundred genomes later
    Celine Brochier-Armanet
    Aix Marseille Universite, Laboratoire de Chimie Bactérienne UPR CNRS 9043, IFR88, 31 Chemin Joseph Aiguier, 13402 Marseilles, Cedex 20, France
    Curr Opin Microbiol 14:274-81. 2011
    Little more than 30 years since the discovery of the Archaea, over one hundred archaeal genome sequences are now publicly available, of which ∼40% have been released in the last two years...
  32. pmc amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions
    Michael Pester
    Departments of Microbial Ecology, Computational Systems Biology Chemical Ecology and Ecosystem Research, University of Vienna, Althanstrasse 14, Vienna, Austria
    Environ Microbiol 14:525-39. 2012
    Ammonia-oxidizing archaea (AOA) play an important role in nitrification and many studies exploit their amoA genes as marker for their diversity and abundance...
  33. ncbi Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil
    Zhongjun Jia
    Max Planck Institute for Terrestrial Microbiology, Karl von Frisch Strasse, D 35043, Marburg, Germany
    Environ Microbiol 11:1658-71. 2009
    ..Recent discoveries have expanded the known ammonia-oxidizing prokaryotes from the domain Bacteria to Archaea. However, in the complex soil environment it remains unclear whether ammonia oxidation is exclusively or ..
  34. ncbi Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria
    Willm Martens-Habbena
    Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98105, USA
    Nature 461:976-9. 2009
    ..nM) closely resemble kinetics of in situ nitrification in marine systems and directly link ammonia-oxidizing Archaea to oligotrophic nitrification...
  35. pmc Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability
    C Vieille
    Biochemistry Department, Michigan State University, East Lansing, Michigan 48824, USA
    Microbiol Mol Biol Rev 65:1-43. 2001
    Enzymes synthesized by hyperthermophiles (bacteria and archaea with optimal growth temperatures of > 80 degrees C), also called hyperthermophilic enzymes, are typically thermostable (i.e...
  36. pmc A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring
    Roland Hatzenpichler
    Department of Microbial Ecology, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    Proc Natl Acad Sci U S A 105:2134-9. 2008
    The recent discovery of ammonia-oxidizing archaea (AOA) dramatically changed our perception of the diversity and evolutionary history of microbes involved in nitrification...
  37. ncbi Physiology and diversity of ammonia-oxidizing archaea
    David A Stahl
    Department of Civil and Environmental Engineering, University of Washington, Seattle, 98195 2700, USA
    Annu Rev Microbiol 66:83-101. 2012
    The discovery of ammonia-oxidizing archaea (AOA), now generally recognized to exert primary control over ammonia oxidation in terrestrial, marine, and geothermal habitats, necessitates a reassessment of the nitrogen cycle...
  38. pmc The complete genome sequence of Haloferax volcanii DS2, a model archaeon
    Amber L Hartman
    Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
    PLoS ONE 5:e9605. 2010
    ..This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general...
  39. ncbi The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains
    Pablo Yarza
    Marine Microbiology Group, Institut Mediterrani d Estudis Avançats CSIC UIB, C Miquel Marqués 21, E 07190 Esporles, Illes Balears, Mallorca, Spain
    Syst Appl Microbiol 31:241-50. 2008
    ..to reconstruct a single 16S rRNA tree harboring all sequenced type strains of the hitherto classified species of Archaea and Bacteria...
  40. pmc Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis
    Paul C Blainey
    Department of Bioengineering, Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America
    PLoS ONE 6:e16626. 2011
    Ammonia-oxidizing archaea (AOA) are thought to be among the most abundant microorganisms on Earth and may significantly impact the global nitrogen and carbon cycles...
  41. ncbi Community structure and metabolism through reconstruction of microbial genomes from the environment
    Gene W Tyson
    Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA
    Nature 428:37-43. 2004
    ..Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment...
  42. ncbi Unusual pathways and enzymes of central carbohydrate metabolism in Archaea
    Bettina Siebers
    Universitat Duisburg Essen, Campus Essen, FB Biologie und Geografie, Mikrobiologie, Universitätsstr 5, D 45117 Essen, Germany
    Curr Opin Microbiol 8:695-705. 2005
    Sugar-utilizing hyperthermophilic and halophilic Archaea degrade glucose and glucose polymers to acetate or to CO2 using O2, nitrate, sulfur or sulfate as electron acceptors...
  43. pmc New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras
    Kevin E Ashelford
    Cardiff School of Biosciences, Cardiff University, Main Building, Park Place, P O Box 915, Cardiff CF10 3TL, United Kingdom
    Appl Environ Microbiol 72:5734-41. 2006
    ..Mallard is freely available from our website at http://www.cardiff.ac.uk/biosi/research/biosoft/...
  44. ncbi Virus population dynamics and acquired virus resistance in natural microbial communities
    Anders F Andersson
    Departments of Earth and Planetary Science and Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
    Science 320:1047-50. 2008
    ..Only the most recently acquired spacers match coexisting viruses, which suggests that community stability is achieved by rapid but compensatory shifts in host resistance levels and virus population structure...
  45. ncbi Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces
    Bedis Dridi
    Unite de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 6236 IDR 198, Faculte de Medecine, IFR48, Aix Marseille Universite, Marseille, France
    Int J Syst Evol Microbiol 62:1902-7. 2012
    During attempts to obtain novel, human-associated species of the domain Archaea, a coccoid micro-organism, designated strain B10(T), was isolated in pure culture from a sample of human faeces collected in Marseille, France...
  46. pmc Phylogenomics of prokaryotic ribosomal proteins
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 7:e36972. 2012
    ..than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes)...
  47. pmc Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms
    Daniel T Verhamme
    Institute of Biological and Environmental Sciences, University of Aberdeen, UK
    ISME J 5:1067-71. 2011
    The first step of nitrification, oxidation of ammonia to nitrite, is performed by both ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in soil, but their relative contributions to ammonia oxidation and existence in ..
  48. ncbi Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes
    Sinan Al-Attar
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, The Netherlands
    Biol Chem 392:277-89. 2011
    ..Despite impressive progress during the last couple of years, the elucidation of several fundamental details will be a major challenge in future research...
  49. ncbi Environmental factors shaping the ecological niches of ammonia-oxidizing archaea
    Tuba H Erguder
    Laboratory of Microbial Ecology and Technology LabMET, Gent University, Gent, Belgium
    FEMS Microbiol Rev 33:855-69. 2009
    ..However, recently, a new strain of archaea bearing a putative ammonia monooxygenase subunit A (amoA) gene and able to oxidize ammonia was isolated from a ..
  50. ncbi Archaeal dominance in the mesopelagic zone of the Pacific Ocean
    M B Karner
    University of Hawaii, Department of Oceanography, Honolulu 96822, USA
    Nature 409:507-10. 2001
    ..Recently, cultivation-independent ribosomal RNA gene surveys have indicated a potential importance for archaea in the subsurface ocean...
  51. ncbi Nitrogenase gene diversity and microbial community structure: a cross-system comparison
    Jonathan P Zehr
    Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
    Environ Microbiol 5:539-54. 2003
    ..The broad analysis of nitrogenase genes provides a basis for developing molecular assays and bioinformatics approaches for the study of nitrogen fixation in the environment...
  52. pmc Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution
    Tal Dagan
    Institut für Botanik III, Heinrich Heine Universitat Dusseldorf, Universitatsstrasse 1, 40225 Dusseldorf, Germany
    Proc Natl Acad Sci U S A 105:10039-44. 2008
    ....
  53. pmc Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre
    Konstantinos T Konstantinidis
    Department of Civil and Environmental Engineering and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Appl Environ Microbiol 75:5345-55. 2009
    ....
  54. ncbi Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea
    Wriddhiman Ghosh
    Department of Microbiology, University of Burdwan, West Bengal, India
    FEMS Microbiol Rev 33:999-1043. 2009
    ..Sulfur-chemolithotrophic metabolism in Archaea, largely restricted to Sulfolobales, is distinct from those in Bacteria...
  55. ncbi Archaeal CRISPR-based immune systems: exchangeable functional modules
    Roger A Garrett
    Archaea Centre, Department of Biology, Ole Maaløes Vej 5, University of Copenhagen, DK2200 Copenhagen N, Denmark
    Trends Microbiol 19:549-56. 2011
    ..target appears to be the DNA of foreign genetic elements, but the CRISPR/Cmr system that is widespread amongst archaea also specifically targets and cleaves RNA in vitro...
  56. pmc Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer
    Yuri I Wolf
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 7:46. 2012
    ..Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs)...
  57. pmc The archaebacterial origin of eukaryotes
    Cymon J Cox
    Department of Zoology, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
    Proc Natl Acad Sci U S A 105:20356-61. 2008
    ..Our analyses favor a topology that supports the eocyte hypothesis rather than archaebacterial monophyly and the 3-domains tree of life...
  58. pmc Role for urea in nitrification by polar marine Archaea
    Laura Alonso-Sáez
    Department of Ecology and Genetics, Limnology, Uppsala University, 75236 Uppsala, Sweden
    Proc Natl Acad Sci U S A 109:17989-94. 2012
    Despite the high abundance of Archaea in the global ocean, their metabolism and biogeochemical roles remain largely unresolved...
  59. ncbi Functional metagenomic profiling of nine biomes
    Elizabeth A Dinsdale
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    Nature 452:629-32. 2008
    ....
  60. ncbi The hydrogen hypothesis for the first eukaryote
    W Martin
    Institut fur Genetik, Technische Universitat Braunschweig, Germany
    Nature 392:37-41. 1998
    ..The host's dependence upon molecular hydrogen produced by the symbiont is put forward as the selective principle that forged the common ancestor of eukaryotic cells...
  61. ncbi A marine microbial consortium apparently mediating anaerobic oxidation of methane
    A Boetius
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    Nature 407:623-6. 2000
    ..Recent data suggest that certain archaea reverse the process of methanogenesis by interaction with sulphate-reducing bacteria...
  62. ncbi Uncultured archaea in deep marine subsurface sediments: have we caught them all?
    Andreas Teske
    Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    ISME J 2:3-18. 2008
    ..biosphere with unknown physiology; the sedimentary subsurface harbors numerous novel phylogenetic lineages of archaea that are at present uncultured...
  63. pmc Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers
    Marc Mussmann
    Department of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
    Proc Natl Acad Sci U S A 108:16771-6. 2011
    ..The discovery of autotrophic ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota has changed our perception of the microbiology of nitrification, in ..
  64. ncbi Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol
    José R de la Torre
    Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195 2700, USA
    Environ Microbiol 10:810-8. 2008
    The widespread occurrence and diversity of ammonia oxidizing Archaea suggests their contribution to the nitrogen cycle is of global significance...
  65. ncbi Genome-wide experimental determination of barriers to horizontal gene transfer
    Rotem Sorek
    Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
    Science 318:1449-52. 2007
    ..coli, a computational analysis of gene-transfer rates across available bacterial and archaeal genomes supports that the barriers observed in our study are general across the tree of life...
  66. pmc Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome
    Carola Simon
    Department of Genomic and Applied Microbiology, Georg August University Gottingen, D 37077 Gottingen, Germany
    Appl Environ Microbiol 75:7519-26. 2009
    ..Thus, analysis of the glacial metagenome provided insights into the microbial life in frozen habitats on Earth, thereby possibly shedding light onto microbial life in analogous extraterrestrial environments...
  67. pmc The future is now: single-cell genomics of bacteria and archaea
    Paul C Blainey
    Broad Institute of Harvard and MIT, Cambridge, MA, USA
    FEMS Microbiol Rev 37:407-27. 2013
    ....
  68. ncbi Mitochondrial evolution
    M W Gray
    Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
    Science 283:1476-81. 1999
    ....
  69. ncbi Predominant archaea in marine sediments degrade detrital proteins
    Karen G Lloyd
    Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus 8000, Denmark
    Nature 496:215-8. 2013
    Half of the microbial cells in the Earth's oceans are found in sediments. Many of these cells are members of the Archaea, single-celled prokaryotes in a domain of life separate from Bacteria and Eukaryota...
  70. pmc Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group
    Takuro Nunoura
    Subsurface Geobiology and Advanced Research Project, Institute of Biogeosciences, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
    Nucleic Acids Res 39:3204-23. 2011
    The domain Archaea has historically been divided into two phyla, the Crenarchaeota and Euryarchaeota...
  71. ncbi Evolution of multisubunit RNA polymerases in the three domains of life
    Finn Werner
    RNA Polymerase Laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
    Nat Rev Microbiol 9:85-98. 2011
    ....
  72. pmc Lateral gene transfer as a support for the tree of life
    Sophie S Abby
    Laboratoire de Biometrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unite Mixte de Recherche 5558, Universite Lyon 1, F 69622 Villeurbanne, France
    Proc Natl Acad Sci U S A 109:4962-7. 2012
    ....
  73. pmc The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity
    Henk Bolhuis
    Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, The Netherlands
    BMC Genomics 7:169. 2006
    ..walsbyi has specialized into its narrow and hostile ecological niche and found ways to cope with the desiccation stress...
  74. ncbi Isotopic signature of N(2)O produced by marine ammonia-oxidizing archaea
    Alyson E Santoro
    Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
    Science 333:1282-5. 2011
    ..Our results suggest that ammonia-oxidizing archaea may be largely responsible for the oceanic N(2)O source.
  75. pmc Genome sequence of an ammonia-oxidizing soil archaeon, "Candidatus Nitrosoarchaeum koreensis" MY1
    Byung Kwon Kim
    Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, 125 Gwahak ro, Yuseong Gu, Daejeon 305 806, Republic of Korea
    J Bacteriol 193:5539-40. 2011
    Ammonia-oxidizing archaea are ubiquitous microorganisms which play important roles in global nitrogen and carbon cycle on earth...
  76. ncbi Significant contribution of Archaea to extant biomass in marine subsurface sediments
    Julius S Lipp
    Organic Geochemistry Group, Department of Geosciences and MARUM Center for Marine Environmental Sciences, University of Bremen, PO Box 330 440, 28334 Bremen, Germany
    Nature 454:991-4. 2008
    ..From recent studies using various culture-independent techniques, no clear picture has yet emerged as to whether Archaea or Bacteria are more abundant in this extensive ecosystem...
  77. ncbi New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation
    Christopher A Francis
    Department of Geological and Environmental Sciences, Stanford University, Stanford, CA 94305 2115, USA
    ISME J 1:19-27. 2007
    ..this time, the processes of anaerobic ammonium oxidation (anammox), and ammonia oxidation within the domain Archaea, have been recognized as two new links in the global nitrogen cycle...
  78. pmc Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    T Z DeSantis
    Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A 3317, Berkeley, CA 94720, USA
    Appl Environ Microbiol 72:5069-72. 2006
    ..Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.
  79. pmc Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea
    On On Lee
    KAUST Global Partnership Program, Department of Biology, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
    ISME J 5:650-64. 2011
    ....
  80. pmc Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria
    Byoung Joon Park
    Department of Microbiology, Chungbuk National University, Heungduk gu, Cheongju 361 763, South Korea
    Appl Environ Microbiol 76:7575-87. 2010
    The role of ammonia-oxidizing archaea (AOA) in nitrogen cycling in marine sediments remains poorly characterized. In this study, we enriched and characterized AOA from marine sediments. Group I...
  81. ncbi Biased gene transfer in microbial evolution
    Cheryl P Andam
    Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, Connecticut 06269 3125, USA
    Nat Rev Microbiol 9:543-55. 2011
    ..We present evidence that prokaryotes (bacteria and archaea) are more likely to transfer genetic material with their close relatives than with distantly related lineages...
  82. ncbi Archaea rather than bacteria control nitrification in two agricultural acidic soils
    Cécile Gubry-Rangin
    Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
    FEMS Microbiol Ecol 74:566-74. 2010
    ..is performed in terrestrial ecosystems by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA)...
  83. ncbi Global ecological patterns in uncultured Archaea
    Jean Christophe Auguet
    Group of Limnology Department of Continental Ecology, Centre d Estudis Avançats de Blanes, CEAB CSIC, Accés Cala Sant Francesc, Girona, Spain
    ISME J 4:182-90. 2010
    We have applied a global analytical approach to uncultured Archaea that for the first time reveals well-defined community patterns along broad environmental gradients and habitat types...
  84. pmc Autotrophic ammonia oxidation by soil thaumarchaea
    Li Mei Zhang
    Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, United Kingdom
    Proc Natl Acad Sci U S A 107:17240-5. 2010
    ..have been cultivated from marine and thermal spring environments, but the relative importance of bacteria and archaea in soil nitrification is unclear and it is believed that soil archaeal ammonia oxidizers may use organic carbon, ..
  85. ncbi Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices
    Ji Zheng He
    State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
    Environ Microbiol 9:2364-74. 2007
    The abundance and composition of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated by using quantitative real-time polymerase chain reaction, cloning and sequencing approaches based on amoA genes...
  86. ncbi Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales
    John A Leigh
    Department of Microbiology, University of Washington, Seattle, WA, USA
    FEMS Microbiol Rev 35:577-608. 2011
    The tree of life is split into three main branches: eukaryotes, bacteria, and archaea. Our knowledge of eukaryotic and bacteria cell biology has been built on a foundation of studies in model organisms, using the complementary approaches ..
  87. ncbi Spatial scaling of microbial biodiversity
    Jessica Green
    School of Natural Sciences, University of California, PO Box 2039, Merced, CA 95344, USA
    Trends Ecol Evol 21:501-7. 2006
    ..Recent empirical analyses of these patterns for microorganisms suggest that there are biodiversity scaling rules common to all forms of life...
  88. ncbi Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment
    James I Prosser
    Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, UK
    Environ Microbiol 10:2931-41. 2008
    ..is now required and this article reviews the current evidence for the relative importance of bacteria and archaea. Much of this evidence is based on metagenomic analysis and molecular techniques for estimation of gene and gene ..
  89. pmc Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru
    Jennifer F Biddle
    Pennsylvania State Astrobiology Research Center, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 103:3846-51. 2006
    ..rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known ..
  90. ncbi Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus
    Erik A Pelve
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, Norbyvagen 18C, SE 752 36, Sweden
    Mol Microbiol 82:555-66. 2011
    ..The findings also have implications for evolutionary issues concerning the last archaeal common ancestor and the relationship between archaea and eukaryotes.
  91. ncbi Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary
    Annika C Mosier
    Department of Environmental Earth System Science, Stanford University, Stanford, CA 94305, USA
    Environ Microbiol 10:3002-16. 2008
    ..Recent reports have shown that the newly discovered ammonia-oxidizing archaea can be both abundant and diverse in aquatic and terrestrial ecosystems...
  92. ncbi Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions
    Hong J Di
    Centre for Soil and Environmental Research, Lincoln University, Lincoln, Christchurch, New Zealand
    FEMS Microbiol Ecol 72:386-94. 2010
    ..The recent discovery of ammonia-oxidizing archaea (AOA) questions the traditional assumption of the dominant role of ammonia-oxidizing bacteria (AOB) in ..
  93. pmc A putative viral defence mechanism in archaeal cells
    Reidun K Lillestøl
    Institute of Molecular Biology, University of Copenhagen, Sølvgade 83H, DK 1307 Copenhagen K, Denmark
    Archaea 2:59-72. 2006
    ..An archaeal database summarizing the data will be maintained at http://dac.molbio.ku.dk/dbs/SRSR/...
  94. ncbi Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets
    Johan Bengtsson
    Department of Plant and Environmental Sciences, University of Gothenburg, Goteborg, Sweden
    Antonie Van Leeuwenhoek 100:471-5. 2011
    ..We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics...
  95. pmc CRISPR loci reveal networks of gene exchange in archaea
    Avital Brodt
    Department of Molecular Microbiology and Biotechnology, George S, Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978, Israel
    Biol Direct 6:65. 2011
    ..Since spacers are accumulated by active CRISPR/Cas systems, the sequences of these spacers provide a record of the past "infection history" of the organism...
  96. ncbi Autotrophic carbon fixation in archaea
    Ivan A Berg
    Mikrobiologie, Fakultat Biologie, Universitat Freiburg, Schanzlestrasse 1, D 79104 Freiburg, Germany
    Nat Rev Microbiol 8:447-60. 2010
    ..Many archaea live in volcanic habitats under such constraints, in high temperatures with only inorganic substances and often ..
  97. pmc A unique cell division machinery in the Archaea
    Ann Christin Lindås
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, Norbyvagen 18C, SE 752 36, Uppsala, Sweden
    Proc Natl Acad Sci U S A 105:18942-6. 2008
    ....
  98. pmc Mapping the tree of life: progress and prospects
    Norman R Pace
    Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309 0347, USA
    Microbiol Mol Biol Rev 73:565-76. 2009
    ..molecular markers have provided the outlines of a universal tree of life (ToL), the three-domain pattern of archaea, bacteria, and eucarya...
  99. pmc Evolution of diverse cell division and vesicle formation systems in Archaea
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Nat Rev Microbiol 8:731-41. 2010
    ..we undertook a comparative genomic analysis of the machineries for cell division and vesicle formation in Archaea. Archaea possess at least three distinct membrane remodelling systems: the FtsZ-based bacterial-type system, the ..
  100. ncbi Life close to the thermodynamic limit: how methanogenic archaea conserve energy
    Uwe Deppenmeier
    Department of Biological Sciences, University of Wisconsin Milwaukee, Milwaukee, WI 53211, USA
    Results Probl Cell Differ 45:123-52. 2008
    Methane-forming archaea are strictly anaerobic, ancient microbes that are widespread in nature...
  101. pmc Enigmatic, ultrasmall, uncultivated Archaea
    Brett J Baker
    Department of Earth and Planetary Science and Environmental Science, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 107:8806-11. 2010
    ..as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge-particularly for Archaea-that occur at relatively low abundance and in extreme environments...

Research Grants67

  1. FUNCTIONAL PROPERTIES OF HEMOGLOBINS AND MYOGLOBINS
    John S Olson; Fiscal Year: 2010
    ..ligand binding, and NO dioxygenation;(b) insight into the evolution of globin structures and functions, from Archaea to Bacteria to Eucarya;and (c) a framework for inhibiting the activities of globins from pathogenic organisms (..
  2. Microbial Diversity in Mechanisms of Disulfide Bond Formation and Reduction
    Dana Boyd; Fiscal Year: 2013
    ..We will establish the nature of two novel protein disulfide bond-forming pathways found in certain bacteria and archaea. E. coli and many other bacteria use two enzymes to introduce disulfide bonds into proteins...
  3. STRUCTURE OF THE VACUOLAR ATPase
    Stephan Wilkens; Fiscal Year: 2013
    ..Structurally similar ATPases have also been identified in the plasma membrane of Archaea and bacteria, where they are called A-ATPases and bacterial A/V-ATPases, respectively...
  4. Coenzyme F420-dependent enzymes in mycobacteria
    Biswarup Mukhopadhyay; Fiscal Year: 2013
    ..60 years ago in a mycobacterial species, but its biological roles have been studied mostly in the methanogenic archaea where it was encountered about 30 years ago...
  5. Structures of RNA processing and Silencing Enzymes in Prokaryotes
    Hong Li; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Like eukarya, bacteria and archaea have evolved a variety of defense systems to protect themselves from selfish genetic elements (phages, transposons, and plasmids)...
  6. The Role of Syntrophic Bacteria in Methanogenic Metabolism in the Human Gut
    Catherine Lozupone; Fiscal Year: 2013
    ..Methanogenic archaea were chosen because 1) they can increase the efficiency of bacterial fermentation by preventing the accumulation ..
  7. CRISPR Cas genes and Legionella pneumophila infection
    Nicholas P Cianciotto; Fiscal Year: 2013
    ..CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci are novel sequences found in Archaea and Bacteria that are comprised of palindromic repeats separated by unique spacer sequences...
  8. Studies of Isoprenoid Biosynthesis
    CHARLES DALE POULTER; Fiscal Year: 2013
    ..1) All available evidence indicates that most, if not all, Archaea synthesize isopentenyl diphosphate from mevalonate differently that eukaryotes...
  9. Investigating Regulation of Integral Membrane Protein Cofactor Biosynthesis using
    Ronald F Peck; Fiscal Year: 2011
    ..The proposed research will study a similar molecular complex in a microbe in order to elucidate the mechanisms that keep proteins and their cofactors in the correct balance. ..
  10. Role of Human Intestinal Microbiota on Success of Surgical Weight Loss Procedures
    BRUCE EDWARD RITTMANN; Fiscal Year: 2013
    ..Also, fermenters and Methanobrevibacter smithii (a methanogen from the Archaea domain) appear to act syntrophically to affect energy uptake...
  11. REGULATION OF METHIONINE METABOLISM IN BACILLUS SUBTILIS
    Tina M Henkin; Fiscal Year: 2013
    ..is widely used in bacteria, including in a number of important pathogens, and has also been identified in archaea and eukaryotes...
  12. Computational Assembly of Beta Barrel Membrane Protein
    Jie Liang; Fiscal Year: 2013
    ..They are essential for protein translocation in all domains of life, except archaea. They regulate metabolism and apoptosis...
  13. Metabolic Engineering Studies of Extreme Thermoacidophily
    Robert M Kelly; Fiscal Year: 2010
    ..The transcriptional and translational mechanisms observed in archaea are closely related to those found in eukaryotes and, thus, provide an excellent alternative perspective...
  14. CHEMOTACTIC SENSORY TRANSDUCTION IN BACILLUS SUBTILIS
    George W Ordal; Fiscal Year: 2012
    ..paradigm might be the ideal one for understanding these diverse mechanisms in the broad sweep of bacteria and archaea because of its inclusion of most known chemotaxis proteins and its similarity to the mechanism used in many ..
  15. Ubiquitin-like Small Archaeal Protein Modification (SAMPylation)
    Julie A Maupin-Furlow; Fiscal Year: 2013
    ..protein modifiers (SAMP1 and SAMP2) that cluster to the 2-grasp fold superfamily, are highly conserved among archaea and are differentially conjugated to a large number of proteins in the halophilic archaeon Haloferax volcanii...
  16. Structural Biology of the Sodium-Calcium Exchanger
    NATHAN KYLE KARPOWICH; Fiscal Year: 2010
    ..As there are NCX1 homologs present in bacteria and archaea, these proteins may provide an avenue to the high-resolution structural information currently unavailable in ..
  17. X-ray crystallographic studies of multi-subunit nucleic acid polymerases
    Katsuhiko Murakami; Fiscal Year: 2013
    ..The transcription apparatus in Archaea can be described as a simplified version of its eukaryotic RNA polymerase II (Pol II) counterpart, comprising a ..
  18. Chlorite dismutase: a novel heme enzyme and its implications for human health
    Jennifer L Dubois; Fiscal Year: 2013
    ..The second objective is to elucidate the broader role of Clds in the hundreds of bacteria and even archaea where cld homologs have been found...
  19. Mechanisms of CRISPR Interference
    Erik J Sontheimer; Fiscal Year: 2013
    ..interspaced, short, palindromic repeat (CRISPR) loci, present in the genomes of many eubacteria and nearly all archaea, have been shown to confer adaptive, heritable, sequence-based immunity against phages...
  20. ELEXSYS E500 CW EPR SPECTROMETER
    Jack H Freed; Fiscal Year: 2010
    ..Recently we presented structural and biochemical evidence that the first step of diphthamide biosynthesis in archaea uses a novel iron-sulfur cluster enzyme, DPH2...
  21. Assembly and Function of Bacterial Chemotaxis Receptor Signaling Complexes
    Robert M Weis; Fiscal Year: 2013
    ..representative of a large family of signal transduction pathways that are distributed throughout the Bacteria and Archaea. These pathways are already known to mediate chemotaxis and phototaxis in free-swimming and surface-associated ..
  22. STRUCTURE AND FUNCTION OF TRANSFER RIBONUCLEIC ACIDS
    Uttam L RajBhandary; Fiscal Year: 2013
    ..relationship between the structure and function of archaeal initiator tRNAs and the translational machinery of archaea in general...
  23. MECHANISMS OF SITE-SPECIFIC RECOMBINATION
    Arthur Landy; Fiscal Year: 2012
    ..or high-energy cofactors and participate in a wide range of biological pathways in prokaryotes, eukaryotes, and archaea. ? Int, which catalyzes integrative and excisive recombination of the ? viral chromosome into and out of the host ..
  24. Characterization of the ferrous iron transporter Feo in Vibrio cholerae
    Shelley M Payne; Fiscal Year: 2013
    ..It is widely distributed in eubacteria and in the Archaea, suggesting that it is a very ancient class of iron transporter...
  25. Biochemical and structural characterization of self-assembling viral particles
    REBECCA ETHEL TAUROG; Fiscal Year: 2010
    The Sulfolobus islandicus rod-shaped virus (SIRV) is a fibrous virus that infects thermophilic, acidophilic Archaea found in thermal vents and hot springs around the world...
  26. Reversible dimerization of a CLC transporter: A model for membrane protein foldin
    Janice L Robertson; Fiscal Year: 2013
    ..by changing the chemical head group, chain length and chain order using unsaturated or tetra-ether lipids from archaea. For all experiments, free energy relationships will also be measured with respect to temperature to extrapolate ..
  27. Assembly dynamics and cellular function of Actin-like proteins in bacteria
    R Dyche Mullins; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Eubacteria and archaea use cytoskeletal elements including, actin-like filaments, tubulin- related polymers, and even intermediate filaments, to: (1) control their shape;(2) to divide;(3) to ..
  28. The Molecular Control of Cell Death in Staphylococcus aureus
    JEFFREY LEE BOSE; Fiscal Year: 2010
    ..These proteins are wide-spread, being found in 46 percent of sequenced genomes including bacteria and archaea, yet none have a predicted or assigned function...
  29. Reversible dimerization of a CLC transporter: A model for membrane protein foldin
    Janice L Robertson; Fiscal Year: 2013
    ..by changing the chemical head group, chain length and chain order using unsaturated or tetra-ether lipids from archaea. For all experiments, free energy relationships will also be measured with respect to temperature to extrapolate ..
  30. Transcription factor positioning and function during promoter opening
    Michael S Bartlett; Fiscal Year: 2010
    ..the position and function of two transcription factors, TFB and TFE, structurally and functionally conserved from archaea to humans...
  31. Genomic and metabolomic foundations of human-microbial symbiosis in the gut
    JEFFREY IVAN GORDON; Fiscal Year: 2013
    ..M. smithii, and E. rectale/E. eligens. These studies should provide new approaches for monitoring and manipulating the functions of the microbiota to promote human health. ..
  32. The Structural Basis of Protein Biogenesis
    Christopher W Akey; Fiscal Year: 2012
    ..This process occurs at the ER membrane in eukaryotes and at the plasma membrane in bacteria and archaea. The mammalian translocon is comprised of Sec61, which forms the channel and a suite of membrane proteins that ..
  33. The function of small RNA-based viral defense system in E. coli
    KONSTANTIN V SEVERINOV; Fiscal Year: 2013
    ..The significance of proposed work will not be limited to E. coli, since CRISPR loci are found in more than 40% eubacteria and in 95% of archaea.
  34. Foregut microbiome in development of esophageal adenocarcinoma
    Zhiheng Pei; Fiscal Year: 2012
    ..Detailed analyses will include pathway-disease and gene-disease associations. Archaea, fungi and viruses, if identified, also will be correlated with the diseases...
  35. Structural Characterization of Archaeal Virus Assembly and Host Interactions
    Chi Yu Fu; Fiscal Year: 2012
    ..The proposal will contribute significantly to our understanding of the cell biology of archaeal virus pathogenesis and viruses in the PRD1-Adeno lineage in general. ..
  36. Structural and Biochemical Characterization of the S. cerevisiae RNA Exosome
    ELIZABETH VICTORINA WASMUTH; Fiscal Year: 2013
    ..substrates targeted by the exosome are threaded through the pore, as they are in RNA degradation assemblies from archaea and bacteria...
  37. Small RNA-based immunity by CRISPR-Cas complexes of Pyrococcus furiosus
    REBECCA TERNS; Fiscal Year: 2013
    ..It was very recently discovered that prokaryotes (archaea and bacteria) have small RNA-based adaptive immune systems, called CRISPR-Cas systems that effectively control ..
  38. Structural basis for transmembrane Mg2+ transport
    EDUARDO A PEROZO; Fiscal Year: 2012
    ..focus on the CorA Mg2+ transporter/channel, which functions as the primary Mg2+ uptake system for Eubacteria and Archaea. The structure of the CorA ortholog from Thermotoga maritima has been recently determined at medium resolution, ..
  39. RNA SPLICING IN ARCHAEA
    Ramesh Gupta; Fiscal Year: 2012
    ..Studying these processes in complex systems is often challenging and sometimes not even feasible. Archaea often have eukaryote-like processes, but at a basic level, thus serving as much simpler model systems to gain ..
  40. Protein Biosensors with Customized Properties for Live-Cell Imaging
    Balaji M Rao; Fiscal Year: 2013
    ..Instead, our starting point is an ensemble of 7 different proteins from hyperthermophilic archaea and bacteria (which thrive at extreme temperatures) as templates, or scaffolds, for engineering biosensors...
  41. A Model Archaeal System: Genetic Tools and Resources for T. kodakarensis
    JOHN NEWTON REEVE; Fiscal Year: 2013
    ..Fortunately, Archaea do have homologues of many of these "eukaryotic" components and research with such simpler archaeal systems can ..
  42. Mre11/Rad50/Nbs1 Structural Biology for DNA Damage Responses
    John A Tainer; Fiscal Year: 2013
    ..The Mre11 nuclease complex with the Rad50 ATPase is conserved from archaea to humans and is regulated by Nbs1 in S. pombe and humans...
  43. The Role of pre-tRNA 3-prime End Processing During Drosophila Development
    EDWARD BORIS DUBROVSKY; Fiscal Year: 2012
    ..The Drosophila RNase ZL (dRNaseZ) gene encodes a protein with homologs in all living organisms: bacteria, archaea, and eukarya...
  44. Identification of Pathways Affected by Essential Proteins of Unknown Function
    SEAN DAVID MOORE; Fiscal Year: 2012
    ..Each of these genes is conserved throughout bacteria and have many homologs in archaea and eukarya;and (2), determine the biochemical pathways most affected by the depletion of the proteins encoded by ..
  45. Design and Use of Novel Bacteriocins
    Shaun Lee; Fiscal Year: 2011
    ..It is believed that about half of all bacteria and archaea produce at least one bacteriocin, and current efforts in genome analysis will likely lead to a tremendous ..
  46. Structure and mechanism of signal peptide peptidase
    Michael S Wolfe; Fiscal Year: 2010
    ..4) What are the characteristics of SPP orthologs from extremophilic archaea? SPP-like proteases from extremophilic archaebacteria should be more stable and amenable to structural studies ..
  47. Structure/Function of Microbial Sensory Rhodopsins
    JOHN LEE SPUDICH; Fiscal Year: 2013
    ..In archaea and bacteria they mediate phototaxis by protein-protein interaction in membrane-embedded receptor-transducer (SR-..
  48. Magnesium Channel Cation Selectivity
    Michael E Maguire; Fiscal Year: 2013
    ..The CorA Mg2+ channel is the primary source of Mg2+ for ~50% of all Bacteria and Archaea while MgtE is the primary source for the other half of each kingdom...
  49. Structural studies of type I topoisomerases
    ALFONSO MONDRAGON; Fiscal Year: 2013
    ..provided by applicant): Topoisomerases are ubiquitous proteins found across all three domains of life (bacteria, archaea, and eukarya)...
  50. STRUCTURE AND FUNCTION OF TRANSFER RIBONUCLEIC ACIDS
    UTTAM RAJBHANDARY; Fiscal Year: 2009
    ..relationship between the structure and function of archaeal initiator tRNAs and the translational machinery of archaea in general...
  51. Molecular Mechanism of Adaptation in Crispr Systems
    Yunzhou Wei; Fiscal Year: 2013
    ..They protect bacteria and archaea from invasions by foreign nucleic acid elements such as phages and plasmids...
  52. The mechanism of signal transduction in photoreceptors
    Hartmut Luecke; Fiscal Year: 2006
    ..SRI and SRII are sensors for phototaxis in Hatobacterium salinarum and related halophilic archaea. SRI mediates attractant motility responses to green-orange wavelengths used by the ion pumps BR and HR, while ..
  53. FINDING NOVEL REAGENTS BY BIOINFORMATICS AND BIOCHEMISTRY
    Richard J Roberts; Fiscal Year: 2013
    ..Enzymes recognizing these modified bases are known to occur in bacterial and archaea strains and in the past, many have been found by random biochemical screening...
  54. Tight Adherence Genes of a Periodontal Pathogen
    David H Figurski; Fiscal Year: 2012
    ..cluster that directs synthesis of surface pili and is broadly conserved in Gram-negatives, Gram-positives, and Archaea. We discovered this locus in the Gram-negative pathogen Aggregatibacter actinomycetemcomitans, the causative ..
  55. Foregut microbiome in development of esophageal adenocarcinoma
    Zhiheng Pei; Fiscal Year: 2009
    ..Detailed analyses will include pathway-disease and gene-disease associations. Archaea, fungi and viruses, if identified, also will be correlated with the diseases...
  56. Structure and Function of DNA Polymerase I of E.coli
    NIGEL DAVID GRINDLEY; Fiscal Year: 2010
    ..DNA polymerases are also a crucial part of many of the diagnostic tools used in modern medicine and will be pivotal in the development of new DNA sequencing technologies for diagnostic purposes. ..
  57. Domain Structure of tRNase ZL, the Long Form of tRNase Z
    LOUIS F LEVINGER; Fiscal Year: 2012
    ..tRNase Z, the pre-tRNA 3'processing endonuclease, is encoded in a short form (tRNase ZS) in bacteria and archaea and in a long form (tRNase ZL) found only in eukaryotes...
  58. Indirect aminoacylation in the Plasmodium apicoplast
    MALCOLM JOHN GARDNER; Fiscal Year: 2010
    ..This pathway is the sole route for the production of Gln-tRNAGln in most bacteria, archaea, and plastids, but is not found in the eukaryotic cytosol...
  59. Methanococcus maripaludis as an emerging model organism
    John A Leigh; Fiscal Year: 2010
    Methanococcus maripaludis is emerging as a premier model for the methanogens and the Archaea. It grows unusually well, has an extensive set of facile genetic tools, and has a known complete annotated genome sequence...
  60. Aminoacyl-tRNA synthetases in Archaea
    Ya Ming Hou; Fiscal Year: 2006
    ..led to general principles of substrate specificity, these are not sufficient to understand synthetases of the archaea domain, which consists of organisms that thrive in extreme environments...
  61. Structural Studies of MCM Complex
    Xiaojiang S Chen; Fiscal Year: 2012
    ..MCM proteins from eukaryotes and archaea form hexamers ring complex, with MWt approximating 0.5-1.0 Mega Dolton...
  62. SERYL-TRNA SYNTHETASES: EVOLUTION AND DIVERSITY
    Dieter Soll; Fiscal Year: 2003
    ..Until recently, the study of aminoacyl-tRNA synthesis in archaea had received little attention...
  63. Interaction of ricin A chain with the ribosomal stalk
    Nilgun E Tumer; Fiscal Year: 2013
    ..for binding RTA, study the interaction of RTA with stalk complexes from different species, including bacteria, archaea, yeast and human and to identify the functional part of the stalk structure...
  64. Mechanims of Archaeal Transcription Termination
    THOMAS JAMES SANTANGELO; Fiscal Year: 2013
    ..b>Archaea offer the advantages of far less complexity but homology in many features of human molecular biology, ..
  65. Pseudouridines, pseudouridine synthases, and ribosomes
    MURRAY DEUTSCHER; Fiscal Year: 2006
    ..Two classes of enzyme systems exist. In eubacteria, all psi are made by a set of site-specific proteins. In archaea and eukarya, psi in tRNA and some sn(o) RNAs are made by specific proteins also, but psi in rRNA and other sn(o)..
  66. 7 FE FDI AS A MODEL FE-S AND REGULATORY PROTEIN
    Thomas Poulos; Fiscal Year: 2002
    Iron-sulfur [Fe-S] proteins are ubiquitous occurring in all life forms from the most primitive bacteria and archaea to the most advanced eucaryotes...
  67. Transcriptional Regulation in Giardia lamblia
    HEIDI ELMENDORF; Fiscal Year: 2006
    ..of transcription have been delineated in higher eukaryotes, extensive work in lower eukaryotes and archaea have clearly indicated many differences in the mechanics of gene expression...