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. doi 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. 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
  3. 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
  4. 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
  5. doi 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
  6. doi 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
  7. 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
  8. 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
  9. 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
  10. 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

Detail Information

Publications260 found, 100 shown here

  1. doi 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. 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 ..
  3. 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...
  4. 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/...
  5. doi 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
    ....
  6. doi 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...
  7. 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...
  8. 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...
  9. 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 ..
  10. 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...
  11. doi 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...
  12. 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 ..
  13. 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...
  14. 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...
  15. doi 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...
  16. doi 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...
  17. doi 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...
  18. 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 ..
  19. 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...
  20. 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...
  21. 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...
  22. doi 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...
  23. 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...
  24. doi 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 ..
  25. doi 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...
  26. 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...
  27. 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...
  28. 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...
  29. 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)...
  30. 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...
  31. doi 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 ..
  32. doi 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...
  33. 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 ..
  34. 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
    ....
  35. 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...
  36. 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...
  37. 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...
  38. 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/...
  39. doi 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...
  40. 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...
  41. 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...
  42. 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
    ....
  43. 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...
  44. 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...
  45. 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...
  46. doi 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.
  47. 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...
  48. doi 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...
  49. 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...
  50. 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.
  51. doi 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...
  52. 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...
  53. 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...
  54. doi 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)...
  55. doi 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 ..
  56. 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...
  57. 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, ..
  58. 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...
  59. 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...
  60. doi 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 ..
  61. 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 ..
  62. 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...
  63. doi 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.
  64. 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...
  65. 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 ..
  66. doi 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...
  67. 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/...
  68. doi 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...
  69. doi 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...
  70. 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 ..
  71. doi 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...
  72. 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
    ....
  73. ncbi Mitochondrial evolution
    M W Gray
    Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
    Science 283:1476-81. 1999
    ....
  74. 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...
  75. 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
    ....
  76. 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...
  77. 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...
  78. 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 ..
  79. ncbi Phylogeny of prokaryotes: does it exist and why should we care?
    Simonetta Gribaldo
    Institut Pasteur, Department of Microbiology, 75015 Paris, France
    Res Microbiol 160:513-21. 2009
    ..Nevertheless, the idea that it is impossible to reconstruct the evolutionary history of prokaryotes because of horizontal gene transfer has become very popular. We review this important debate and how it can be solved...
  80. ncbi Supertrees disentangle the chimerical origin of eukaryotic genomes
    Davide Pisani
    Department of Biology, The National University of Ireland, Maynooth, Maynooth, County Kildare, Ireland, UK
    Mol Biol Evol 24:1752-60. 2007
    ..The results reject all but two of the current hypotheses for the origin of eukaryotes: those assuming a sulfur-dependent or hydrogen-dependent syntrophy for the origin of mitochondria...
  81. pmc Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
    Zasha Weinberg
    Howard Hughes Medical Institute, Yale University, New Haven, CT 06520 8103, USA
    Genome Biol 11:R31. 2010
    ..Structured RNAs can be detected by comparative genomics, in which homologous sequences are identified and inspected for mutations that conserve RNA secondary structure...
  82. ncbi The respiratory complex I of bacteria, archaea and eukarya and its module common with membrane-bound multisubunit hydrogenases
    T Friedrich
    Institut fur Biochemie, Heinrich Heine Universitat Dusseldorf, Germany
    FEBS Lett 479:1-5. 2000
    ..Homologues of this complex exist in bacteria, archaea, in mitochondria of eukaryotes and in chloroplasts of plants...
  83. pmc Global occurrence of archaeal amoA genes in terrestrial hot springs
    Chuanlun L Zhang
    Department of Marine Sciences, University of Georgia, Athens, Georgia 30602, USA
    Appl Environ Microbiol 74:6417-26. 2008
    ..bulk water pH, suggesting that geography may play a role in structuring communities of putative ammonia-oxidizing archaea (AOA)...
  84. doi Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea
    Yuchen Liu
    Department of Microbiology, University of Georgia, 541 Biological Sciences Building, Athens, GA 30605, USA
    Ann N Y Acad Sci 1125:171-89. 2008
    Although of limited metabolic diversity, methanogenic archaea or methanogens possess great phylogenetic and ecological diversity...
  85. doi Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales
    Junichi Sugahara
    Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
    Mol Biol Evol 25:2709-16. 2008
    ..9% of the codon tables in Archaea. Previously, the content of intron-containing tRNA genes in Archaea was estimated to be approximately 15% of the ..
  86. pmc Archaea dominate the ammonia-oxidizing community in the rhizosphere of the freshwater macrophyte Littorella uniflora
    Martina Herrmann
    Department of Biological Sciences, Microbiology, University of Aarhus, Ny Munkegade, Building 1540, DK 8000 Aarhus C, Denmark
    Appl Environ Microbiol 74:3279-83. 2008
    ..submersed macrophyte Littorella uniflora, archaeal amoA was 500- to >8,000-fold enriched compared to bacterial amoA, suggesting that the enhanced nitrification activity observed in the rhizosphere was due to ammonia-oxidizing Archaea.
  87. pmc Distribution and diversity of archaeal and bacterial ammonia oxidizers in salt marsh sediments
    Nicole S Moin
    Connecticut College, Department of Biology, New London, CT 06320, USA
    Appl Environ Microbiol 75:7461-8. 2009
    Diversity and abundance of ammonia-oxidizing Betaproteobacteria (beta-AOB) and archaea (AOA) were investigated in a New England salt marsh at sites dominated by short or tall Spartina alterniflora (SAS and SAT sites, respectively) or ..
  88. ncbi Methane and sulfate profiles within the subsurface of a tidal flat are reflected by the distribution of sulfate-reducing bacteria and methanogenic archaea
    Reinhard Wilms
    Institut für Chemie und Biologie des Meeres, Carl von Ossietzky Universitat Oldenburg, Oldenburg, Germany
    FEMS Microbiol Ecol 59:611-21. 2007
    ..Therefore, a quantitative PCR approach was applied using primers targeting the domains of Bacteria and Archaea, and key functional genes for sulfate reduction (dsrA) and methanogenesis (mcrA)...
  89. pmc Diversity and abundance of ammonia-oxidizing archaea in hydrothermal vent chimneys of the juan de fuca ridge
    Shufang Wang
    Third Institute of Oceanography, State Oceanic Administration, Xiamen, People s Republic of China
    Appl Environ Microbiol 75:4216-20. 2009
    ..The majority of the retrieved archaeal amoA sequences exhibited identities of less than 95% to those in the GenBank database. Novel ammonia-oxidizing archaea may exist in the hydrothermal vent environments.
  90. ncbi Classification of Bacteria and Archaea: past, present and future
    Karl Heinz Schleifer
    Department of Microbiology, Technical University Munich, Am Hochanger 4, D 85350 Freising, Germany
    Syst Appl Microbiol 32:533-42. 2009
    ..Later on, chemotaxonomic and genotypic methods were widely used for a more satisfactory classification. Archaea were first classified as a separate group of prokaryotes in 1977...
  91. doi Disrupted tRNA gene diversity and possible evolutionary scenarios
    Junichi Sugahara
    Institute for Advanced Biosciences, Keio University, Tsuruoka, 403 1 Nipponkoku, Tsuruoka, Yamagata, 997 0017, Japan
    J Mol Evol 69:497-504. 2009
    The following unusual tRNAs have recently been discovered in the genomes of Archaea and primitive Eukaryota: multiple-intron-containing tRNAs, which have more than one intron; split tRNAs, which are produced from two pieces of RNA ..
  92. ncbi Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia
    Jane M Caffrey
    Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, FL, USA
    ISME J 1:660-2. 2007
    ..We evaluate the relationships between the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) amoA genes; potential nitrification rates and environmental variables ..
  93. doi The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?
    Simonetta Gribaldo
    Institut Pasteur, Department of Microbiology, Paris, France
    Nat Rev Microbiol 8:743-52. 2010
    The origin of eukaryotes and their evolutionary relationship with the Archaea is a major biological question and the subject of intense debate...
  94. ncbi Diversity and spatio-temporal distribution of ammonia-oxidizing Archaea and Bacteria in sediments of the Westerschelde estuary
    Emel Sahan
    Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
    FEMS Microbiol Ecol 64:175-86. 2008
    The diversity and spatio-temporal distribution of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) were investigated along a salinity gradient in sediments of the Westerschelde estuary...
  95. pmc Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function
    James A Cotton
    Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland
    Proc Natl Acad Sci U S A 107:17252-5. 2010
    ..This importance reflects these genes' origin as the ancestral nuclear component of the eukaryotic genome...
  96. pmc Spatial distribution and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in mangrove sediments
    Meng Li
    School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People s Republic of China
    Appl Microbiol Biotechnol 89:1243-54. 2011
    We investigated the diversity, spatial distribution, and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in sediment samples of different depths collected from a transect with different distances to ..
  97. doi Diversity and spatial distribution of amoA-encoding archaea in the deep-sea sediments of the tropical West Pacific Continental Margin
    H Dang
    Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
    J Appl Microbiol 106:1482-93. 2009
    The ecological characteristics of the deep-sea amoA-encoding archaea (AEA) are largely unsolved...
  98. pmc Effect of lake trophic status and rooted macrophytes on community composition and abundance of ammonia-oxidizing prokaryotes in freshwater sediments
    Martina Herrmann
    Department of Biological Sciences, Microbiology, Aarhus University, Ny Munkegade, Building 1540, DK 8000 Aarhus C, Denmark
    Appl Environ Microbiol 75:3127-36. 2009
    Communities of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in freshwater sediments and those in association with the root system of the macrophyte species Littorella uniflora, Juncus bulbosus, and Myriophyllum alterniflorum were ..
  99. pmc Transfer RNA processing in archaea: unusual pathways and enzymes
    Ilka U Heinemann
    Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, 266 Whitney Avenue, New Haven, CT 06520 8114, USA
    FEBS Lett 584:303-9. 2010
    ..However, mostly in archaea, the short genes encoding tRNAs can be found disrupted, fragmented, with permutations or with non-functional ..
  100. ncbi Ammonia-oxidising archaea--physiology, ecology and evolution
    Christa Schleper
    Department of Genetics in Ecology, University of Vienna, Vienna, Austria
    Adv Microb Physiol 57:1-41. 2010
    ..studies and subsequent cultivation efforts have recently demonstrated that microorganisms of the domain archaea are also capable of performing this process...
  101. 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...

Research Grants83

  1. Unique Isoprenoid Biosynthesis Machinery of the Hyperthermophilic Archaea
    HAROLD MONBOUQUETTE; Fiscal Year: 2007
    ..The archaea necessarily have higher throughput isoprenoid biosynthesis machinery; as their membrane lipids are based solely ..
  2. Unique Isoprenoid Biosynthesis Machinery of the Hyperthermophilic Archaea
    HAROLD MONBOUQUETTE; Fiscal Year: 2006
    ..The archaea necessarily have higher throughput isoprenoid biosynthesis machinery; as their membrane lipids are based solely ..
  3. X-ray crystallographic studies of multi-subunit nucleic acid polymerases
    Katsuhiko Murakami; Fiscal Year: 2010
    ..The transcription apparatus in Archaea can be described as a simplified version of its eukaryotic RNA polymerase II (Pol II) counterpart, comprising a ..
  4. X-ray crystallographic studies of multi-subunit nucleic acid polymerases
    Katsuhiko Murakami; Fiscal Year: 2010
    ..The transcription apparatus in Archaea can be described as a simplified version of its eukaryotic RNA polymerase II (Pol II) counterpart, comprising a ..
  5. Mechanism of signal transduction in photoreceptors
    Hartmut Luecke; Fiscal Year: 2003
    ..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 ..
  6. The mechanism of signal transduction in photoreceptors
    Hartmut Luecke; Fiscal Year: 2004
    ..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 ..
  7. The mechanism of signal transduction in photoreceptors
    Hartmut Luecke; Fiscal Year: 2005
    ..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 ..
  8. 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 ..
  9. Resequencing microarray for rapid detection & antimicrobial resistance profiling
    Susan Lynch; Fiscal Year: 2009
    ..g. the 16S rRNA PhyloChip that detects all known bacteria and archaea. Drs...
  10. Resequencing microarray for rapid detection & antimicrobial resistance profiling
    SUSAN VERONICA LYNCH; Fiscal Year: 2010
    ..g. the 16S rRNA PhyloChip that detects all known bacteria and archaea. Drs...
  11. Resequencing microarray for rapid detection & antimicrobial resistance profiling
    Susan Lynch; Fiscal Year: 2007
    ..g. the 16S rRNA PhyloChip that detects all known bacteria and archaea. Drs...
  12. 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...
  13. Foregut microbiome in development of esophageal adenocarcinoma
    ZHIHENG contact PEI; Fiscal Year: 2010
    ..Detailed analyses will include pathway-disease and gene-disease associations. Archaea, fungi and viruses, if identified, also will be correlated with the diseases...
  14. Genomic and metabolomic foundations of human-microbial symbiosis in the gut
    Jeffrey Gordon; Fiscal Year: 2009
    ..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. ..
  15. Genomic and metabolomic foundations of human-microbial symbiosis in the gut
    Jeffrey Gordon; Fiscal Year: 2007
    ..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. ..
  16. Genomic and metabolomic foundations of human-microbial symbiosis in the gut
    JEFFREY IVAN GORDON; Fiscal Year: 2010
    ..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. ..
  17. Genomic and metabolomic foundations of human-microbial symbiosis in the gut
    Jeffrey Gordon; Fiscal Year: 2006
    ..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. ..
  18. Genomic and metabolomic foundations of human-microbial symbiosis in the gut
    JEFFREY IVAN GORDON; Fiscal Year: 2010
    ..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. ..
  19. RNA SPLICING IN ARCHAEA
    Ramesh Gupta; Fiscal Year: 2009
    ..Broad long-term objectives of this application are to characterize various RNA processing events in Archaea. The specific aims of this proposal are: Structural and functional characterization of archaeal box C/D sRNPs;In ..
  20. RNA SPLICING IN ARCHAEA
    Ramesh Gupta; Fiscal Year: 2009
    ..Broad long-term objectives of this application are to characterize various RNA processing events in Archaea. The specific aims of this proposal are: Structural and functional characterization of archaeal box C/D sRNPs;In ..
  21. REGULATORY DOMAINS OF PROTEIN PHOSPHATASE 1
    PETER KENNELLY; Fiscal Year: 1999
    ..Successful completion of this project may increase the understanding of how PP1 is regulated in cells, and do so in molecular detail. ..
  22. STRUCTURE/FUNCTION OF ARCHAEAL SENSORY RHODOPSINS
    John Spudich; Fiscal Year: 1999
    ..Additionally, the SR-I transducer is eubacterial in origin and this novel receptor/transducer combination may reveal a new mechanism of signal transduction. ..
  23. Indirect aminoacylation in the Plasmodium apicoplast
    Malcolm Gardner; Fiscal Year: 2009
    ..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...
  24. 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...
  25. STRUCTURE/FUNCTION OF ARCHAEAL SENSORY RHODOPSINS
    John Spudich; Fiscal Year: 2001
    ..Additionally, the SR-I transducer is eubacterial in origin and this novel receptor/transducer combination may reveal a new mechanism of signal transduction. ..
  26. STRUCTURE/FUNCTION OF ARCHAEAL SENSORY RHODOPSINS
    John Spudich; Fiscal Year: 2002
    ..Additionally, the SR-I transducer is eubacterial in origin and this novel receptor/transducer combination may reveal a new mechanism of signal transduction. ..
  27. STRUCTURE/FUNCTION OF ARCHAEAL SENSORY RHODOPSINS
    John Spudich; Fiscal Year: 2000
    ..Additionally, the SR-I transducer is eubacterial in origin and this novel receptor/transducer combination may reveal a new mechanism of signal transduction. ..
  28. CHEMOTACTIC SENSORY TRANSDUCTION IN BACILLUS SUBTILIS
    George W Ordal; Fiscal Year: 2010
    ..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 ..
  29. CHEMOTACTIC SENSORY TRANSDUCTION IN BACILLUS SUBTILIS
    GEORGE ORDAL; Fiscal Year: 2009
    ..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 ..
  30. Archaeal gene recruitment by the Chlamydiales
    David Graham; Fiscal Year: 2007
    ..Results from these experiments will support future microbiological studies of the role of this system in chlamydial infection and survival in the host cell. [unreadable] [unreadable] [unreadable]..
  31. Aminoacyl-tRNA synthetases in Archaea
    Ya Ming Hou; Fiscal Year: 2003
    ..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...
  32. Aminoacyl-tRNA synthetases in Archaea
    Ya Ming Hou; Fiscal Year: 2004
    ..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...
  33. 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...
  34. Aminoacyl-tRNA synthetases in Archaea
    Ya Ming Hou; Fiscal Year: 2005
    ..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...
  35. RNA SPLICING IN ARCHAEA
    Ramesh Gupta; Fiscal Year: 2005
    ..Broad long-term objectives of this AREA application are to characterize various RNA processing events in Archaea. Both Archaea and Bacteria are prokaryotes; yet Archaea exhibit several molecular features resembling Eukaryotes...
  36. STUDIES ON TRANSFER RNA
    Dieter Soll; Fiscal Year: 2009
    ..characterization of a novel tRNA ligase(s) will lead to a better understanding of tRNA processing in humans and archaea. PUBLIC HEALTH RELEVANCE: The unexpected diversity of aminoacyl-tRNA synthesis (processes that maintain the ..
  37. STUDIES ON TRANSFER RNA
    Dieter Soll; Fiscal Year: 2009
    ..characterization of a novel tRNA ligase(s) will lead to a better understanding of tRNA processing in humans and archaea. PUBLIC HEALTH RELEVANCE: The unexpected diversity of aminoacyl-tRNA synthesis (processes that maintain the ..
  38. STUDIES ON TRANSFER RNA
    Dieter Soll; Fiscal Year: 2009
    ..characterization of a novel tRNA ligase(s) will lead to a better understanding of tRNA processing in humans and archaea. PUBLIC HEALTH RELEVANCE: The unexpected diversity of aminoacyl-tRNA synthesis (processes that maintain the ..
  39. SERYL-TRNA SYNTHETASES: EVOLUTION AND DIVERSITY
    Dieter Soll; Fiscal Year: 2002
    ..Until recently, the study of aminoacyl-tRNA synthesis in archaea had received little attention...
  40. SERYL-TRNA SYNTHETASES: EVOLUTION AND DIVERSITY
    Dieter Soll; Fiscal Year: 2001
    ..Until recently, the study of aminoacyl-tRNA synthesis in archaea had received little attention...
  41. 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...
  42. STRUCTURE AND FUNCTION OF TRANSFER RIBONUCLEIC ACIDS
    Uttam L RajBhandary; Fiscal Year: 2010
    ..relationship between the structure and function of archaeal initiator tRNAs and the translational machinery of archaea in general...
  43. Mechanisms of CRISPR Interference
    Erik J Sontheimer; Fiscal Year: 2010
    ..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...
  44. Ubiquitin-like Small Archaeal Protein Modification (SAMPylation)
    Julie A Maupin Furlow; Fiscal Year: 2010
    ..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...
  45. RNA SPLICING IN ARCHAEA
    Ramesh Gupta; Fiscal Year: 2001
    ..Broad, long-term objectives of this AREA application are to characterize various RNA processing events in archaea. Both archaea and bacteria are prokaryotes; yet archaea exhibit several molecular features resembling eukaryotes...
  46. 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...
  47. 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)..
  48. Pseudouridines, pseudouridine synthases, and ribosomes
    MURRAY DEUTSCHER; Fiscal Year: 2004
    ..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)..
  49. Pseudouridines, pseudouridine synthases, and ribosomes
    MURRAY DEUTSCHER; Fiscal Year: 2005
    ..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)..
  50. Pseudouridines, pseudouridine synthases, and ribosomes
    James Ofengand; Fiscal Year: 2003
    ..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)..
  51. 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...
  52. Biochemical and structural characterization of self-assembling viral particles
    REBECCA TAUROG; Fiscal Year: 2009
    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...
  53. CHEMOTACTIC SENORY TRANSDUCTION IN BACILLUS SUBTILIS
    GEORGE ORDAL; Fiscal Year: 2003
    ..study of chemotaxis during the past decade is that the well-studied enteric model may not be representative of archaea and eubacteria ("bacteria')...
  54. CHEMOTACTIC SENORY TRANSDUCTION IN BACILLUS SUBTILIS
    GEORGE ORDAL; Fiscal Year: 2001
    ..study of chemotaxis during the past decade is that the well-studied enteric model may not be representative of archaea and eubacteria ("bacteria')...
  55. CHEMOTACTIC SENSORY TRANSDUCTION IN BACILLUS SUBTILIS
    GEORGE ORDAL; Fiscal Year: 1991
    ..This operon is over 26 kb and contains at least 27 genes. We will also examine the mechanism by which both hag and mot transcription and methanol formation on chemotactic stimulation depend on the morphology of the basal body...
  56. Biochemical and structural characterization of self-assembling viral particles
    REBECCA TAUROG; Fiscal Year: 2007
    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...
  57. CHEMOTACTIC SENORY TRANSDUCTION IN BACILLUS SUBTILIS
    GEORGE ORDAL; Fiscal Year: 2000
    ..study of chemotaxis during the past decade is that the well-studied enteric model may not be representative of archaea and eubacteria ("bacteria')...
  58. CHEMOTACTIC SENSORY TRANSDUCTION IN BACILLUS SUBTILIS
    GEORGE ORDAL; Fiscal Year: 1999
    ..This operon is over 26 kb and contains at least 27 genes. We will also examine the mechanism by which both hag and mot transcription and methanol formation on chemotactic stimulation depend on the morphology of the basal body. ..
  59. CHEMOTACTIC SENORY TRANSDUCTION IN BACILLUS SUBTILIS
    GEORGE ORDAL; Fiscal Year: 2002
    ..study of chemotaxis during the past decade is that the well-studied enteric model may not be representative of archaea and eubacteria ("bacteria')...
  60. PHYSIOLOGY OF PROTEASOMES IN HALOFERAX VOLCANII
    Julie Maupin Furlow; Fiscal Year: 2000
    ..understanding of energy-dependent proteolysis in the cell, especially as it relates to the metabolically diverse Archaea which play a major role in global carbon mineralization and the production of greenhouse gases...
  61. PHYSIOLOGY OF PROTEASOMES IN HALOFERAX VOLCANII
    Julie Maupin Furlow; Fiscal Year: 2001
    ..understanding of energy-dependent proteolysis in the cell, especially as it relates to the metabolically diverse Archaea which play a major role in global carbon mineralization and the production of greenhouse gases...
  62. PHYSIOLOGY OF PROTEASOMES IN HALOFERAX VOLCANII
    Julie Maupin Furlow; Fiscal Year: 2002
    ..understanding of energy-dependent proteolysis in the cell, especially as it relates to the metabolically diverse Archaea which play a major role in global carbon mineralization and the production of greenhouse gases...
  63. PHYSIOLOGY OF PROTEASOMES IN HALOFERAX VOLCANII
    Julie Maupin Furlow; Fiscal Year: 2003
    ..understanding of energy-dependent proteolysis in the cell, especially as it relates to the metabolically diverse Archaea which play a major role in global carbon mineralization and the production of greenhouse gases...
  64. PHYSIOLOGY OF PROTEASOMES IN HALOFERAX VOLCANII
    Julie Maupin Furlow; Fiscal Year: 2004
    ..understanding of energy-dependent proteolysis in the cell, especially as it relates to the metabolically diverse Archaea which play a major role in global carbon mineralization and the production of greenhouse gases...
  65. 7 FE FDI AS A MODEL FE-S AND REGULATORY PROTEIN
    Barbara Burgess; Fiscal Year: 2000
    Iron-sulfur [Fe-S] proteins are ubiquitous occurring in all life forms from the most primitive bacteria and archaea to the most advanced eucaryotes...
  66. 7 FE FDI AS A MODEL FE-S AND REGULATORY PROTEIN
    Barbara Burgess; Fiscal Year: 1999
    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. 7 FE FDI AS A MODEL FE-S AND REGULATORY PROTEIN
    Barbara Burgess; Fiscal Year: 2001
    Iron-sulfur [Fe-S] proteins are ubiquitous occurring in all life forms from the most primitive bacteria and archaea to the most advanced eucaryotes...
  68. 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...
  69. Structural study of enzymes of inositol biosynthesis
    Boguslaw Stec; Fiscal Year: 2002
    ..A collection of enzymes from primitive to more advanced organisms (Archaea to Eukarya) will be created that will allow us to extract conserved or noel structures and to correlate them with ..
  70. The Molecular Control of Cell Death in Staphylococcus aureus
    JEFFREY BOSE; Fiscal Year: 2009
    ..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...
  71. Biosynthesis of hypermodified guanosines
    Valerie De Crecy Lagard; Fiscal Year: 2007
    ..separate Domains; queuosine is ubiquitous among Bacteria and Eukarya, while archaeosine is only present in the Archaea. The 7-deazapurine structure in general is widespread in biology, where it is found in a variety of natural ..
  72. Biosynthesis of hypermodified gaunosines.
    Valerie De Crecy Lagard; Fiscal Year: 2009
    ..separate Domains; queuosine is ubiquitous among Bacteria and Eukarya, while archaeosine is only present in the Archaea. The 7-deazapurine structure in general is widespread in biology, where it is found in a variety of natural ..
  73. Biosynthesis of hypermodified gaunosines.
    Valerie De Crecy Lagard; Fiscal Year: 2007
    ..separate Domains; queuosine is ubiquitous among Bacteria and Eukarya, while archaeosine is only present in the Archaea. The 7-deazapurine structure in general is widespread in biology, where it is found in a variety of natural ..
  74. CHEMOTACTIC SENSORY TRANSDUCTION IN BACILLUS SUBTILIS
    GEORGE ORDAL; Fiscal Year: 2009
    ..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 ..
  75. ENZYMATIC MECHANISMS OF SULFUR NUCLEOSIDE METABOLISM
    GEORGE MARKHAM; Fiscal Year: 2002
    ..AdoMet synthetases from Archaea have very different sequences from those of the eukarya and prokarya, suggesting an altered catalytic strategy; ..
  76. ENZYMATIC MECHANISMS OF SULFUR NUCLEOSIDE METABOLISM
    GEORGE MARKHAM; Fiscal Year: 2000
    ..AdoMet synthetases from Archaea have very different sequences from those of the eukarya and prokarya, suggesting an altered catalytic strategy; ..
  77. Role of Human Intestinal Microbiota on Success of Surgical Weight Loss Procedures
    BRUCE EDWARD RITTMANN; Fiscal Year: 2012
    ..Also, fermenters and Methanobrevibacter smithii (a methanogen from the Archaea domain) appear to act syntrophically to affect energy uptake...
  78. STATIONARY PHASE GENE REGULATION IN THE HALOARCHAEA
    RICHARD SHAND; Fiscal Year: 1999
    ..that are involved in regulating stationary phase expressed genes in extremely halophilic members of the domain Archaea. This is of interest for two reasons...
  79. Characterization of the ferrous iron transporter Feo in Vibrio cholerae
    Shelley M Payne; Fiscal Year: 2011
    ..It is widely distributed in eubacteria and in the Archaea, suggesting that it is a very ancient class of iron transporter...
  80. Transcriptional Regulation in Giardia lamblia
    HEIDI ELMENDORF; Fiscal Year: 2005
    ..rules' 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...
  81. 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...