- RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex
Caryn R Hale
Department of Biochemistry, University of Georgia, Athens, GA 30602, USA
Cell 139:945-56. 2009
..Our results indicate that prokaryotes possess a unique RNA silencing system that functions by homology-dependent cleavage of invader RNAs...
- Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity
Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
Mol Cell 45:303-13. 2012
..Both target and guide RNAs can be cleaved, although a single molecule of guide RNA can support the degradation of multiple targets...
- A single-base resolution map of an archaeal transcriptome
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
Genome Res 20:133-41. 2010
..This study highlights transcriptome sequencing as a key tool for understanding the mechanisms and extent of RNA-based regulation in Bacteria and Archaea...
- Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis
Max Planck Institute for Terrestrial Microbiology, Karl von Frisch Strasse 10, D 35037 Marburg, Germany
Nucleic Acids Res 40:9887-96. 2012
..These effects will need to be considered for the application of CRISPR clusters that are designed to produce synthetic crRNAs...
- Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs
Caryn R Hale
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
Mol Cell 45:292-302. 2012
..Our findings indicate that the CRISPR RNA-Cmr protein pathway may be exploited to cleave RNAs of interest...
- Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota
University of Vienna, Department of Genetics in Ecology, Althanstrasse 14, A 1090 Vienna, Austria
Trends Microbiol 18:331-40. 2010
- Identification of genes that are associated with DNA repeats in prokaryotes
Department of Infectious Diseases and Immunology, Bacteriology Division, Veterinary Faculty, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
Mol Microbiol 43:1565-75. 2002
..The spatial coherence of CRISPR and cas genes may stimulate new research on the genesis and biological role of these repeats and genes...
- Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax
Institute of Biology, Microbiology I, University of Duisburg Essen, Essen, Germany
J Bacteriol 194:2491-500. 2012
..These data provide insights into the specialized mechanisms of an archaeal CRISPR/Cas system and allow selective functional analyses of Cas protein complexes in the future...
- Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling
Alexander H Treusch
University of Bergen, Department of Biology, Jahnebakken 5, N 5020 Bergen, Norway
Environ Microbiol 7:1985-95. 2005
..Taken together, our findings suggest that mesophilic terrestrial and marine crenarchaeota might be capable of ammonia oxidation under aerobic and potentially also under anaerobic conditions...
- Phylogenomics of prokaryotic ribosomal proteins
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
PLoS ONE 7:e36972. 2012
..These alignments, available for download, can be used as search profiles to improve genome annotation of r-proteins and for further comparative genomics studies...
- Archaeal nitrification in the ocean
Department of Marine Biogeochemistry and Toxicology, Royal Netherlands Institute for Sea Research NIOZ, P O Box 59, 1790 AB, Den Burg, The Netherlands
Proc Natl Acad Sci U S A 103:12317-22. 2006
..Our data thus suggest a major role for Archaea in oceanic nitrification...
- Origin and evolution of DNA topoisomerases
Institut de Genetique et Microbiologie, UMR8621, Universite Paris Sud 11, Bat 400 409, 91405 Orsay Cedex, France
Biochimie 89:427-46. 2007
- Revealing the essentiality of multiple archaeal pcna genes using a mutant propagation assay based on an improved knockout method
State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
Microbiology 156:3386-97. 2010
..Because the only prerequisite for this assay is the generation of a MID transformant, this approach can be applied generally to any micro-organisms proficient in homologous recombination...
- The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, New Haven, CT 06520 8114, USA
Science 289:905-20. 2000
..Most of the proteins stabilize the structure by interacting with several RNA domains, often using idiosyncratically folded extensions that reach into the subunit's interior...
- 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
- A role for the ESCRT system in cell division in archaea
Rachel Y Samson
Medical Research Council MRC Cancer Cell Unit, Hills Road, Cambridge CB2 0XZ, UK
Science 322:1710-3. 2008
..Overexpression of a catalytically inactive mutant Vps4 in Sulfolobus resulted in the accumulation of enlarged cells, indicative of failed cell division. Thus, the archaeal ESCRT system plays a key role in cell division...
- Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases
Fachbereich Biologie, Chemie, Pharmazie, Freie Universitat Berlin, Takustrasse 3, 14195 Berlin, Germany
Mol Cell 30:360-8. 2008
..This mechanism differs from that of PA26/28, which lacks the HbYX motif and does not cause alpha subunit rotation. These findings demonstrated how the ATPases' C termini function to facilitate substrate entry...
- The HAMP domain structure implies helix rotation in transmembrane signaling
Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
Cell 126:929-40. 2006
..coli chemotaxis receptor. Structural and functional studies show that the equilibrium between the two forms is dependent on the side-chain size of residue 291, which is alanine in the wild-type protein...
- Development of additional selectable markers for the halophilic archaeon Haloferax volcanii based on the leuB and trpA genes
Institute of Genetics, University of Nottingham, Queen s Medical Centre, Nottingham NG7 2UH, United Kingdom
Appl Environ Microbiol 70:943-53. 2004
..We constructed both integrative and replicative plasmids carrying the leuB or trpA gene under control of a constitutive promoter. The use of these selectable markers in deletion of the lhr gene of H. volcanii is described...
- The mechanisms of HAMP-mediated signaling in transmembrane receptors
Hedda U Ferris
Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
Structure 19:378-85. 2011
..These are correlated with activity and ligand response in vitro and in vivo by incorporating Af1503 HAMP into mycobacterial adenylyl cyclase assay systems...
- Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes
Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
PLoS ONE 6:e20237. 2011
..The extremely halophilic archaea are present worldwide in saline environments and have important biotechnological applications. Ten complete genomes of haloarchaea are now available, providing an opportunity for comparative analysis...
- 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
..Overall, this study significantly enhances our understanding of estuarine ammonia-oxidizing microbial communities and highlights the environmental conditions and niches under which different AOA and beta-AOB phylotypes may thrive...
- Crystal structure of Argonaute and its implications for RISC slicer activity
Ji Joon Song
Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
Science 305:1434-7. 2004
..The architecture of the molecule and the placement of the PAZ and PIWI domains define a groove for substrate binding and suggest a mechanism for siRNA-guided mRNA cleavage...
- The principle of gating charge movement in a voltage-dependent K+ channel
Howard Hughes Medical Institute, Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
Nature 423:42-8. 2003
..Our findings lead us to conclude that the voltage-sensor paddles operate somewhat like hydrophobic cations attached to levers, enabling the membrane electric field to open and close the pore...
- Structure of Alba: an archaeal chromatin protein modulated by acetylation
B N Wardleworth
Centre for Biomolecular Science, St Andrews University, North Haugh, St Andrews, Fife KY16 9ST, UK
EMBO J 21:4654-62. 2002
..We present a model for the Alba-DNA interaction consistent with the available structural, biophysical and electron microscopy data...
- A methylaspartate cycle in haloarchaea
Mikrobiologie, Fakultat Biologie, Universitat Freiburg, Schanzlestrasse 1, D 79104 Freiburg, Germany
Science 331:334-7. 2011
..Moreover, it requires elevated intracellular glutamate concentrations, as well as coupling carbon assimilation with nitrogen metabolism...
- The UCSC Archaeal Genome Browser
Kevin L Schneider
Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
Nucleic Acids Res 34:D407-10. 2006
..We encourage submission of new experimental and bioinformatic analysis from contributors. The purpose of this tool is to aid biological discovery and facilitate greater collaboration within the archaeal research community...
- Recognition and cleavage of a nonstructured CRISPR RNA by its processing endoribonuclease Cas6
Institute of Molecular Biophysics, Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
Structure 21:385-93. 2013
..The distinct RNA binding and cleavage mechanisms underline the diversity in CRISPR RNA processing...
- The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes
Kira S Makarova
National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, Maryland 20894, USA
Biol Direct 7:7. 2012
..Here we present the results of in-depth phylogenomic analysis of RecJ homologs in archaea...
- Proteomic characterization of archaeal ribosomes reveals the presence of novel archaeal-specific ribosomal proteins
Gene Center and Department of Biochemistry, Ludwig Maximilians Universitat, Feodor Lynen Str 25, 81377 Munich, Germany
J Mol Biol 405:1215-32. 2011
..The discovery of novel archaeal r-proteins and factors may be the first step to understanding how archaeal ribosomes cope with extreme environmental conditions...
- How do thermophilic proteins deal with heat?
Laboratory of Experimental and Computational Biology, NCI Frederick, Maryland 21702, USA
Cell Mol Life Sci 58:1216-33. 2001
..At the same time, surface loop deletion contributes to decreased conformational entropy and decreased heat capacity change between the folded and unfolded states of the protein...
- DNA bending, compaction and negative supercoiling by the architectural protein Sso7d of Sulfolobus solfataricus
Institute of Protein Biochemistry and Enzymology, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Naples, Italy
Nucleic Acids Res 30:2656-62. 2002
..The proposed biological relevance of these observations is that these proteins might model the behaviour of DNA in constrained chromatin environments...
- E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea
Hugo V Miranda
Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611 0700, USA
Proc Natl Acad Sci U S A 108:4417-22. 2011
..In sulfur transfer, SAMP1 and SAMP2 appear specific for MoCo biosynthesis and the thiolation of tRNA, respectively. Overall, this study provides a fundamental insight into the diverse cellular functions of the Ubl system...
- Molecular mechanisms of proteasome assembly
Laboratory of Protein Metabolism, Department of Integrated Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
Nat Rev Mol Cell Biol 10:104-15. 2009
..By contrast, little is known about the assembly of the 19S regulatory particles, but several hints have emerged...
- Diversity and spatio-temporal distribution of ammonia-oxidizing Archaea and Bacteria in sediments of the Westerschelde estuary
Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
FEMS Microbiol Ecol 64:175-86. 2008
..Variability in net primary production rates was also correlated with species composition of both groups, but changes in the nitrite concentration only to the distribution of the AOA...
- Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group
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 presence of such a eukaryote-type system is unprecedented in prokaryotes, and indicates that a prototype of the eukaryotic protein modifier system is present in the Archaea...
- X-ray structure of a voltage-dependent K+ channel
Howard Hughes Medical Institute, Laboratory of Molecular Neurobiology and Biophysics, Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
Nature 423:33-41. 2003
..Flexible hinges suggest that the voltage-sensor paddles move in response to membrane voltage changes, carrying their positive charge across the membrane...
- 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
..2009) ISME J 3:159-167], and many genes previously only affiliated with Crenarchaea or Bacteria indicate extensive unique physiology in organisms that branched close to the time that Cren- and Euryarchaeotal lineages diverged...
- Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi protein
Jin Biao Ma
Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
Nature 434:666-70. 2005
- Improved and versatile transformation system allowing multiple genetic manipulations of the hyperthermophilic archaeon Thermococcus kodakaraensis
Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
Appl Environ Microbiol 71:3889-99. 2005
..Likewise, a triple deletion mutant, KUWH1 (DeltapyrF DeltatrpE DeltahisD), could also be constructed. The transformation systems developed here now provide the means for extensive genetic studies in this hyperthermophilic archaeon...
- Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes
Nicholas P Robinson
Medical Research Council Cancer Cell Unit, Hutchison Medical Research Council Research Center, Hills Road, Cambridge CB2 0XZ, United Kingdom
Proc Natl Acad Sci U S A 104:5806-11. 2007
- Diversity in chemotaxis mechanisms among the bacteria and archaea
Department of Biochemistry, College of Medicine, University of Illinois, Urbana, IL 61801, USA
Microbiol Mol Biol Rev 68:301-19. 2004
..coli and B. subtilis have been discovered in other organisms. This review emphasizes those used by B. subtilis and these other organisms but also gives an account of the mechanism in E. coli...
- A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro
Department of Research and Development, MJ Bioworks Inc, 7000 Shoreline Court, South San Francisco, CA 94080, USA
Nucleic Acids Res 32:1197-207. 2004
..This technology has the potential to broadly improve the performance of nucleic acid modifying enzymes...
- The relationship of protein conservation and sequence length
David J Lipman
National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
BMC Evol Biol 2:20. 2002
..However, additional evolutionary forces that affect the length of a protein may be revealed by studying the length distributions of proteins evolving under weaker functional constraints...
- Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes
R S Gupta
Department of Biochemistry, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
Microbiol Mol Biol Rev 62:1435-91. 1998
..In this model, the ancestral eukaryotic cell is a chimera that resulted from a unique fusion event between the two separate groups of prokaryotes followed by integration of their genomes...
- Crystal structure of the crenarchaeal conserved chromatin protein Cren7 and double-stranded DNA complex
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People s Republic of China
Protein Sci 19:1253-7. 2010
- Structural insights into the interaction of the crenarchaeal chromatin protein Cren7 with DNA
State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No 1 West Beichen Road, Chaoyang District, Beijing 100101, China
Mol Microbiol 76:749-59. 2010
..Structural comparison of Cren7-DNA complexes with Sac7d-DNA complexes reveals significant differences between the two proteins in DNA binding surface, suggesting that Cren7 and Sul7d serve distinct functions in chromosomal organization...
- The structure and function of MCM from archaeal M. Thermoautotrophicum
Ryan J Fletcher
Department of Biochemistry and Molecular Genetics, University of Colorado Health Science Center, School of Medicine, Denver, Colorado 80262, USA
Nat Struct Biol 10:160-7. 2003
..Yeast bypass experiments using MCM5 mutant proteins support the hypothesis for the bypass mechanism...
- 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
..By contrast, eukaryotes seem to have inherited all three ancestral systems...
- Structure of the archaeal Cascade subunit Csa5: relating the small subunits of CRISPR effector complexes
Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, UK
RNA Biol 10:762-9. 2013
..A definitive answer awaits structural studies of further small subunits from other CRISPR effector complexes. ..
- Structure of a dimeric crenarchaeal Cas6 enzyme with an atypical active site for CRISPR RNA processing
Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
Biochem J 452:223-30. 2013
- Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends
Rosalie P C Driessen
Molecular Genetics, Leiden Institute of Chemistry and Cell Observatory, Physics of Life Processes, Leiden Institute of Physics and Cell Observatory, Leiden University, 2333 CC Leiden, The Netherlands
Nucleic Acids Res 41:196-205. 2013
..Moreover, we investigate the flexibility of the bending angle induced by Cren7 and Sul7 and show that the protein-DNA complexes differ in flexibility from analogous bacterial and eukaryotic DNA-bending proteins...
- A genetic investigation of the KEOPS complex in halophilic Archaea
Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
PLoS ONE 7:e43013. 2012
..volcanii. Deletion of pcc1 led to pleiotropic phenotypes, including decreased growth rate, reduced levels of t(6)A modification, and elevated levels of intra-cellular glycation products...
- Change of carbon source causes dramatic effects in the phospho-proteome of the archaeon Sulfolobus solfataricus
Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Faculty of Chemistry, University of Duisburg Essen, Universitätsstraße 5, 45141 Essen, Germany
J Proteome Res 11:4823-33. 2012
- Characterization of DNA primase complex isolated from the archaeon, Thermococcus kodakaraensis
Wiebke Chemnitz Galal
Program of Molecular Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
J Biol Chem 287:16209-19. 2012
..Supplementation of such reactions with the DNA primase complex supported lagging strand formation as well...
- Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin
EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
EMBO J 18:3451-62. 1999
..We also identified archaeal proteins related to Sm and Sm-like proteins...
- Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine
Daniel Y L Mao
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
Mol Cell 32:259-75. 2008
..Lastly, as Bud32 lacks the conventional substrate-recognition infrastructure of eukaryotic protein kinases including an activation segment, Bud32 may provide a glimpse of the evolutionary history of the protein kinase family...
- Crystal structure of the Mre11-Rad50-ATPγS complex: understanding the interplay between Mre11 and Rad50
Hye Seong Lim
Department of Life Science, Pohang University of Science and Technology, Pohang, South Korea
Genes Dev 25:1091-104. 2011
..Our structural and biochemical data provide insights into understanding the interplay between Mre11 and Rad50 to facilitate efficient DNA damage repair...
- The role of the DNA sliding clamp in Okazaki fragment maturation in archaea and eukaryotes
Thomas R Beattie
Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, UK
Biochem Soc Trans 39:70-6. 2011
..This conformational malleability may be key to the co-ordination of these enzymes' activities...
- The archaeal DNA primase: biochemical characterization of the p41-p46 complex from Pyrococcus furiosus
Department of Molecular Biology, Binomolecular Engineering Research Institute, Suita, Osaka 565 0874, Japan
J Biol Chem 276:45484-90. 2001
..furiosus, in a similar fashion to the eukaryotic polymerase alpha-primase complex...
- The archaeal eIF2 homologue: functional properties of an ancient translation initiation factor
Department of Cellular Biotechnology and Hematology, University of Rome La Sapienza Viale Regina Elena 324, 00161 Rome, Italy
Nucleic Acids Res 33:1804-12. 2005
..The detailed analysis of the complete trimer and of its isolated subunits is discussed in light of the evolutionary history of the eIF2-like proteins...
- The impact of CRISPR repeat sequence on structures of a Cas6 protein-RNA complex
Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
Protein Sci 21:405-17. 2012
..Substitutions of these bases result in structural changes in the protein-RNA complex including its oligomerization state...
- Distinct regulators control the expression of methanol methyltransferase isozymes in Methanosarcina acetivorans C2A
Department of Microbiology, University of Illinois at Urbana Champaign, B103 CLSL, 601 S Goodwin, Urbana, IL 61801, USA
Mol Microbiol 67:649-61. 2008
..We refer to these genes as methanol-specific regulators and designate MA0459, MA0460, MA4383, MA4397 and MA4398 as msrA, msrB, msrC, msrD and msrE respectively...
- Archaeal intrinsic transcription termination in vivo
Thomas J Santangelo
Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
J Bacteriol 191:7102-8. 2009
- The P. furiosus mre11/rad50 complex promotes 5' strand resection at a DNA double-strand break
Ben B Hopkins
The Howard Hughes Medical Institute, Department of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712, USA
Cell 135:250-60. 2008
..This work elucidates how the conserved Mre11/Rad50 complex promotes DNA end resection in archaea and may serve as a model for DSB processing in eukaryotes...
- Diversity and spatial distribution of amoA-encoding archaea in the deep-sea sediments of the tropical West Pacific Continental Margin
Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
J Appl Microbiol 106:1482-93. 2009
..Our aim was to study the diversity, structure and distribution of the AEA community in the sediments of the tropical West Pacific Continental Margin, to develop a general view of the AEA biogeography in the deep-sea extreme environment...
- The evolutionary history of archaeal MCM helicases: a case study of vertical evolution combined with hitchhiking of mobile genetic elements
Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
Mol Biol Evol 27:2716-32. 2010
- Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus
Susana L A Andrade
Institut fur Mikrobiologie und Genetik, Abteilung Molekulare Strukturbiologie, Georg August Universitat, Justus von Liebig Weg 11, 37077 Gottingen, Germany
Proc Natl Acad Sci U S A 102:14994-9. 2005
..In this model, GlnB-1 binds tightly to the cytoplasmic face of the transporter, effectively blocking conduction through the three individual substrate channels...
- The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
New York University, Biology Department, Center for Comparative Functional Genomics, New York, NY 10003, USA
Genome Biol 7:R36. 2006
..Several specific regulatory predictions were experimentally tested and verified...
- ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair
Gareth J Williams
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Nat Struct Mol Biol 18:423-31. 2011
- Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
Biochemistry 41:8152-61. 2002
..At buried sites, statistically significant hydrophobic amino acid substitutions are typically consistent with decreased side chain conformational entropy...
- Reconstitution, activities, and structure of the eukaryotic RNA exosome
Structural Biology Program, Sloan Kettering Institute, New York, NY 10021, USA
Cell 127:1223-37. 2006
..To elucidate the architecture of a eukaryotic exosome, its conserved surfaces, and the structural basis for RNA decay, we report the X-ray structure determination for the 286 kDa nine-subunit human exosome at 3.35 A...
- Archaeal ribosomal protein L7 is a functional homolog of the eukaryotic 15.5kD/Snu13p snoRNP core protein
Jeffrey F Kuhn
Department of Molecular and Structural Biochemistry, North Carolina State University, Box 7622, Raleigh, NC 27695 7622, USA
Nucleic Acids Res 30:931-41. 2002
..L7 functioning as both an sRNP core protein and a ribosomal protein could potentially regulate and coordinate sRNP assembly with ribosome biogenesis...
- 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
..Our study demonstrates the global occurrence of putative archaeal amoA genes in a wide variety of terrestrial hot springs and suggests that geography may play an important role in selecting different assemblages of AOA...
- The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation
Stephen D Bell
Medical Research Council MRC Cancer Cell Unit, The Hutchison MRC Research Centre, Hills Road, Cambridge, CB2 2QH, UK
Science 296:148-51. 2002
..These data provide a paradigm for how Sir2 family proteins influence transcription and suggest that modulation of chromatin structure by acetylation arose before the divergence of the archaeal and eukaryotic lineages...
- Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes
Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
Genome Res 15:352-63. 2005
- Biogeography of the Sulfolobus islandicus pan-genome
Michael L Reno
Department of Microbiology and Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
Proc Natl Acad Sci U S A 106:8605-10. 2009
..islandicus exposes the process of allopatric speciation in thermophilic Archaea and brings us closer to a generalized framework for understanding microbial genome evolution in a spatial context...
- The many faces of the helix-turn-helix domain: transcription regulation and beyond
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 5N50, Bethesda, MD 20894, USA
FEMS Microbiol Rev 29:231-62. 2005
..This differential relationship of their basal and specific transcriptional machinery poses an apparent conundrum regarding the origins of their transcription apparatus...
- Archaeal DNA replication and repair
University of Maryland Biotechnology Institute, Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
Curr Opin Microbiol 8:669-76. 2005
..Recent biochemical and structural studies of the proteins that participate in archaeal DNA replication and repair have increased our understanding of these processes...
- Structure and function in the uracil-DNA glycosylase superfamily
L H Pearl
Section of Structural Biology and CRC DNA Repair Enzyme Group, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, SW3 6JB, London, UK
Mutat Res 460:165-81. 2000
- A novel DNA nuclease is stimulated by association with the GINS complex
Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
Nucleic Acids Res 39:6114-23. 2011
..This novel archaeal nuclease, designated GINS-associated nuclease (GAN), also forms a complex in vivo with the euryarchaeal-specific DNA polymerase D. Roles for GAN in replisome assembly and DNA replication are discussed...
- The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
Nucleic Acids Res 31:365-70. 2003
..Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at firstname.lastname@example.org...
- Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea
Centre for Bioengineering and Biotechnology, China University of Petroleum East China, Qingdao 266555, China
Microbiology 154:2084-95. 2008
..Besides freshwater, nutrients, organic matter and suspended particles, the Changjiang Diluted Water might also contribute to the transport of terrestrial archaea into the seawater and sediments along its flow path...
- Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments
Melissa M Kendall
Biology Department, Portland State University, PO Box 751, Portland, OR 97207 0751, USA
Int J Syst Evol Microbiol 56:1525-9. 2006
..The name Methanococcus aeolicus sp. nov. is proposed, with strain Nankai-3(T) (=OCM 812(T)=DSM 17508(T)) as the type strain...
- Spatial variability in nitrification rates and ammonia-oxidizing microbial communities in the agriculturally impacted Elkhorn Slough estuary, California
Scott D Wankel
Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, USA
Appl Environ Microbiol 77:269-80. 2011
..This is the first report measuring AOA and β-AOB amoA abundance in conjunction with (15)N-based nitrification rates in estuary sediments...
- Genetic technologies for Archaea
Institut fur Mikrobiologie, Johann Wolfgang Goethe Universitat, Marie Curie Strasse 9, D 60439 Frankfurt Main, Germany
Curr Opin Microbiol 8:745-51. 2005
- Crystal structure of a near-full-length archaeal MCM: functional insights for an AAA+ hexameric helicase
Aaron S Brewster
Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
Proc Natl Acad Sci U S A 105:20191-6. 2008
..These structural and biochemical results provide a basis for future study of the helicase mechanisms of the archaeal and eukaryotic MCM complexes in DNA replication...
- Nitrogen fixation at 92 degrees C by a hydrothermal vent archaeon
Mausmi P Mehta
School of Oceanography, University of Washington, Seattle, WA 98195, USA
Science 314:1783-6. 2006
..This increase in the temperature limit of nitrogen fixation could reveal a broader range of conditions for life in the subseafloor biosphere and other nitrogen-limited ecosystems than previously estimated...
- The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation
Jan P Erzberger
Biochemistry and Molecular Biology Division, Department of Molecular and Cell Biology, 229 Stanley Hall, University of California, Berkeley, CA 94720, USA
EMBO J 21:4763-73. 2002
- Characterization of Sac10a, a hyperthermophile DNA-binding protein from Sulfolobus acidocaldarius
Stephen P Edmondson
Laboratory for Structural Biology, Department of Chemistry, Graduate Program in Biotechnology and Bioengineering, University of Alabama in Huntsville, Huntsville, Alabama 35899, USA
Biochemistry 43:13026-36. 2004
..Sac10a shows no sequence similarity to the other Sulfolobus chromatin proteins Sac7d, Sac8, Sso10b2, and Alba...
- A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability
Amy K Schmid
Institute for Systems Biology, Seattle, WA 98103 8904, USA
Mol Syst Biol 5:282. 2009
..Simultaneous analysis of metabolic and gene regulatory network architectures suggests an ongoing process of co-evolution in which TrmB integrates the expression of metabolic enzyme-coding genes of diverse origins...
- A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq
Elizabeth G Wilbanks
University of California Davis, Department of Biomedical Engineering and Genome Center, One Shields Avenue, Davis, CA 95616, USA
Nucleic Acids Res 40:e74. 2012
..While this study focuses on the application of ChIP-seq in H. salinarum sp. NRC-1, our workflow can also be adapted for use in other archaea and bacteria with basic genetic tools...
- The Mre11 protein interacts with both Rad50 and the HerA bipolar helicase and is recruited to DNA following gamma irradiation in the archaeon Sulfolobus acidocaldarius
Univ Paris Sud, Institut de Genetique et Microbiologie, CNRS UMR 8621, Batiment 409, F 91405 Orsay cedex, France
BMC Mol Biol 9:25. 2008
..Since genetic tools for hyperthermophilic archaea are just emerging, we utilized immuno-detection approaches to get the first in vivo data on the role(s) of these proteins in the hyperthermophilic crenarchaeon Sulfolobus acidocaldarius...
- The core and unique proteins of haloarchaea
Melinda D Capes
Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland, 701 East Pratt Street, Baltimore, MD 21202 USA
BMC Genomics 13:39. 2012
..However, few previous attempts have been made to identify novel genes that would permit survival in such extreme conditions...
- DNA replication: archaeal oriGINS
Stephen D Bell
Sir William Dunn School of Pathology, Oxford OX1 3RE, UK
BMC Biol 9:36. 2011
..The structure reveals the anticipated similarity to the previously determined eukaryotic complex but also has some intriguing differences in the relative disposition of subunit domains...
- Tantalizing evidence for caspase-like protein expression and activity in the cellular stress response of Archaea
Kelly A Bidle
Department of Biology, Rider University, Lawrenceville, NJ, USA
Environ Microbiol 12:1161-72. 2010
..By playing a role in normal cell function, caspase-like proteases in Archaea appear to have co-evolved with other metabolic pathways, broadening their biological roles beyond apoptosis and cell death...
- Genetic and biochemical analysis of the twin-arginine translocation pathway in halophilic archaea
Department of Biology, University of Pennsylvania, Philadelphia, 19104, USA
J Bacteriol 187:8104-13. 2005
..Using size exclusion chromatography to further characterize cytoplasmic and membrane TatA proteins, we find these proteins present in high-molecular-weight complexes in both cellular fractions...
- Identification and characterization of an archaeon-specific riboflavin kinase
Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
J Bacteriol 190:2615-8. 2008
..Some divalent metals were found to be potent inhibitors of the reaction. The enzyme represents a unique CTP-dependent family of kinases...
- Archaeal RNA polymerase is sensitive to intrinsic termination directed by transcribed and remote sequences
Thomas J Santangelo
Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
J Mol Biol 355:196-210. 2006
- Nucleoid-associated proteins in Crenarchaea
Rosalie P C Driessen
Leiden Institute of Chemistry, Gorlaeus Laboratories, Laboratory of Molecular Genetics and Cell Observatory, Leiden University, P O Box 9502, 2300 RA Leiden, The Netherlands
Biochem Soc Trans 39:116-21. 2011
..It relies on the action of a large set of small, abundant and generally basic proteins to compact and organize their genome and to modulate its activity...
- Structure and catalysis of acylaminoacyl peptidase: closed and open subunits of a dimer oligopeptidase
Laboratory of Structural Chemistry and Biology and HAS ELTE Protein Modeling Group, Institute of Chemistry, Eotvos Lorand University, Pázmány P sétány 1 A, H 1117 Budapest, Hungary
J Biol Chem 286:1987-98. 2011
..The mutations affected the closed, active form of the enzyme, disrupting its catalytic triad. We concluded that the two forms are at equilibrium and the substrates bind by the conformational selection mechanism...