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Keywords: archaeon
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Articles
Homing endonucleases residing within inteins: evolutionary puzzles awaiting genetic solutions
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2011) 39 (1): 169–173.
Published: 19 January 2011
... ). 16 8 2010 © The Authors Journal compilation © 2011 Biochemical Society 2011 archaeon endonuclease halophile homing endonuclease (HEN) intein HENs are a large and diverse class of selfish elements found in archaea, bacteria and lower eukaryotes, and their respective viruses...
Articles
Insights into chaperonin function from studies on archaeal thermosomes
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2011) 39 (1): 94–98.
Published: 19 January 2011
... © The Authors Journal compilation © 2011 Biochemical Society 2011 archaeon chaperonin heat shock molecular chaperone protein folding thermosome Genes encoding one or more thermosome subunits are found in all complete archaeal genomes which are currently available. A few also...
Articles
Archaeal promoter architecture and mechanism of gene activation
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2011) 39 (1): 99–103.
Published: 19 January 2011
... or inactive [ 14 ], and gene expression from such promoters has to be activated from an upstream activation sequence such as the ara -box element. © The Authors Journal compilation © 2011 Biochemical Society 2011 activator archaeon transcriptional regulation transcription factor B-recognition...
Articles
Assembly and function of the archaeal flagellum
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2011) 39 (1): 64–69.
Published: 19 January 2011
... be an interesting topic of research. archaeon flagellum motility type II secretion system type IV pilus assembly In general, prokaryotes possess a variety of cellular structures on their surface, e.g. flagella and pili, that are thought to be involved in survival under various environmental...
Articles
Structure and function of the primase domain of the replication protein from the archaeal plasmid pRN1
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2011) 39 (1): 104–106.
Published: 19 January 2011
... data, we propose a model of the catalytic cycle of primer synthesis by the pRN1 replication protein. 1 email [email protected] 1 10 2010 © The Authors Journal compilation © 2011 Biochemical Society 2011 archaeon plasmid polymerase primase pRN1 The plasmid...
Articles
The archaeal PCNA proteins
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2011) 39 (1): 20–24.
Published: 19 January 2011
... in reduced DNA binding [ 21 ]. In contrast with the PCNA proteins from the thermophilic archaea P. furiosus , A. fulgidus , S. solfataricus and T. kodakaraensis , and the eukaryotic PCNA, the protein from the halophilic archaeon H. volcanii has very few positively charged residues within...
Articles
Archaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit
Available to PurchaseMagdalena Wojtas, Bibiana Peralta, Marina Ondiviela, Maria Mogni, Stephen D. Bell, Nicola G.A. Abrescia
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2011) 39 (1): 25–30.
Published: 19 January 2011
... step towards the understanding of Rpo13's role in archaeal transcription. 1 To whom correspondence should be addressed (email [email protected] ). 29 9 2010 © The Authors Journal compilation © 2011 Biochemical Society 2011 archaeon RNA polymerase Rpo13...
Articles
Bacterial and eukaryotic systems collide in the three Rs of Methanococcus
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2011) 39 (1): 111–115.
Published: 19 January 2011
...Richard P. Parker; Alison D. Walters; James P.J. Chong Methanococcus maripaludis S2 is a methanogenic archaeon with a well-developed genetic system. Its mesophilic nature offers a simple system in which to perform complementation using bacterial and eukaryotic genes. Although information-processing...
Articles
Structure and function of a novel endonuclease acting on branched DNA substrates
Available to PurchaseChristophe Creze, Roxane Lestini, Joelle Kühn, Alessio Ligabue, Hubert F. Becker, Mirjam Czjzek, Didier Flament, Hannu Myllykallio
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2011) 39 (1): 145–149.
Published: 19 January 2011
...) complex with DNA will be crucial for identification of its physiologically relevant activities. 1 To whom correspondence should be addressed (email [email protected] ). 21 9 2010 © The Authors Journal compilation © 2011 Biochemical Society 2011 archaeon...
Articles
Assembling the archaeal ribosome: roles for translation-factor-related GTPases
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2011) 39 (1): 45–50.
Published: 19 January 2011
... (email [email protected] ). 22 7 2010 © The Authors Journal compilation © 2011 Biochemical Society 2011 archaeon GTPase ribosome assembly translation-factor-related GTPase (TRAFAC GTPase) Translation of the genetic information from nucleic acids into proteins...
Articles
Regulatory RNAs in Haloferax volcanii
Available to PurchaseSusan Fischer, Juliane Benz, Bettina Späth, Angelika Jellen-Ritter, Ruth Heyer, Marcella Dörr, Lisa-Katharina Maier, Clemens Menzel-Hobeck, Matthias Lehr, Katharina Jantzer, Julia Babski, Jörg Soppa, Anita Marchfelder
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2011) 39 (1): 159–162.
Published: 19 January 2011
... knowledge about sRNAs and their function in the halophilic archaeon Haloferax volcanii . Using two different experimental approaches, 111 intergenic and 38 antisense sRNAs were identified, as well as 42 tRFs (tRNA-derived fragments). Observation of differential expression under various conditions suggests...
Articles
Protein–protein interactions in the archaeal core replisome
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2011) 39 (1): 163–168.
Published: 19 January 2011
... Biochemical Society 2011 archaeon chromosome replication DNA replication protein–protein interaction replication machinery replisome In all forms of cellular life, chromosomal DNA replication requires the complex interplay of a large number of essential and non-essential protein factors...
Articles
The role of the DNA sliding clamp in Okazaki fragment maturation in archaea and eukaryotes
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2011) 39 (1): 70–76.
Published: 19 January 2011
... archaeon Sulfolobus solfataricus Mol. Cell 2003 11 275 282 42 Hutton R.D. Roberts J.A. Penedo J.C. White M.F. PCNA stimulates catalysis by structure-specific nucleases using two distinct mechanisms: substrate targeting and catalytic step Nucleic Acids Res. 2008 36 6720...
Articles
Structure, function and evolution of the XPD family of iron–sulfur-containing 5′→3′ DNA helicases
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (3): 547–551.
Published: 20 May 2009
... compilation © 2009 Biochemical Society 2009 archaeon Fanconi's anaemia complementation group J (FancJ) helicase iron–sulfur-cluster-binding domain molecular evolution xeroderma pigmentosum complementation group D (XPD) The XPD/Rad3 helicase family comprises a group of related superfamily 2...
Articles
Reactions to UV damage in the model archaeon Sulfolobus solfataricus
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 36–41.
Published: 20 January 2009
... ). 28 10 2008 © The Authors Journal compilation © 2009 Biochemical Society 2009 aggregation archaeon DNA repair hyperthermophile Sulfolobus UV damage All living organisms, from bacteria to archaea and eukaryotes, have an impressive number of proteins and pathways that seem...
Articles
Methanococcus maripaludis : an archaeon with multiple functional MCM proteins?
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 1–6.
Published: 20 January 2009
..., revealing that the MCM complex has ATPase, DNA-binding and -unwinding activities. Unusually, the genome of the methanogenic archaeon Methanococcus maripaludis contains four MCM homologues, all of which contain the conserved motifs required for function. The availability of a wide range of genetic tools...
Articles
Expanding and understanding the genetic toolbox of the hyperthermophilic genus Sulfolobus
Available to PurchaseMichaela Wagner, Silvia Berkner, Malgorzata Ajon, Arnold J.M. Driessen, Georg Lipps, Sonja-Verena Albers
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 97–101.
Published: 20 January 2009
... Society 2009 archaeon deletion mutant genetics plasmid recombination Sulfolobus To recombine plasmid DNA into the chromosome via single-cross-over events leading to a markerless deletion strain, the up- and down-stream flanking regions were cloned consecutively upstream of the pyrEF...
Articles
Reverse gyrase and genome stability in hyperthermophilic organisms
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 69–73.
Published: 20 January 2009
... of the three-dimensional structure of the reverse gyrase of the archaeon Archaeoglobus fulgidus confirmed the two-domain structure and revealed other interesting features [ 13 ]. The C-terminal domain forms a toroidal shape typical of IA-type topoisomerases, comprising four subdomains arranged around...
Articles
The interaction of Nanoarchaeum equitans with Ignicoccus hospitalis : proteins in the contact site between two cells
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 127–132.
Published: 20 January 2009
... Society 2009 archaeon Ignicoccus Nanoarchaeum transporter Ignicoccus hospitalis [ 1 ] and Nanoarchaeum equitans [ 2 ] form a stable intimate association of hyperthermophilic archaea. I. hospitalis is a chemolithoautotrophic micro-organism; it can thrive alone in a stable axenic...
Articles
How is the archaeal MCM helicase assembled at the origin? Possible mechanisms
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 7–11.
Published: 20 January 2009
... MCM protein from the archaeon M. thermautotrophicus . These studies suggest that the protein can adopt multiple forms; hexamers, heptamers, dodecamers, filaments and open circles were identified (see [ 14 ] and references therein). Conformational changes upon DNA and nucleotide binding have also been...
Articles
Molecular biology of Hel308 helicase in archaea
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 74–78.
Published: 20 January 2009
... molecular biology of Hel308, drawing together ideas of how it may contribute to genome stability through the control of recombination, with reference to paradigms developed in bacteria. archaeon Hel308 helicase recombination repair replication Since many stages of replication, repair...
Articles
RecA family proteins in archaea: RadA and its cousins
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 102–107.
Published: 20 January 2009
... ). 4 8 2008 © The Authors Journal compilation © 2009 Biochemical Society 2009 archaeon homologous recombination RadA RadB Rad51 RecA Recombinases are enzymes that are essential for HR (homologous recombination), since they catalyse homologous base-pairing and strand exchange...
Articles
Small RNAs of the halophilic archaeon Haloferax volcanii
Available to PurchaseJörg Soppa, Julia Straub, Mariam Brenneis, Angelika Jellen-Ritter, Ruth Heyer, Susan Fischer, Michaela Granzow, Björn Voss, Wolfgang R. Hess, Brian Tjaden, Anita Marchfelder
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 133–136.
Published: 20 January 2009
... for the presence of sRNAs in the model archaeon Haloferax volcanii , resulting in more than 150 putative sRNA genes being identified. Northern blot analyses were used to study (differential) expression of sRNA genes. Several chromosomal deletion mutants of sRNA genes were generated and compared with the wild-type...
Articles
Chaperones and protein folding in the archaea
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 46–51.
Published: 20 January 2009
.... Our studies on the type II chaperonins of the genetically tractable archaeon Haloferax volcanii have shown that only one of the three genes has to be present for the organisms to grow, but that there is some evidence for functional specialization between the different chaperonin proteins. All archaea...
Articles
Molecular mechanisms of archaeal RNA polymerase
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 12–17.
Published: 20 January 2009
... the molecular mechanisms of transcription. 1 To whom correspondence should be addressed (email [email protected] ). 25 9 2008 © The Authors Journal compilation © 2009 Biochemical Society 2009 archaeon evolution RNA polymerase transcription The structure and function...
Articles
Role of multiprotein bridging factor 1 in archaea: bridging the domains?
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 52–57.
Published: 20 January 2009
... of a GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 2007 63 239 241 46 Sabina J. Söll D. The RNA-binding PUA domain of archaeal tRNA-guanine transglycosylase is not required for archaeosine...
Articles
Genetics, biochemistry and structure of the archaeal virus STIV
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 114–117.
Published: 20 January 2009
...) are indicated. archaeal virus archaeon Sulfolobus solfataricus Sulfolobus turreted icosahedral virus (STIV) References 1 Rice G. Tang L. Stedman K. Roberto F. Spuhler J. Gillitzer E. Johnson J.E. Douglas T. Young M. The structure...
Articles
Homologous recombination in Sulfolobus acidocaldarius : genetic assays and functional properties
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 88–91.
Published: 20 January 2009
.... 1 email [email protected] 29 7 2008 © The Authors Journal compilation © 2009 Biochemical Society 2009 archaeon conjugation electroporation homologous recombination oligonucleotide Sulfolobus acidocaldarius Figure 1 Assays for OMT Upper panel...
Articles
Evolution and assembly of ESCRTs
Available to PurchaseSara Ghazi-Tabatabai, Takayuki Obita, Ajaybabu V. Pobbati, Olga Perisic, Rachel Y. Samson, Stephen D. Bell, Roger L. Williams
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 151–155.
Published: 20 January 2009
... ] ( Figure 2 B). This alternative MIM has been referred to as a MIM2. In contrast with the MIM1 sequences of Vps2 and Vps46, the Vps20 MIM2 has an extended conformation in its complex with the MIT domain rather than the helical conformation that is characteristic of Vps2 and Vps46. archaeon...
Articles
Recognition of deaminated bases by archaeal family-B DNA polymerases
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 65–68.
Published: 20 January 2009
... seem likely in the archaea. archaeon DNA polymerase DNA replication and repair hypoxanthine read-ahead recognition uracil Bioscientists are most familiar with archaeal family-B DNA polymerases, such as the enzyme from Pyrococcus furiosus (Pfu-Pol), as reagents for PCR. In several...
Articles
Genetic analyses in the hyperthermophilic archaeon Sulfolobus islandicus
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 92–96.
Published: 20 January 2009
... archaeon gene knockout hyperthermophile marker gene plasmid Sulfolobus islandicus Figure 1 Schematic diagram of gene-knockout plasmids Gene-knockout plasmids are constructed with an E. coli cloning vector, e.g. pGEM3z, pUC18 or pUC19. Either pyrEF or pyrEF + lacS can be used...
Articles
Role of vapBC toxin–antitoxin loci in the thermal stress response of Sulfolobus solfataricus
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 123–126.
Published: 20 January 2009
.... Microbiol. 2005 7 789 797 32 Han C.J. Park S.H. Kelly R.M. Acquired thermotolerance and stressed-phase growth of the extremely thermoacidophilic archaeon Metallosphaera sedula in continuous culture Appl. Environ. Microbiol. 1997 63 2391 2396 33 Peeples T.L. Kelly...
Articles
Lessons from structural and biochemical studies on the archaeal exosome
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 83–87.
Published: 20 January 2009
..., polyadenylation and nuclease activities in the human exosome and associated factors have been separated. 1 To whom correspondence should be addressed (email [email protected] ). 10 10 2008 © The Authors Journal compilation © 2009 Biochemical Society 2009 archaeon exonuclease...
Articles
Mutational studies of archaeal RNA polymerase and analysis of hybrid RNA polymerases
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 18–22.
Published: 20 January 2009
...). archaeon RNA polymerase transcription transcription factor E (TFE) The multisubunit structure of RNAP (RNA polymerase) was one of the first eukaryotic features of the archaeal transcriptional machinery to be discovered [ 1 ], and biochemical structural analyses have revealed a high similarity...
Articles
Respiratory nitrate and nitrite pathway in the denitrifier haloarchaeon Haloferax mediterranei
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2006) 34 (1): 115–117.
Published: 20 January 2006
... and preliminary EPR studies. 1 To whom correspondence should be addressed (email [email protected] ). 19 9 2005 © 2006 The Biochemical Society 2006 archaeon denitrification halophile Haloferax mediterranei respiratory nitrate pathway transcription Bacterial nitrate...
