Tesis sobre el tema "Archaebacteria"
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1
Stevens, A. F. "Studies on the extremely halophilic archaebacteria". Thesis, University of Leicester, 1985. http://hdl.handle.net/2381/35419.
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A variety of techniques have been employed to study the taxonomic relationships within a large number of extremely halophilic archaebacteria, including both alkaliphilic and neutrophilic isolates. These techniques include a computer-assisted analysis of whole cell and ribosomal protein patterns, after separation by one-dimensional SDS- polyacrylamide gel electrophoresis. The API-ZYM system has been applied to the extreme halophiles to produce, and then compare, the partial enzyme profiles of a large number of strains. The serotaxonomy of the major cell envelope component of the archaebacterial halophiles (a 200 KD glycoprotein) has been investigated. The cell envelope structure was further investigated by the use of scanning and transmission electron microscopes to study the cell surface topography and composition of a number of extreme halophiles, both rodshaped and coccoid is elites. A brief investigation of the plasmid DNA present in many of the isolates was carried out by preforming hybridization experiments between plasmids from different strains. Ross and Grant (1985) have suggested that the taxonomy of the extremely halophilic archaebacteria should be revised and that these organisms should be divided into two families, comprising a total of nine genera. The work reported in this thesis provides further evidence that, in general, these suggestions are valid.
2
Galada, Ncebakazi. "Exploring diversity and ecology of nonarchaea in hydrothermal biotopes". Thesis, University of the Western Cape, 2005. http://etd.uwc.ac.za/index.php?module=etd&.
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The Nanoarchaeota were proposed as the fourth archaeal sub-division in 2002, and the only fully characterized nanoarchaeon was found to exist in a symbiotic association with the crenarchaeote, Ignicoccus sp. This nanoarchaeote, named Nanoarchaeum equitans could not be detected with &ldquouniversal&rdquo
archaeal 16S PCR primers and could only be amplified using specifically designed primers. In order to identify and access a wide diversity of archaeal phylotypes a new set of &ldquo
universal&rdquo
archaeal primers A571F (5&rsquo
-GCY TAA AGS RIC CGT AGC-3&rsquo
) and UA1204R (5&rsquo
-TTM GGG GCA TRC IKA CCT-3&rsquo
) was designed, that could amplify the 16S rRNA genes of all four archaeal sub-divisions. Using these primers community DNA was amplified from Chinese and New Zealand hydrothermal systems.
3
Lin, Xinli. "Isolation and characterization of new pterins from nonmethanogenic archaebacteria". Diss., Virginia Polytechnic Institute and State University, 1987. http://hdl.handle.net/10919/77823.
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Several new pterins have been discovered in halophilic and thermoacidophilic archaebacteria. Two of these were identified in the extreme halophiles and were thus called halopterins. One of these halopterins is produced by Halobacterium salinarium, Halobacterium halobium, and Halococcus morrhuae and is called phosphohalopterin-1. It was given this name because it was the first halopterin discovered and it has four monophosphate esters per dimeric pterin. The proposed structure of phosphohalopterin-1 is as follows. [see document for diagram of chemical structure]
The other halopterin, which is produced by Halobacterium marismortui, Halobacterium volcanii, and Halobacterial strain GN-1, is called sulfohalopterin-2 because it has two sulfate esters per dimeric pterin and it was isolated and recognized after the isolation of phosphohalopterin-1. The proposed structure of sulfohalopterin-2 is as follows. [see document for diagram of chemical structure]
As shown above, both pterins are dimers with an ether linkage connecting the polyol side chains. Both of the halopterins are negatively charged because of the phosphate and sulfate esters on the side chains. In addition to the halopterins, a positively charged pterin has been isolated from Sulfolobus solfataricus. This pterin is very special since no positively charged unconjugated pterin had ever been found in nature before. This pterin is named solfapterin after the species name of the bacteria from which it was obtained. The structure of this pterin is still unknown but the preliminary data indicate that it is an unconjugated pterin with a polyol containing an amine on the side chain. Another positively charged pterin which is different from solfapterin was found in Thermoplasma. All of the above pterins are different from any previously described pterins and thus represent new pterins in the archaebacterial kingdom.
The discovery of these new pterins is important both to pterin biochemistry and to archaebacterial taxonomy. These discoveries also open up a new field, that is, the exploration of the function of these new pterins in norunethanogenic archaebacteria.Ph. D.
4
Brown, James W. "RNA polymerase binding sites and polyadenylated RNAs in archaebacteria /". The Ohio State University, 1988. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487591658174843.
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5
Giaquinto, Laura School of Biotechnology & Biomolecular Science UNSW. "The characterization of Csp (Cold Shock Protein) from the Antarctic archaeon, Methanogenium frigidum". Awarded by:University of New South Wales. School of Biotechnology and Biomolecular Science, 2006. http://handle.unsw.edu.au/1959.4/26148.
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Cold shock proteins (Csp) are small acidic proteins that fold into ??-barrel structures with five anti-parallel ??-strands and are involved in essential cellular processes. Upon temperature downshift the synthesis of Csp proteins is drastically increased to enable cells to restore growth in the cold. These proteins facilitate transcription and translation at low temperature by functioning as RNA chaperones. Csp proteins have been most extensively studied in Bacteria but very few Csp homologues have been identified and studied in Archaea. This is the first study examining structural, functional and biophysical properties of Csp from the Antarctic archaeon Methanogenium frigidum. The fastidious growth requirements of M. frigidum make it difficult to cultivate, therefore recombinant methods have been developed for the expression and characterization of the protein. The analysis by transverse urea gradient gel electrophoresis (TUG-GE) revealed that M. frigidum Csp folds by a reversible two-state mechanism and has a low conformational stability. The spectroscopic analysis of the protein performed by Circular Dichroism (CD) spectroscopy disclosed features typical of other homologous proteins. A possible association between Csp and RNA has been proposed according to MALDI-TOF mass spectrometry analysis. The effect of a Nterminal polyhistidine affinity tag on the biophysical properties of Csp was also examined. The biological activity of Csp was investigated by complementation of an E. coli cold sensitive mutant. These studies revealed that the M. frigidum Csp is biologically active and can function in E. coli.
6
Morozova, Daria. "Tolerance limits and survival potential of methanogenic archaea from Siberian permafrost under extreme living conditions = Toleranzgrenzen und Überlebensstrategien von methanogenen Archaeen aus sibirischen Permafrosthabitaten unter Extrembedingungen /". Bremerhaven : Alfred-Wegener-Institut für Polar- und Meeresforschung, 2007. http://www.loc.gov/catdir/toc/fy0804/2008384365.html.
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7
Beckler, Gregory Scott. "Structure and analysis of the hisA and hisI genes of the archaebacterium Methanococcus vannielii /". The Ohio State University, 1987. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487330761219015.
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8
Munro, Stacey. "Investigation of the transcriptional response of Sulfolobus solfataricus to damaging agents". Thesis, St Andrews, 2009. http://hdl.handle.net/10023/743.
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9
Stewart, John E. B. (John Edward Bakos). "Characterization of Aspartate Transcarbamoylase in the Archaebacterium Methanococcus Jannaschii". Thesis, University of North Texas, 1996. https://digital.library.unt.edu/ark:/67531/metadc935724/.
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Asparate transcarbamoylase catalyzes the first committed step in the de novo synthesis of pyrmidine nucleotides UMP, UDP, UTP, and CTP. The archetype enzyme found in Escherichia coli (310 kDa) exhibits sigmodial substrate binding kinetics with positive control by ATP and negative control with CTP and UTP. The ATCase characterized in this study is from the extreme thermophilic Archaebacterium, Methanococcus jannaschii. The enzyme was very stable at elevated temperatures and possessed activity from 20 degrees Celsius to 90 degrees Celsius. M. Jannaschii ATCase retained 75% of its activity after incubation at 100 degrees Celsius for a period of 90 minutes. No sigmodial allosteric response to substrate for the enzyme was observed. Velocity substrate plots gave Michaelis-Menten (hyperbolic) kinetics. The Km for aspartate was 7 mM at 30 degrees Celsius and the KM for carbamoylphosphate was .125 mM. The enzyme from M. jannaschii had a broad pH response with an optimum above pH 9. Kinetic measurements were significantly affected by changes in pH and temperature. The enzyme catalyzed reaction had an energy of activation of 10,300 calories per mole. ATCase from M. jannaschii was partially purified. The enzyme was shown to have a molecular weight of 110,000 Da., with a subunit molecular weight of 37,000 Da. The enzyme was thus a trimer composed of three identical subunits. The enzyme did not possess any regulatory response and no evidence for a regulatory polypeptide was found, DNA from M. jannaschii did hybridize to probes corresponding to genes for both the catalytic and regulatory subunits from E. coli. Analysis of DNA sequences for the M. jannaschii ATCase genes showed that the gene for the catalytic subunits shares significant homology with the pyrB genes from E. coli, and maximum homology amongst known ATCase genes to pyrB from Bacillus. An unlinked gene homologous to E. coli pyrl encoding the regulatory subunit was identified, though its expression and true function remain uncharacterized.
10
Richards, Jodi Dominique. "Helicases and DNA dependent ATPases of Sulfolobus solfataricus /". St Andrews, 2008. http://hdl.handle.net/10023/474.
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11
Wiedenheft, Blake Alan. "Sulfolobus as a model organism for the study of diverse biological interests forays into thermal virology and oxidative stress /". Diss., Montana State University, 2006. http://etd.lib.montana.edu/etd/2006/wiedenheft/WiedenheftB1206.pdf.
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12
Smith, Leon David. "Studies of dehydrogenases from thermoacidophilic archaebacteria with a view to cofactor regeneration". Thesis, University of Bath, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.328734.
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13
Morris, Christina Jane. "DNA sequences and comparison of argininosuccinate synthetase genes from two methanogenic archaebacteria /". The Ohio State University, 1987. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487332636476356.
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14
Yu, Zhiliang. "Use of ValRS-IleRS interparalog distance for the analysis of the phylogenetic relationships between methanopyrus isolates from the atlantic, pacific and indian oceans /". View abstract or full-text, 2007. http://library.ust.hk/cgi/db/thesis.pl?AMCE%202007%20YU.
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15
Orofino, Maria J. "Heavy Metal ATPases from Archaeabacteria to Plants". Digital WPI, 2006. https://digitalcommons.wpi.edu/etd-theses/662.
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PIB-ATPases are membrane proteins that transport heavy metal ions across biological membranes upon ATP-hydrolysis. These enzymes contribute to metal homeostasis in archaeal, prokaryotic and eukaryotic cells. Typically, most PIB-ATPases have eight transmembrane segments, one or more metal binding domains in the cytoplasmic N-terminal region and a series of amino acids conserved in all the members of this family. By sequence homology analysis, the metal specificity for most ATPases has been predicted. Here, we report studies on PIB-ATPases from different organisms. The first part of this work focuses in a group of ATPases from Arabidopsis thaliana plants. Transcription levels of HMA3, 4 and 8 were analyzed in different plant organs and in seedlings upon metal exposure. Tissue specificity was studied for HMA8 by generation of transgenic plants carrying a reporter gene downstream its promoter region. Attempts to determine metal specificity of proteins expressed in yeast cells were performed. Finally, in order to study the effects of removing the genes products from the plants, HMA4 and 8 mutant plants were identified. The second part describes a novel Pb-transport ATPase from a thermophilic archaeabacterium, Aeropyrum pernix. This enzyme is predicted to have only six transmembrane segments, no regulatory metal binding domains and unusual metal specificity. PbTP was cloned, expressed in Escherichia coli and partially purified. The enzyme retained its thermophilicity characteristics when isolated from its native lipid environment. The metal dependent ATPase activity was determined in the presence of different metals at 75ºC. The enzyme was highly activated by Pb2+ (Vmax: 23.6 µmol Pi/mg/h) and to a lesser extent by Zn2+, Hg2+ and Cd2+. Lead interacts with PbTP with high apparent affinity (K1/2: 4.6 µM). The enzymatic ATP hydrolysis was independent of cysteine or glutathione, suggesting direct interaction of the metal ions with the transmembrane transport sites.
16
Menaia, Jose Antonio Gomes Ferreira. "Osmotics of halophilic methanogenic archaeobacteria /". Full text open access at:, 1992. http://content.ohsu.edu/u?/etd,239.
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17
Srinivasan, Gayathri. "Translation of the amber codon in methylamine methyltransferase genes of a methanogenic archaeon". Columbus, Ohio Ohio State University, 2003. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1072732858.
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Thesis (Ph.D.)--Ohio State University, 2003.Title from first page of PDF file. Document formatted into pages; contains xvi, 147 p.; also includes graphics (some col.). Includes abstract and vita. Advisor: Joseph A. Krzycki, Dept. of Microbiology. Includes bibliographical references (p. 122-147).
18
Finn, Michael W. "Discovery of a biochemical pathway to generate ribulose 1,5-bisphosphate and subsequent CO2 fixation through ribulose carboxylase/oxygenase (rubisCO) in Methanococcus jannaschii". Columbus, Ohio : Ohio State University, 2004. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1077915999.
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Thesis (Ph. D.)--Ohio State University, 2004.Title from first page of PDF file. Document formatted into pages; contains xiii, 149 p.; also includes graphics. Includes abstract and vita. Advisor: F. Robert Tabita, Dept. of Microbiology. Includes bibliographical references (p. 144-149).
19
Jem, Kwan-min Jim. "Development of a low-cost industrial recovery process to produce a novel hyperthermophilic alpha amylase overexpressed as inclusion bodies /". Thesis, Connect to Dissertations & Theses @ Tufts University, 2002.
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Thesis (Ph.D.)--Tufts University, 2002.Adviser: Eliana De Bernardez Clark. Submitted to the Dept. of Chemical Engineering. Includes bibliographical references. Access restricted to members of the Tufts University community. Also available via the World Wide Web;
20
Laughery, Marian Frances. "Cellular response of the hyperthermophilic archaeon Sulfolobus solfataricus to radiation damage". Pullman, Wash. : Washington State University, 2009. http://www.dissertations.wsu.edu/Thesis/Fall2009/m_laughery_111609.pdf.
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Thesis (M.S. in biochemistry)--Washington State University, December 2009.Title from PDF title page (viewed on Jan. 20, 2010). "School of Molecular Biosciences." Includes bibliographical references.
21
Larson, Eric Thomas. "X-Ray Crystallographic Studies of Sulfolobus Turetted Icosahedral Virus (STIV): A Hyperthermophilic Virus from Yellowstone National Park". Thesis, Montana State University, 2006. http://etd.lib.montana.edu/etd/2006/larson/LarsonE1206.pdf.
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Sulfolobus turreted icosahedral virus (STIV) was isolated from acidic hot springs of Yellowstone National Park and was the first hyperthermophilic virus described with icosahedral capsid architecture. Structural analysis of the STIV particle and its major capsid protein suggests that it belongs to a lineage of viruses that predates the division of the three domains of life. Functional predictions of the viral proteins are hindered because they lack similarity to sequences of known function. Protein structure, however, may suggest functional relationships that are not apparent from the sequence. Thus, we have initiated crystallographic studies of STIV and expect to gain functional insight into its proteins while illuminating the viral life cycle. These studies may also provide genetic, biochemical, and evolutionary insight into its thermoacidophilic host and the requirements for life in these harsh environments. The first three proteins studied in structural detail are A197, B116, and F93. As anticipated, these structures suggest possible functions. The structure of A197 reveals a glycosyltransferase GT-A fold. Within the context of the GT-A fold, are the canonical DXD motif and a putative catalytic base, hallmarks of this family of enzymes, strongly suggesting glycosyltransferase activity for A197. B116 is a unique structure that lacks significant homology to known protein structures. However, sequence similarity to proteins from other hyperthermophilic viruses reveals conserved surface features suggesting interaction with a host macromolecule, likely DNA. The F93 structure reveals a winged-helix fold common among DNA-binding proteins, in particular, the MarR-like family of transcriptional regulators. The most likely role for F93 is thus regulation of viral transcription. Interestingly, B116 contains an intramolecular disulfide bond while F93 contains an intermolecular disulfide bond. The presence of these disulfide bonds was not anticipated because these proteins are expected to be localized within the host cell. This prompted analysis of the cysteine distribution in the STIV genome, which suggests that disulfide bonds are common in intracellular (cytoplasmic) proteins encoded by STIV. This work is in accordance with accumulating evidence that disulfide bonds are common stabilizing elements in the intracellular proteins of thermophilic organisms in general, and extends the observation to genomes of hyperthermophilic viruses.
22
Geary, Joella Suzanne. "DNA binding proteins of archaeal viruses". Thesis, Montana State University, 2008. http://etd.lib.montana.edu/etd/2008/geary/GearyJ1208.pdf.
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Archaea are single-celled organisms comprising the third domain of life. The Achaeal species Sulfolobus are infected by the Fuselloviridae virus family: SSV1, SSV2, SSV-RH, and SSV-K. The genomes of these viruses have been annotated and contain putative DNA-binding proteins. The purpose of this work is to identify DNA sequences bound by the SSV1 putative DNA-binding protein C43. C43 protein was cloned, expressed, purified, and assayed at various temperatures for interaction with three SSV1 DNA sequences. C43 binds the T5-promoter, T6-promoter, and C43-promoter sequentially and consistently. Additionally, C43 protein is functional at temperatures of 50°C and 65°C. Thus, C43 appears to be an important regulator of the Fuselloviridae SSV1 viral genome.
23
Tarlykov, Pavel Victorovich. "Chemical approaches to probe environmental stress in Archaea". Thesis, Montana State University, 2009. http://etd.lib.montana.edu/etd/2009/tarlykov/TarlykovP0509.pdf.
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Little is known about strategies and mechanisms employed by thermophilic organisms to adapt to environmental stress. Sulfolobus solfataricus is a thermophile that belongs to Archaea, the third domain of life, and can be found in unusual habitats, such as the hot springs of Yellowstone National Park. This archaeon can tolerate high temperature, extreme acidity and high concentrations of heavy metals and other toxic substances. Thus, S. solfataricus has been chosen by many researchers as a model system for biochemical, structural, and genetic studies. In this work S. solfataricus has been exposed to hydrogen peroxide as a natural mild oxidant and arsenic as a common toxic metalloid. One of the aims was to quantitatively define the regulation of proteins upon treatment with hydrogen peroxide or arsenic species in different time periods and concentrations. In this sense, two-dimensional gel electrophoresis approach in conjunction with novel chemical tagging probes has been applied to detect changes on the level of regulation and chemical modification of individual proteins within the whole proteome in response to the stressors. Proteins expression levels have been monitored, redox-sensitive and phosphoproteomic profiles of the S. solfataricus proteome have been identified. Synthesis of the results has allowed a general scheme for how S. solfataricus fights H2O2- and As-induced stress. Lists of mapped proteins have been created and potential biomarkers for oxidative stress have been identified, which can guide further research to better understand mechanisms of proteomic response to the environmental stress in Archaea on the example of thermophilic archaeon S. solfataricus.
24
Zhou, Dan. "Biosynthesis of Caldariellaquinone in Sulfolobus acidocaldarius". Diss., Virginia Tech, 1991. http://hdl.handle.net/10919/39854.
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25
Eustis, Robyn Lynn. "The Role of Pyrococcus furiosus Transcription Factor E in Transcription Iniitiation". PDXScholar, 2015. https://pdxscholar.library.pdx.edu/open_access_etds/2522.
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All sequenced archaeal genomes encode a general transcription factor, TFE, which is highly conserved and homologous to the alpha subunit of the eukaryotic transcription factor TFIIE. TFE functions to increase promoter opening efficiency during transcription initiation, although the mechanism for this is unclear. The N-terminus of TFE contains a common DNA binding motif, a winged helix. At the tip of this winged helix is a highly conserved region of aromatic amino acids that is close to DNA during initiation. TFE activation can compensate for mutations in another transcription factor, TFB2, which is homologous to TFIIB. P. furiosus encodes two paralogs of the eukaryotic RNA polymerase II transcription factor TFIIB: TFB1 and TFB2. TFB2 lacks a portion of the highly conserved N-terminus, and functions in transcription complexes at a lower efficiency than TFB1. It has been demonstrated that the presence of TFE is able to assist in transcription with TFB2 in vitro bringing its efficiency to almost TFB1 levels. Thus, TFB2 provides a unique opportunity to evaluate the function of the TFE winged helix in transcription. In this study the aromatic patch of the TFE winged helix was mutated to test its role in activation of TFB1 and TFB2-containing transcription complexes, because this aromatic patch is required for full TFE activity especially when NTP concentrations are low.
26
Bhattarai, Arati. "The orientation of the Pyrococcus furiosus transcription factor TFB2 in the transcription initiation complex". PDXScholar, 2014. https://pdxscholar.library.pdx.edu/open_access_etds/1938.
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The hyperthermophile archaeon, Pyrococcus furiosus encodes two eukaryotic TFIIB family proteins, TFB1 and TFB2. TFB1 is very similar to TFIIB in terms of sequence homology and function, whereas TFB2 is unusual as it is missing highly conserved sequences in its N-terminal domain that are present in TFIIB and TFB1. Despite this, TFB2 is effective in transcription process, albeit with lower efficiency compared to TFB1. Other archaea also contain multiple TFBs, but unlike Pyrococcus furiosus TFB2, these multiple TFBs have higher sequence homology to each other and have similar transcription efficiencies. Photochemical cross-linking experiments have shown that the B-reader of TFB in archaea and TFIIB in eukaryotes is close to transcription start site and is very important in RNAP recruitment to promoter DNA and transcription start site selection. Thus the lack of the highly conserved B reader region in P. furiosus TFB2 presents the opportunity to further study the functional importance of this region.
In this study several amino acids in N-terminal domain of TFB2 were mutated with photoactivable unnatural amino acid p-benzoyl L- phenylalanine (pBpa) and the proximity of TFB2 relative to DNA was determined by photochemical cross-linking experiments. The results showed that TFB2 interacts with DNA near the TATA box via its C-terminal domain, and interacts with both strands of DNA near the transcription start site via its divergent B-reader and the B-linker sequences. The B-reader loop region is close to transcription start site and interacts with the transcribed strand of promoter DNA while the B-linker strand cross-links with the non-transcribed strand. Some of the amino acids in between the B-reader loop and the B-linker strand region in TFB2 are seen to cross-link both the transcribed and the non-transcribed strand. Thus, despite the absence of strong homology to conserved B-reader and B-linker sequences, TFB2 is likely to interact with DNA in the transcription bubble and facilitate in transcription initiation.
27
Kelley, John Forad. "Expanding Metabolic Diversity of Two Archaeal Phyla: Nanoarchaeota and Korarchaeota". PDXScholar, 2017. https://pdxscholar.library.pdx.edu/open_access_etds/3835.
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Culture independent studies have revealed a greater diversity of Archaea than the two kingdoms initially defined by Carl Woese. Culturing species from the newly discovered archaeal lineages, as with the majority of microbes, has been difficult. To overcome the culturing dilemma, metagenomics is being used to reconstruct environmental genomes. Two metagenomic studies are presented in this thesis, with the aim of recovering newly proposed archaeal genomes from the Nanoarchaeota and Korarchaeota.
In the first study, a sediment sample, NZ13, was collected from a terrestrial New Zealand hot spring. Along with the sediment sample, two complex enrichments were sequenced on an Illumina MiSeq platform. Assembly and differential binning recovered two nearly complete genomes of a nanoarchaeote and a korarchaeote. The NZ13 nanoarchaeote is similar to other terrestrial nanoarchaeotes, which lack an ATP synthase and encode genes for glycolysis/gluconeogenesis and archaella. One notable difference is the NZ13 nanoarchaeote contains CRISPR genes, which are absent in other terrestrial nanoarchaeotes, although present in a marine nanoarchaeote, Nanoarchaeum equitans. The NZ13 korarchaeote mirrors Candidatus Korarchaeum cryptofilum, lacking genes for de novo synthesis of purines and several cofactors, while containing an abundance of peptide transporters and amino acid fermentation pathways.
The second study focused on sulfide samples collected from deep-sea hydrothermal vent fields in southwestern Pacific Ocean along the Eastern Lau Spreading Center. Ten sulfide samples were sequenced on an Illumina HiSeq platform. Small subunit ribosomal RNA genes were extracted from the metagenome reads and aligned against the SILVA Ref NR 99 123 database. The preliminary results identified which samples could be prioritized for genome reconstruction of uncultured bacterial and archaeal lineages. Three uncultured bacteria, candidate division SR1, Gracilibacteria (GN02), and Parcubacteria (OD1) were identified in several samples. Many uncultured deep-sea hydrothermal archaeal lineages were identified in all samples. In particular, korarchaeotal sequences were in high relative archaeal abundances in two samples, ABE 1 and Vai Lili-2, while few nanoarchaeotal reads were classified.
28
Sheffield, Kimberly Kay. "Interplay of Transcription Factor E and Spt4/5 During Transcription Initiation in Pyrococcus furiosus". PDXScholar, 2018. https://pdxscholar.library.pdx.edu/open_access_etds/4444.
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Transcription, the first step in gene expression, is a highly regulated process which relies on a multi-protein complex to occur. Among these proteins are transcription factors, including initiation and elongation factors, which play differing roles in early and late stages of transcription. The mechanisms of transition from transcription initiation to elongation are not well understood in archaea, nor are the structures of the transcription factors involved. For transcription to occur in vitro, transcription factors TATA binding protein (TBP) and Transcription Factor B (TFB) are sufficient to allow RNA polymerase (RNAP) to synthesize RNA from template DNA. Another factor, Transcription Factor E (TFE), can also join the initiation complex and is likely to be essential in vivo. TFE is known to contribute to initiation by enhancing promoter opening, and while it has been shown to persist in elongation complexes, its role after initiation is unknown. Spt4/5, the archaeal homolog of the only universally conserved RNAP-associated factor, is known to join complexes in elongation steps and enhance processivity of the polymerase. However, if Spt4/5 joins pre-initiated complexes, it has been shown to inhibit transcription activity. The experiments in this thesis show that TFE and Spt4/5 participate in a crucial interchange at the upstream fork of the transcription bubble that helps define the timing of Spt4/5 binding. Using unnatural amino acid crosslinking techniques, the points of proximity between specific regions of these two factors and the template DNA have been mapped to identify possible sites of interaction. Competitive crosslinking assays indicate the exact timing of the shift in affinity between TFE and Spt4/5 for their shared binding site on RNAP. These data, combined with transcription assays, suggest a new role for TFE in preventing premature Spt4/5 binding, corresponding with a unique localized mobility within the winged helix of TFE.
29
Mackay, Dale Tara. "Characterisation of Sulfolobus solfataricus Ard1, a promiscuous N-acetyltransferase". Thesis, St Andrews, 2008. http://hdl.handle.net/10023/468.
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30
Arp, Jennifer Rebecca. "Quantification of marine archaea in the Cape Fear River Estuary in southeastern North Carolina using fluorescence in situ hybridization /". Electronic version (PDF), 2003. http://dl.uncw.edu/etd/2003/arpj/jenniferarp.html.
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31
Iverson, Eric Alexander. "A Genetic and Biochemical Analysis of Sulfolobus Spindle-Shaped Virus 1". PDXScholar, 2015. https://pdxscholar.library.pdx.edu/open_access_etds/2641.
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Viruses infecting the Archaea exhibit a tremendous amount of morphological and genetic diversity. This is especially true for crenarchaeal viruses from the family Fuselloviridae, which possess spindle-shaped capsids and genomes that harbor a great number of uncharacterized genes. The functions of these unidentified gene products are of interest as they have the potential to provide valuable insights into the fusellovirus infection cycle and archaeal viruses in general. In an effort to better characterize the genetic requirements of the Fuselloviridae, we have performed genetic and biochemical experiments using the best studied fusellovirus, Sulfolobus spindle-shaped virus 1 (SSV1).
A comprehensive genetic analysis of SSV1 was conducted using long inverse PCR and transposon mutagenesis. The results of this work illustrate that SSV1 is highly tolerant of mutagenesis. A robust protocol for the purification of recombinant VP2 protein from E. coli was developed and should be useful for future studies aimed at characterizing the biochemical and structural characteristics of this SSV1 structural protein. Finally, the first insights into a fusellovirus infection are presented and provide the framework for a detailed characterization of the fusellovirus infection cycle. The results and significance of this work are presented in the chapters that follow.
32
Goodman, David Andrew. "Comparative Genetic and Genomic Analysis of the Novel Fusellovirus Sulfolobus Spindle-shaped Virus 10". PDXScholar, 2018. https://pdxscholar.library.pdx.edu/open_access_etds/4496.
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Viruses that infect thermophilic Archaea are unique in both their structure and genetic makeup. The lemon-shaped fuselloviruses - which infect members of the order Sulfolobales, growing optimally at 80º C and pH 3 - are some of the most ubiquitous and best studied viruses of the thermoacidophilic Archaea. They provide a malleable and useful genetic tool for probing into the functions of their host, as well as the host responses to infection. Nonetheless, much about these viruses remains to be learned to further understand their morphological, genetic, and life cycle characteristics.
In order to investigate these aspects of these Fuselloviridae, as well as their evolution, this work reports the isolation and characterization of a novel fusellovirus, Sulfolobus Spindle-shaped virus 10 (formerly SSV-L1). Genetic and genomic analyses highlight significant homology with both SSV8 and SSV9, as well as conservation of promoter elements within the Fuselloviridae. SSV10 encodes five ORFs with no homology within or outside of the Fuselloviridae, as well as a putatively functional Cas4-like ORF which may play a role in anti-CRISPR host evasion. Moreover, we demonstrate the ability of SSV10 to withstand mutation in a fashion consistent with mutagenesis in SSV1. Lastly, analysis of predicted protein structures from SSV10 provide new insights into virus-host interactions. These analyses help to expand our understanding of the viral life cycle while contextualizing the mutagenesis data presented in the following chapters.
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Janzen, Timothy William y University of Lethbridge Faculty of Arts and Science. "Subunit interactions within box C/D sRNPs". Thesis, Lethbridge, Alta. : University of Lethbridge, Dept. of Chemistry and Biochemistry, c2010, 2010. http://hdl.handle.net/10133/2547.
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Box C/D small ribonucleoproteins (box C/D sRNPs) are responsible for the 2’-O-methylation required for the complete maturation of precursor rRNA. Archaeal box C/D sRNPs, like eucarya, are composed of four components: a guide RNA (box C/D sRNA), an RNA binding protein (L7ae), a 2’-O-methyltransferase (Fibrillarin) and a structural protein (Nop5). Here we develop several approaches for studying box C/D sRNP assembly. In particular, we have used pulldown and mobility shift assays to identify box C/D sRNP assembly intermediates (Nop5-aFib and L7ae-sR1). We have also demonstrated that isothermal titration calorimetry (ITC) can be utilized to quantitatively characterize the energetics of formation for the L7ae-sRNA assembly intermediate.xi, 98 leaves : ill. (some col.) ; 29 cm
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Burke, Paula Louise y University of Lethbridge Faculty of Arts and Science. "The oligomeric state of archaeal fibrillarin : implications in the organization and function of essential box C/D sRNP particles". Thesis, Lethbridge, Alta. : University of Lethbridge, Faculty of Arts and Science, 2006, 2006. http://hdl.handle.net/10133/540.
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Several vital cellular processes are preformed by large ribonucleoprotein (RNP)
complexes. In archaeal and eukaryotic cells one example of these essential RNP particles
is the box C/D sRNP. In archaea, this complex is responsible for methylation of
ribosomal RNA (rRNA) and transfer RNA (tRNA) during their maturation. Archaeal
fibrillarin (aFib) is the 2'-O methyltransferase responsible for catalysis by this complex.
In this work we have identified the ability of aFib from Sulfolobus acidocaldarius to
form dimers at biologically relevant concentrations and the structural determinants
essential for this association. Based on our model we have predicted the ability of aFibs
to form dimers in different archaeal and eukaryotic species. The ability of aFibs and their
eukaryotic homologs to potentially adopt multiple conformations provides insight into
the dynamics of the box C/D sRNP complex. As observed in the study of other essential
RNP particles, the ability of these complexes to be conformationally diverse is integral to
efficient catalysis of their varied substrates.viii, 74 leaves ; 29 cm.
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Leng, Jie. "Purification and characterization of a protein phosphatase (PP1-Arch) from the archaebacterium Sulfolobus solfataricus, isolation and expression of its gene". Diss., Virginia Tech, 1994. http://hdl.handle.net/10919/39141.
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PP1-Arch was verified as a protein phosphatase by both acid molybdate extraction and thin layer electrophoresis. Soluble fraction was prepared from Sulfolobus solfataricus, from which PP1-Arch was purified over 1OOO-fold by DE-52 ion-exchange, hydroxyapatite, gel filtration (G- 100), and Mono Q FPLC chromatography. PP1-Arch was identified from the final purified sample by renaturation on an SDS-polyacrylamide gel. The molecular size of PP1-Arch was determined by both gel filtration chromatography and SDS-PAGE as 28 kDa and 33 kDa, respectively, which suggests that PP1-Arch is a monomer. PP1-Arch was found stable at temperatures as high as 90°C. Activation constants for the divalent metal ions Mn²⁺ and Ni²⁺, and the Km for phosphocasein were determined. Myosin light chain was found to be a substrate for PP1-Arch in vitro. EDTA, Cu²⁺, Zn²⁺, Pi' and PPi were shown to be inhibitors of PP1-Arch, while many compounds known to affect eukaryotic protein phosphatase activities were found to be without noticeable effect.
N-terminal and an internal peptide sequence of the enzyme were obtained. The gene for PP1-Arch was cloned by a combination of "touchdown" PCR and conventional cloning techniques. The PP1-Arch gene was sequenced on both strands, and the sequence was compared with ones from eukaryotes and bacteriophage λ. The sequence homology between PP1-Arch and PP1/PP2A/PP2B suggests that they belongs to the same genetic family.
A recombinant plasmid which was derived from pT7-7 was constructed for expression of PP1-Arch. The PP1-Arch gene was expressed in E. coli and the activity of the expressed enzyme was tested and shown to be divalent metal ion-dependent. Formation of inclusion bodies of expressed PP1-Arch was demonstrated.Ph. D.
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Holden, James Francis. "Ecology, diversity, and temperature-pressure adaptation of the deep-sea hyperthermophilic Archaea Thermococcales /". Thesis, Connect to this title online; UW restricted, 1996. http://hdl.handle.net/1773/11044.
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Xie, Yunwei. "Nucleosomes, transcription and transcription regulation in Archaea". Connect to resource, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1127830717.
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Thesis (Ph. D.)--Ohio State University, 2005.Title from first page of PDF file. Document formatted into pages; contains xiv, 200 p.; also includes graphics (some col.). Includes bibliographical references (p. 167-197). Available online via OhioLINK's ETD Center
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Wu, Ming-Hsiao. "Temperature Dependent Transcription Initiation in Archaea: Interplay between Transcription Factor B and Promoter Sequence". PDXScholar, 2014. https://pdxscholar.library.pdx.edu/open_access_etds/2021.
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In Pyrococcus furiosus (Pfu), a hyperthermophile archaeon, two transcription factor Bs, TFB1 and TFB2 are encoded in the genomic DNA. TFB1 is the primary TFB in Pfu, and is homologous to transcription factor IIB (TFIIB) in eukaryotes. TFB2 is proposed to be a secondary TFB that is compared to TFB1, TFB2 lacks the conserved B-finger / B-reader / B-linker regions which assist RNA polymerase in transcription start site selection and promoter opening functions respectively. P. furiosus, like all Archaea, encodes a single transcription factor E (TFE), that is homologous to the N-terminus of transcription factor II E (TFIIE) α subunit in eukaryotes. TFE stabilizes the transcription bubble when present, although it is not required for in vitro transcription. In this study, in vitro transcription is used to reveal how TFB2 responds to different temperature (65 °C, 70 °C, 75 °C, 80 °C, and 85 °C) at promoters for three different kinds of gene: non-temperature responsive, heat-shock induced, and cold-shock induced in the absence or presence of TFE. The activity of transcription complexes formed by TFB2 is always lower than by TFB1 in all temperatures and promoters. However, with heat-shock gene promoters, the activity of transcription complexes formed by TFB2 increases more than those formed with TFB1 with increasing temperatures. The temperature-dependent activities of TFB1 and TFB2 are similar with the non-temperature responsive gene promoter. With the cold-shock gene promoter, the activity of transcription complexes formed by both TFB1 and TFB2 has the highest activity in lower temperatures. When TFE is present, the activity of transcription complexes formed by TFB2 is enhanced with heat-shock gene promoters particularly at lower temperatures, and makes TFB2 behave more similarly to TFB1. With the non-temperature responsive gene promoter, TFB2 still behaves similarly to TFB1 when TFE is present. However, with the cold-shock gene promoter, most of the activity of transcription complexes formed by TFB1 and TFB2 remain the same, but only the activity of TFB1 decreases at 75 °C. The results suggest that TFB2 may play a role in heat-shock response through its increased sensitivity to temperature, and that TFE can modulate this temperature response.
39
Kreel, Nathaniel Edward. "Examination of Mutants that Alter Oxygen Sensitivity and CO2/O2 Substrate Specificity of the Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) from Archaeoglobus fulgidus". Columbus, Ohio : Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1204513403.
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Rutherford, Alexander Fenner. "Abundance and Distribution of Major and Understudied Archaeal Lineages at Globally Distributed Deep-Sea Hydrothermal Vents". PDXScholar, 2014. https://pdxscholar.library.pdx.edu/open_access_etds/1555.
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Deep-sea hydrothermal vents are some of the most biologically productive ecosystems on Earth, yet receive little to no input of photosynthetically derived organic matter. The trophic system at hydrothermal vents is based primarily on the reduction-oxidation (redox) of inorganic chemicals by Bacteria and Archaea. However, the distributional patterns of the microorganisms that colonize deep-sea hydrothermal vent deposits and their link to the geologic setting are still not deeply understood.
The goal of the studies presented in this thesis was to quantify the abundance, and distribution of major and understudied vent colonizing archaeal groups from globally distributed and geochemically distinct hydrothermal vent fields. The archaeal community composition was analyzed using quantitative PCR with lineage specific functional gene primers that target methanogens, and 16S rRNA gene primers designed or optimized from this study for the Thermococcales, Archaeoglobus, Ignicoccus and marine Nanoarchaeota.
Overall, a general relationship was demonstrated between the geochemical differences of the hydrothermal vent fields and the archaeal community structure. The archaeal community assemblage varied dramatically from hydrothermal vents with different vent host rocks along the Mid-Atlantic Ridge and Eastern Lau Spreading Center. In contrast, two vent fields in the East Pacific, 9°N on the EPR and Guaymas Basin that are basalt and basalt-sediment hosted were found to have similar community composition. These observed differences may be driven in part by the metabolically available chemical energy as hydrogen oxidizing lineages of the methanogens and Archaeoglobus were found in higher abundance in the samples from vent field that had a high concentration of end-member hydrogen and the heterotrophic Thermococcales constituted a higher proportion of the archaeal community at the less enriched vent fields. Interestingly, the Nanoarchaeota and the genus of its only confirmed symbiont, Ignicoccus, were found to have an inconsistent proportional relationship, with the Nanoarchaeota comprising a larger proportion of the archaeal community at the ultramafic and fast spreading basalt vent fields and Ignicoccus at the ultra-slow spreading basalt and andesite hosted vent fields.
There was also a more localized pattern identified within the hydrothermal vent deposit. The chemosynthetic lineages of the methanogens and Archaeoglobus constituted a higher proportion of the archaeal community in chimney samples compared to Thermococcales that was found in a higher proportion at horizontal flange samples. This archaeal proportional shift could be driven by energetic micro-niches within the vent deposit, as the chemolithotrophic lineages colonize the area closest to the venting source, and the heterotrophic Thermococcales dominate in more mature structures further from the venting source.
Quantitative assessments of the archaeal community composition from this study provided added insight into the dynamic geologic influence on the archaeal lineages that colonize deep-sea hydrothermal vents, on a global and local scale.
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Rudolf, Jana. "Characterisation of XPD from Sulfolobus acidocaldarius : an iron-sulphur cluster containing DNA repair helicase". Thesis, St Andrews, 2007. http://hdl.handle.net/10023/159.
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Cao, Huiluo y 曹慧荦. "Molecular ecology of ammonia oxidizing archaea and bacteria". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B47155358.
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The newly recognized ammonia-oxidizing archaea (AOA) makes re-evaluation of the contribution to ammonia oxidization by both AOA and ammonia-oxidizing bacteria (AOB) necessary and meaningful. The growing population and increasing anthropogenic activities around coastlines have affected wetland and coastal marine ecosystems through discharging polluted water containing large amounts of reactive inorganic nitrogen. The objectives of this study were to detect the phylogenetic diversity and abundance of ammonia oxidizers including AOA and AOB on different scales and to elucidate the distribution patterns along an anthropogenic pollution gradient from the coastal wetland of the Mai Po Nature Reserve in Hong Kong to the South China Sea (SCS).
Generally, besides lineages shared by similar environments, various endemic lineages were also observed in the polluted mangrove sediments of Hong Kong, and in the coastal, and deep-sea surface and subsurface sediments from the SCS indicating their geographical distance should be responsible for these phylogenetic distinctions. The community structures of AOA and AOB observed were proposed to be associated with environmental parameters including metals and total phosphorus (TP) separately in the sediments while their abundance was correlated with the pH value and temperature. On the other hand, along a profile of surface sediments with stable salinity from the coastal margin to the slope in the SCS, a clear community structure transition was detected for both AOA and AOB, showing major differences in each of their responses. Although the abundance of AOA was lower than that of AOB in the subsurface sediment samples from the SCS, the statistical support for relationships between AOA and nitrite concentration shed new light on the active contributor to the subsurface nitrogen cycle in the oxygen minimum zone from the deep-sea sediments.
On a large scale, along the anthropogenic pollution gradient from the Pearl River Delta to the coastal margin and then the SCS, the dominant genus transition from Nitrosomonas to Nitrosospira was detected in response to the salinity and anthropogenic influences. Among a wide spectrum of environmental conditions in the western Pacific, a suite of statistical analyses clearly delineated the shallow and deep-sea sediments clusters suggesting that the depth and other contributing environmental factors involved shape the current distribution pattern of AOA. On a global scale, our understanding about the systematics and evolution of AOA was advanced through phylogenetic analyses. Salinity, lifestyle and temperature were proposed to be responsible for the global distribution patterns of AOA. On the basis of studies in the anthropogenic influence areas, the methods to detect specific responses of ammonia oxidizers to known anthropogenic pollution were concluded.
Highlights of this study advance not only our understandings about phylogenetic diversity of ammonia oxidizers and the driving forces shaping their community structure and distribution patterns, but also a revised comprehensive view about them on the larger scale.published_or_final_version
Biological Sciences
Doctoral
Doctor of Philosophy
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McRobbie, Anne-Marie M. "Splitting, joining and cutting : mechanistic studies of enzymes that manipulate DNA". Thesis, University of St Andrews, 2010. http://hdl.handle.net/10023/951.
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DNA is a reactive and dynamic molecule that is continually damaged by both exogenous and endogenous agents. Various DNA repair pathways have evolved to ensure the faithful replication of the genome. One such pathway, nucleotide excision repair (NER), involves the concerted action of several proteins to repair helix-distorting lesions that arise following exposure to UV light. Mutation of NER proteins is associated with several genetic diseases, including xeroderma pigmentosum that can arise upon mutation of the DNA helicase, XPD. The consequences of introducing human mutations into the gene encoding XPD from Sulfolobus acidocaldarius (SacXPD) were investigated to shed light on the molecular basis of XPD-related diseases. XPD is a 5’-3’ DNA helicase that requires an iron-sulphur (FeS) cluster for activity (Rudolf et al., 2006). Several proteins related to SacXPD, including human XPD, human FancJ and E. coli DinG, also rely on an FeS cluster for DNA unwinding (Rudolf et al., 2006; Pugh et al., 2008; Ren et al., 2009). Sequence analysis of the homologous protein, DinG, from Staphylococcus aureus (SarDinG) suggests that this protein does not encode a FeS cluster. In addition, SarDinG comprises an N-terminal extension with homology to the epsilon domain of polymerase III from E. coli. This thesis describes the purification and characterisation of SarDinG. During replication, DNA lesions or other ‘roadblocks’, such as DNA-bound proteins, can lead to replication fork stalling or collapse. To maintain genomic integrity, the fork must be restored and replication restarted. In archaea, the DNA helicase Hel308 is thought to play a role in this process by removing the lagging strands of stalled forks, thereby promoting fork repair by homologous recombination. Potential roles of Hel308 during replication fork repair are discussed in this thesis. The mechanism by which Hel308 moves along and unwinds DNA was also investigated using a combined structural and biophysical approach. The exchange of DNA between homologous strands, catalysed by a RecA family protein (RecA in bacteria, RAD51 in eukaryotes, and RadA in archaea), defines homologous recombination. While bacteria encode a single RecA protein, both eukaryotes and archaea encode multiple paralogues that have implications in the regulation of RAD51 and RadA activity, respectively. This thesis describes the purification and characterisation of one of the RadA paralogues (Sso2452) in archaea.
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Lundgren, Magnus. "Exploring the Cell Cycle of Archaea". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7848.
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St, John Emily Joyce. "Symbiosis in Archaea: Functional and Phylogenetic Diversity of Marine and Terrestrial Nanoarchaeota and their Hosts". PDXScholar, 2019. https://pdxscholar.library.pdx.edu/open_access_etds/4939.
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The Nanoarchaeota are an enigmatic lineage of Archaea found in deep-sea hydrothermal vents and geothermal springs across the globe. These small (~100-400 nm) hyperthermophiles live ectosymbiotically with diverse hosts from the Crenarchaeota. Despite their broad distribution in high-temperature environments, very few Nanoarchaeota have been successfully isolated in co-culture with their hosts and nanoarchaeote genomes are poorly represented in public databases. However, the Nanoarchaeota provide unique insights into the structure and function of symbiosis in the archaeal domain. This study describes novel nanoarchaeotes from multiple geothermal habitats, using a combination of direct cultivation techniques and genomic analysis. A new nanoarchaeote from a New Zealand hot spring, Candidatus Nanoclepta minutus, was isolated in co-culture with its host. Like other terrestrial Nanoarchaeota, Cand. Ncl. minutus harbors genes for gluconeogenesis and archaeal flagella. Zestosphaera tikiterensis, the New Zealand host, was also isolated in pure culture and characterized. Phylogenetic analysis showed that both Cand. Ncl. minutus and Z. tikiterensis are new genera in the Nanoarchaeota and Crenarchaeota, respectively. Metagenome-assembled genomes (MAGs) from the Nanoarchaeota were also recovered from deep-sea hydrothermal vent sites. These MAGs capture a wide range of diversity in the Nanoarchaeota, representing three new species and two novel genera. Key nanoarchaeotal features were identified in the MAGs, including marker genes for archaeal flagella, gluconeogenesis and CRISPR-Cas regions. These studies greatly contribute to our understanding of nanoarchaeotal ecophysiology and provide key insights into the coding potential and diversity of Nanoarchaeota and their hosts.
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Longstaff, David Gordon. "Requirements and rationale for amber translation as pyrrolysine". Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1196107921.
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Shimmin, Lawrence Charles. "An archaebacterial ribosomal protein gene cluster". Thesis, University of British Columbia, 1990. http://hdl.handle.net/2429/30994.
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The eubacteria, archaebacteria and eucaryota evolved from a common ancestral state, the progenote, approximately 4,000 million years ago. The archaebacteria flourish in extreme environments, exhibiting unusual macromolecular structures and metabolism of which much has recently been elucidated. Less, however, is known of the genetics of archaebacteria. In order to investigate gene structure, organization, regulation and evolution in the archaebacteria a gene cluster encoding the ribosomal proteins of the GTPase domain was cloned from the extremely halophilic archaebacterium Halobacterium cutirubrum, characterized and compared with the homologous genes and proteins from eubacteria and eucaryota.
A clone containing a 5146 basepair insert of genomic Halobacterium cutirubrum NRCC 34001 DNA encoding the GTPase domain ribosomal proteins was characterized and discovered to retain the identical gene order (i.e. L11e, Lie, L10e and L12e) as the homologous Escherichia coli genes and in addition two transcribed upstream open reading frames encoding the potential proteins ORF, of unknown function and NAB, bearing sequence similarity to nucleic acid binding proteins.
The predominant transcripts are monocistronic L11e and tricistronic Lie - L10e - L12e transcripts; monocistronic NAB and bicistronic NAB - L11e transcripts are present at reduced levels and the ORF is present as a very rare transcript. Common elements upstream of the transcription initiation sites include the motif TTCGA ... 4-15 bp ... TTAA ... 20-26 bp ... A or G transcription start. The NAB and some of the ORF transcripts are divergently transcribed from a single TTAA promotor element. The NAB and some of the ORF transcripts initiate 1 nucleotide before the coding region; the L11e monocistronic transcript initiates precisely at the first A of the initiator methionine ATG codon. The Lie - L10e - L12e tricistronic transcript has a 75 nucleotide leader that is probably involved in the autogenous regulation of the transcript at the translational level by the Lie protein. Termination of transcription occurs, with a single exception, within T tracts after GC rich regions. Although classic Shine-Dalgarno (eubacterial) type ribosome binding sites are present upstream of the Lie and L10e genes, the mechanism of translation initiation for transcripts with nil or negligible 5' leaders remains to be elucidated.
Alignments between the deduced amino acid sequences of the L1le, Lie, Ll0e and L12eribosomal proteins and other available homologous proteins of archaebacteria, eubacteria and eucaryota have been made and show that the L11e, Lie and L10e proteins are colinear whereas the L12e protein has suffered a rearrangement through what appears to be gene fusion events. The L11e proteins exhibit (i) sequence conservation in the region interacting with release factor 1, (ii) conserved proline residues (probably contributing to the elongated shape of the molecule) and (iii) sites of methylation in Eco L11 are not conserved in the archaebacterial L11e proteins. The Lie proteins have regions of very high sequence similarity near the center and carboxy termini of the proteins but the relationships between protein structure and function remain unknown. Intraspecies comparisons between L10e and L12e sequences indicate the archaebacterial and eucaryotic L10e proteins contain a partial copy of the L12e protein fused to their carboxy terminus. In the eubacteria most of this fusion has been removed by a carboxy terminal deletion. Within the L12e derived region a 26 amino acid long internal modular sequence reiterated thrice in the archaebacterial L10e, twice in the eucaryotic L10e and once in the eubacterial L10e was discovered. This modular sequence also appears to be present in single copy in all Ll2e proteins and may play a role in L12e dimerization, L10e - L12e complex formation and the function of L10e - L12e complex in translation. From these sequence comparisons a model depicting the evolutionary progression gene cluster and proteins from the primordial state to the contemporary archaebacterial, eucaryotic and eubacterial states is presented.Medicine, Faculty of
Biochemistry and Molecular Biology, Department of
Graduate
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Herbold, Craig William. "Ribosomal mosaicism in the archaebacterial eocytes". Diss., Restricted to subscribing institutions, 2009. http://proquest.umi.com/pqdweb?did=1930912501&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.
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Pulukkunat, Dileep K. "Biochemical studies on archaeal ribonuclease P reveal thematic convergence in protein-facilitated RNA catalysis". Columbus, Ohio : Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1206094060.
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HAMAL, ABDELLAH. "Etude des adn polymerases chez les archaebacteries". Paris 11, 1991. http://www.theses.fr/1991PA112195.
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Une adn polymerase thermophile a ete purifiee a homogeneite chez l'archaebacterie thermoplasma acidophilum. L'analyse de l'adn polymerase purifiee sur gel de polyacrylamide en conditions denaturantes revele qu'elle correspond a polypeptide de 588 kda qui co-sedimente avec l'activite adn polymerase sur gradient de saccharose. La combinaison de la sedimentation et du gel filtration ont permis de conclure que l'adn polymerase purifiee est une enzyme monomerique constituee d'un unique polypeptide de 88 kda. Cette adn polymerase est resistante a l'aphidicoline, peu sensible au ddttp et inhibee par le nem lorsqu'elle est prealablement pre-incubee a haute temperature. L'adn polymerase purifiee chez t. Acidophilum possede une activite exonuclease 35 associee qui est stimulee en presence du manganese; les deux activites adn polymerase et exonuclease sont optimales a 65c mais l'activite exonuclease est beaucoup plus thermostable que l'activite adn polymerase. Par la suite, on a mis en evidence une activite exonuclease 35 manganese-dependante associee a l'adn polymerase purifiee chez s. Acidocaldarius. Ce resultat a ete confirme par la co-precipitation de l'activite exonuclease avec l'activite adn polymerase, et sa neutralisation par des anticorps anti-adn polymerase purifies. L'analyse des extraits bruts de differentes archaebacteries, par la technique d'immunotransfert, en presence d'anticorps prepares contre l'adn polymerase chez s. Acidocaldarius nous a permis de montrer qu'une adn polymerase apparentee a celle de s. Acidocaldarius existe chez d'autres archaebacteries. On a detecte d'autres activites adn polymerase dans differents extraits bruts d'archaebacteries; ces activites sont plus thermostables chez les hyperthermophiles que chez les sulfolobales. Enfin, dans l'extrait brut d'archaeglobus, l'activite adn polymerase est inhibee a 50% en presence de 100 m d'aphidicol