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Dissertations / Theses on the topic 'Archaeon'

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Published: 4 June 2021

Last updated: 20 February 2023

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1

Berger, Stefanie [Verfasser]. "Energy conservation in aceticlastic methanogenic archaea and the human gut archaeon Methanomassiliicoccus luminyensis / Stefanie Berger." Bonn : Universitäts- und Landesbibliothek Bonn, 2015. http://d-nb.info/1077290292/34.

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2

Lower, Brian Howard. "Protein O-Kinases in the Archaeon Sulfolobus solfataricus." Diss., Virginia Tech, 2001. http://hdl.handle.net/10919/28471.

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For many years, it has been understood that protein phosphorylation-dephosphorylation constitutes one of the most ubiquitous mechanisms for controlling the functional properties of proteins. Although originally believed to be a eukaryotic phenomenon, protein phosphorylation is now known to occur in all three domains of life Eukarya, Bacteria, and Archaea. Very little is known, however, concerning the origins and evolution of protein phosphorylation-dephosphorylation. Knowledge of the structure and properties of the protein kinases resident in the members of the Archaea represents a key piece of this puzzle. The extreme acidothermophilic archaeon, Sulfolobus solfataricus, exhibits a membrane-associated protein kinase activity. Solubilization of the kinase activity requires the presence of detergent such as Triton X-100 or octyl glucoside, indicating its activity reside in an integral membrane protein. This protein kinase utilizes purine nucleotides as phosphoryl donors in vitro with a requirement for a divalent metal ion cofactor, favoring Mn⁺². A preference for NTPs over NDPs and for adenyl nucleotides over the analogous guanyl nucleotides was observed. The enzyme appears to be a glycoprotein that displays catalytic activity on SDS-PAGE corresponding to a molecular mass of ≈67 kDa, as well as an apparent molecular mass of –125 kDa on a gel filtration column. Challenged with several exogenous substrates revealed the protein kinase to be relatively selective. Only casein, reduced carboxyamidomethylated and maleylated lysozyme (RCM lysozyme), histone H4 proved, and a peptide modeled after myosin light chains (KKRAARATSNVFA) were phosphorylated to appreciable levels in vitro. All of the aforementioned substrates were phosphorylated on threonine, while histone H4 was phosphorylated on serine as well. When the phosphoacceptor threonine in the MLC peptide was substituted with serine an appreciable decrease in phosphorylation was noted. The protein kinase underwent autophosphorylation on threonine and was relatively insensitive to several known "eukaryotic" protein kinase inhibitors. Primary sequence motifs based on known conserved subdomains of eukaryotic protein kinases were used to search the genome of S. solfataricus for eukaryotic-like protein kinase sequences. Six hypothetical proteins were identified from S. solfataricus whose primary sequence exhibited noticeable similarities to eukaryotic protein kinases. The hypothetical protein encoded by ORF sso0197 contained 7 putative subdomains, ORFs sso0433, sso2291, sso2387, and sso3207 contained 8 putative subdomains, and ORF sso3182, contained 9 putative subdomains of the 12 characteristically conserved subdomains found within eukaryotic protein kinases. ORF sso2387 was cloned and expressed in Escherichia coli. The expressed protein, SsPK2, was solubilized from inclusion bodies using 5 M urea. SsPK2 was able to phosphorylate casein, BSA, RCM lysozyme, and mixed histones in vitro. Phosphoamino acid analysis of casein, BSA, and mixed histones revealed that they were all phosphorylated on serine. SsPK2 underwent autophosphorylation on serine at elevated temperature using both purine nucleotide triphosphates as phosphoryl donors in vitro, but exhibited a noticeable preference for ATP. Autophosphorylate of SsPK2 also occurred at elevated temperature using a variety of divalent metals cofactors in order of Mn⁺² > Mg⁺² >> Ca²⁺ ≈ Zn⁺². Polycations such as polyLys stimulated the phosphorylation of exogenous substrates while polyanions such as poly(Glu:Tyr) were shown to inhibit the phosphorylation of exogenous substrates. Of the "eukaryotic" protein kinases inhibitors tested, only tamoxifen had any noticeable effect of the catalytic activity of SsPK2 towards itself and exogenous substrates. A truncated form of SsPK2 containing the perceived catalytic domain also exhibited protein kinase activity towards itself and exogenous substrates. The observed protein kinase activity for SsPK2trunk was similar to that observed for SsPK2. Proteins from the membrane fraction of S. solfataricus subject to phosphorylation in vitro on serine or threonine residues were identified using MALDI-MS / peptide fingerprinting techniques. Nine phosphoproteins were assigned a tentative identification using the ProFound protein search engine from Rockefeller University. The identity of two of nine phosphoproteins, a translational endoplasmic reticulum ATPase and an ≈ 42 kDa hypothetical protein, were determined with a relatively high degree of confidence. Collectively the results suggested MALDI-MS peptide mapping coupled with [³²P] labeling in vivo will have a tremendous potential for mapping out a major portion of the phosphoproteome of S. solfataricus.
Ph. D.

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3

Cong, Xinyu. "Genetic stability in the hyperthermophilic archaeon Sulfolobus acidocaldarius." University of Cincinnati / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1439309763.

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4

Maddocks, Deborah G. "Citrate synthase from the halophilic archaeon Haloferax volcanii." Thesis, University of Bath, 1999. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301966.

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5

Muir, Jacqueline M. "Citrate synthase from the hyperthermophilic archaeon, Pyrococcus furiosus." Thesis, University of Bath, 1995. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.260247.

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6

Heyer, Narinder Isabel. "Glucose dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus." Thesis, University of Bath, 1999. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301967.

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7

Daifuku, Takashi. "Genomic analysis of the marine hyperthermophilic archaeon Aeropyrum." Kyoto University, 2015. http://hdl.handle.net/2433/199358.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第19034号
農博第2112号
新制||農||1031(附属図書館)
学位論文||H27||N4916(農学部図書室)
31985
京都大学大学院農学研究科応用生物科学専攻
(主査)教授左子芳彦, 教授澤山茂樹, 准教授吉田天士
学位規則第4条第1項該当

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8

Kessler, Peter S. "Nitrogen fixation in the mesophilic marine archaeon Methanococcus maripaludis /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/11520.

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9

Kydd, Catriona L. "A novel aldolase from the hyperthermophilic archaeon Sulfolobus solfataricus." Thesis, University of Bath, 1999. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.311181.

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10

Qu, Qiuhao. "Sugar metabolism and regulation in the hyperthermophilic archaeon Thermococcus litoralis." Konstanz, 2004. http://www.ub.uni-konstanz.de/kops/volltexte/2004/1409/index.html.

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11

Martusewitsch, Erika. "Differentielle Genexpression in dem hyperthermophilen Archaeon Sulfolobus solfataricus nach Hitzeschock." Phd thesis, [S.l. : s.n.], 2004. http://elib.tu-darmstadt.de/diss/000484.

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12

Auxilio, Maria. "Non-protein coding RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus." Thesis, University of British Columbia, 2006. http://hdl.handle.net/2429/31192.

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The archaeal L7Ae protein is an integral component of three functionally distinct macromolecular ribonucleoprotein complexes: the 50S large ribosomal subunit, the C/D box modification particles and the H/ACA box particles To better understand the function of the L7Ae protein and to investigate the diversity of RNAs specifically associated with this protein, immuno-affinity chromatography was used to isolate the sRNAs associated with L7Ae and RT-PCR was employed to construct a cDNA library. The isolated sRNAs were divided in different groups based on the presence of common known sequence and structural motifs and/or genomic location. Group one contained six RNAs that exhibited the, features characteristic of the canonical C/D box archaeal sRNAs and one RNA representative of the archaeal H/ACA sRNA family. Group two contained fourteen sequences that were encoded either within, or overlapping the 5' end or 3' end of ORFs mostly coding for transposases. Interestingly, one of the clones in this group corresponded to the 5'-untranslated region (UTR) of L7Ae mRNA, indicating that L7Ae protein is able to interact with its own mRNA. The relevance of this interaction for the expression of L7Ae protein was further analyzed using a S. solfataricus in vitro translation system. Group three contained three sequences form intergenic regions. Group four contained five antisense sequences complementary to the 5' end, 3' end or internal regions within annotated open-reading frames (ORFs) and two sequences antisense to bona-fide C/D box sRNAs. Group five contained two sequences corresponding to internal regions of 7S RNA of the signal recognition particle (SRP). Additionally, in the aim to better understand the versatility of L7Ae in the interaction with various sRNA substrates, we introduced mutations in a model C/D box sRNA and monitored the impact of mutation on the protein binding ability and on the methylation function of the sRNA. My data suggest that L7Ae protein might have an important regulatory role in archaeal cells, serving as a primary RNA-binding factor in various complexes with distinct function. In addition, the results obtained in this study set the stage to further characterize all the sequences identified in this screening and to elucidate their function.
Medicine, Faculty of
Biochemistry and Molecular Biology, Department of
Graduate

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13

Singleton, Martin Robert. "Studies on pyrrolidone carboxyl peptidase from the archaeon Thermococcus litoralis." Thesis, University of Exeter, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.245927.

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14

Sakofsky, Cynthia J. "Mechanisms Of Genome Stability In The Hyperthermophilic Archaeon Sulfolobus acidocaldarius." University of Cincinnati / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1321370182.

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15

Nakatani, Masaru. "Studies on a thermostable DNA ligase from a hyperthermophilic archaeon." 京都大学 (Kyoto University), 2003. http://hdl.handle.net/2433/148883.

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16

James, Keith D. "Cloning of citrate synthase from the halophilic archaeon Haloferax volcanii." Thesis, University of Bath, 1994. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.385349.

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17

Rossjohn, Jamie. "The crystal structure of glucose dehydrogenase from a thermophilic archaeon." Thesis, University of Bath, 1994. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.387316.

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18

Jolley, Keith A. "Studies of dihydrolipoamide dehydrogenase from the halophilic archaeon Haloferax volcanii." Thesis, University of Bath, 1996. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.321841.

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19

Wende, Andy. "Signaltransduktion durch Zwei-Komponenten-Systeme in dem halophilen Archaeon Halobacterium salinarum." Diss., [S.l.] : [s.n.], 2006. http://edoc.ub.uni-muenchen.de/archive/00005579.

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20

Maruyama, Hugo. "Analysis of the genome architecture of the hyperthermopholic archaeon Thermococcus kodakarensis." 京都大学 (Kyoto University), 2011. http://hdl.handle.net/2433/142451.

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21

Beattie, Thomas R. "The molecular biology of DNA replication in the archaeon Sulfolobus solfataricus." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:99d668a5-2d7a-4c7f-a1f8-b514e699347e.

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DNA replication is essential for the propagation of all living organisms. The ability of a cell to accurately duplicate its entire genome is dependent upon the activity of numerous proteins. Identifying the molecular mechanisms by which these proteins act, and determining how they are physically and functionally coordinated at sites of active DNA replication, is central to understanding this essential cellular process. Archaea possess a DNA replication machinery which is ancestral to the one present in eukaryotes, and thus these organisms serve as simplified model systems for understanding the complexities of eukaryotic DNA replication. This thesis investigates the molecular mechanisms underlying Okazaki fragment maturation in the crenarchaeon Sulfolobus solfataricus, which is essential to the completion of lagging strand DNA replication. Reconstitution of Okazaki fragment maturation in vitro demonstrated that the activities of three enzymes – PolB1, Fen1, and Lig1 – are required for this process in S. solfataricus. Furthermore, it was shown that optimum coordination of their three distinct activities is dependent on the ability of PolB1, Fen1 and Lig1 to simultaneously interact with a single PCNA ring, providing evidence for a mechanism of multi-enzyme coordination which may be universally employed by DNA sliding clamp proteins. The importance of protein flexibility in the accommodation of multiple proteins around a single PCNA was also investigated. Finally, the physical coordination of one of these key maturation enzymes – PolB1 – with other replisome proteins was examined. It was demonstrated that PolB1 exists in a trimeric complex in vivo with two previously unidentified factors, raising the possibility of uncharacterised activities and interactions for this crucial enzyme. Taken together, these data provide new insights into functionally important protein-protein interactions within the archaeal replisome, and facilitate a greater understanding of the DNA replication machinery in both archaea and eukaryotes.

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22

Gamble-Milner, Rebecca. "Genetic analysis of the Hel308 helicase in the archaeon Haloferax volcanii." Thesis, University of Nottingham, 2016. http://eprints.nottingham.ac.uk/37153/.

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Hel308 is a RecQ family DNA helicase that is conserved in metazoans and archaea but is absent from bacteria and fungi. Hel308 family helicases are implicated in DNA repair, homologous recombination and genome stability, but the exact role of Hel308 is largely unknown. Strains deleted for hel308 are sensitive to DNA inter-strand crosslinks, which are potent blocks to DNA replication. In this study, the archaeon Haloferax volcanii was used as a model organism to study the role of Hel308. In archaea, homologous recombination is catalysed by polymerisation of the RadA recombinase onto ssDNA; the mediator RadB assists this process. Strains deleted for radB exhibit decreased levels of recombination and an increased sensitivity to DNA damaging agents. In this study, strains deleted for hel308 in combination with radB exhibited in an improvement in both these phenotypes, suggesting that Hel308 acts as an anti-recombinase to antagonise RadA filament formation. Genetic analysis of point mutants in Hel308 revealed that that the helicase activity of Hel308 is separate to its role in the regulation of recombination, which appears to rely heavily on the correct structural conformation of Hel308. Analysis of these point mutations suggests that Hel308 may act in regulating the pathway choice for the resolution of homologous recombination intermediates. This study showed that H. volcanii contains a second Hel308 helicase named Hel308b, which lacks the ‘auto-inhibitory’ domain 5 found in canonical Hel308 helicases. Deletion of hel308b does not lead to sensitivity to DNA inter-strand crosslinks but does result in defects in homologous recombination.

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23

Mao, Dominic M. "Genetic fidelity and genome stability in the hyperthermophilic archaeon Sulfolobus acidocaldarius." University of Cincinnati / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1342103504.

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24

MacAuley, Sheridan Rose. "Expression of recombinant proteins in the methane-producing archaeon (Methanosarcina acetivorans)." College Park, Md. : University of Maryland, 2005. http://hdl.handle.net/1903/3285.

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Thesis (M.S.) -- University of Maryland, College Park, 2005.
Thesis research directed by: Marine, Estuarine, Environmental Sciences Graduate Program. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.

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25

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.

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26

Andersson, Anders. "Microarray-based investigation of genome and transcriptome organisation in the archaeon Sulfolobus /." Stockholm, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-142.

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27

Jackson, Brian Robert. "DNA repair pathways of the extremely acidophilic archaeon 'Ferroplasma acidarmanus' Fer 1." Thesis, University of East Anglia, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.445236.

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28

Giaquinto, Laura School of Biotechnology &amp 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.

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29

Mutowo, Prudence. "Thermodynamic characterization of DNA binding proteins from an extreme halophilic archaeon Haloferax volcanii." Thesis, University of Nottingham, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.478927.

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30

Srinivasan, Gayathri. "Translation of the amber codon in methylamine methyltransferase genes of a methanogenic archaeon." The Ohio State University, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=osu1072732858.

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31

Rahman, Raja Noor Zaliha Raja Abd. "Studies on enzymes for ammonium assimilation in hyperthermophilic archaeon Pyrococcus sp. strain KOD1." Kyoto University, 1998. http://hdl.handle.net/2433/182328.

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32

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).

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33

Angelov, Angel Stoyanov. "Genome sequence analysis and characterization of recombinant enzymes from the thermoacidophilic archaeon Picrophilus torridus." [S.l. : s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=974034916.

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34

Kasiviswanathan, Rajesh. "Structural and functional analysis of dna replication initiation proteins from the archaeon methanothermobacter thermautotrophicus." College Park, Md. : University of Maryland, 2005. http://hdl.handle.net/1903/3152.

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Thesis (Ph. D.) -- University of Maryland, College Park, 2005.
Thesis research directed by: Cell Biology & Molecular Genetics. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.

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35

Offermann, Stefanie. ""Shotgun-Kristallisation"- Strukturaufklärung eines Ferritins und einer Glyzerin-Dehydrogenase aus dem Archaeon H. salinarum." Diss., lmu, 2003. http://nbn-resolving.de/urn:nbn:de:bvb:19-9349.

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36

Ji, Mikyoung Lee. "Superoxide Reductase from the Hyperthermophilic Archaeon Pyrococcus furiosus: its Function, Regulation, and Biotechnological Applications." NCSU, 2007. http://www.lib.ncsu.edu/theses/available/etd-04172007-095920/.

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The anaerobic hyperthermophilic archaeon, Pyrococcus furious, possesses a system for the detoxification of reactive oxygen species, which is different from the classical defense mechanisms present in aerobes. P. furiosus employs a novel enzyme system centered on the enzyme superoxide reductase (SOR), which reduces superoxide molecules to hydrogen peroxide without producing oxygen. Surprisingly, P. furiosus SOR, unlike many P. furiosus enzymes, was shown to function at low temperature (<25o C). A model for superoxide reduction by SOR was proposed where the electrons used by SOR to reduce superoxide are supplied by a small iron containing protein, rubredoxin (Rd), and Rd is reduced by the oxidoreductase, NAD(P)H-rubredoxin oxidoreductase (NROR). The first objective of this study was to evaluate the validity of the proposed superoxide reduction pathway by using the recombinant SOR, Rd and NROR enzymes in an in vitro assay as well as to demonstrate in vivo function via complementation studies in superoxide detoxification deficient Escherichia coli strains. The second objective was to investigate the transcriptional expression levels of genes that are involved in the SOR-centered superoxide reduction pathway in order to determine how these genes are expressed and regulated in response to various oxidative stresses. The third objective was to evaluate the efficacy of the biotechnological application of this superoxide detoxification system by expressing SOR in plant cells, which enhanced their survival at high temperature and from drought indicating that it functions successfully in vivo. The fourth objective of this study was the characterization of glutathione reductase (GR) from a psychrophile, Colwellia psychrerythraea, which is stable at low temperatures and protects cells from free radicals by serving as a reductant. The C. psychrerythraea GR gene was cloned into an E. coli-based recombinant expression system. Recombinant C. psychrerythrae GR was expressed and purified. The recombinant GR showed significant activity at low temperature (4C). The P. furiosus superoxide reduction system genes and GR from C. psychrerythraea can be engineered into plants (Arabidopsis) to aid in combating damage caused by oxidative stress when plants undergo rapid changes in temperature, high light or UV exposure, or drought conditions.

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37

Duan, Zhenhong. "Genetic analysis of two structure-specific endonucleases Hef and Fen1 in archaeon Haloferax volcanii." Thesis, University of Nottingham, 2009. http://eprints.nottingham.ac.uk/10656/.

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Nucleotide excision repair (NER) is a versatile pathway of DNA repair that deals with a variety of DNA lesions, such as UV-induced DNA damage and interstrand crosslinks. In bacteria, the UvrABC system carries out NER. In human cells, XPF and XPG are two structure-specific endonucleases that act in NER. XPF is responsible for a 5' incision at the DNA lesion and XPG carries out the 3' incision. In Archaea, the third domain of life, most species have homologues of some eukaryal NER proteins. Interestingly, Haloferax volcanii encodes homologues of both the eukaryotic NER genes (XPF, XPG, XPB and XPD) and bacterial NER genes (uvrA, uvrB, uvrC and uvrD). In this study, the function of XPG, XPF and UvrA in H. volcanii is investigated. XPG is related to FEN1, a structure-specific 5' flap endonuclease that acts in Okazaki fragment maturation. H. volcanii has a single gene homologous to both XPG and FEN1. The helicase/nuclease hef gene in H. volcanii is the archaeal homologue of human XPF, but also shows homology to Mus81 and FANCM. Mus81 has been found to resolve joint molecules in yeast, while FANCM is required for the repair of interstrand crosslinks in vertebrates. The uvrA gene in H. volcanii is the archaeal homologue of bacterial uvrA, which encodes a protein that plays a vital role in NER at the DNA damage recognition step. This study demonstrates that in H. volcanii, UvrA is involved in the major pathway for repair of UV induced DNA damage. By contrast, Hef and UvrA are involved in two different pathways for the repair of mitomycin C induced DNA crosslinks. Fen1 and Hef have overlapping functions for the repair of DNA cross-links, but not oxidative damage. We also obtain a spontaneous suppressor sfnA, which can suppress the slow growth and MMC sensitivity, but not the UV sensitivity of fen1 deletion mutants. Using plasmid assays, it has been shown that the hef deletion mutant is deficient in accurate end-joining and homologous recombination, including both crossover and non-crossover recombination. In contrast, Fen1 has no significant role in accurate end-joining, but Fen1 may regulate the ratio of non-crossover recombination to crossover recombination.

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38

Shinka, Yasuhiro. "Studies on the Oxidative Stress and Heat Stress Response Systems in a Hyperthermophilic Archaeon." 京都大学 (Kyoto University), 2008. http://hdl.handle.net/2433/57284.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(工学)
甲第13852号
工博第2956号
新制||工||1436(附属図書館)
26068
UT51-2008-C768
京都大学大学院工学研究科合成・生物化学専攻
(主査)教授今中忠行, 教授青山安宏, 教授森泰生
学位規則第4条第1項該当

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39

Darcy, Trevor J. "In Vitro analysis of transcription from the Thermophilic Archaeon Methanobacterium Thermoautotrophicum strain (delta)H /." The Ohio State University, 1999. http://rave.ohiolink.edu/etdc/view?acc_num=osu1488192447430803.

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40

Nunoura, Takuro. "Study of Aerobic Respiratory Chain of Novel Facultative Aerobic and Hyperthermophilic Archaeon Pyrobaculum oguniense." Kyoto University, 2002. http://hdl.handle.net/2433/149916.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第9630号
農博第1258号
新制||農||844(附属図書館)
学位論文||H14||N3662(農学部図書室)
UT51-2002-G388
京都大学大学院農学研究科応用生物科学専攻
(主査)教授内田有恆, 教授加藤暢夫, 助教授左子芳彦
学位規則第4条第1項該当

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41

Imanaka, Hiroyuki. "Studies on enzymes involved in sugar metabolism in the hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1." 京都大学 (Kyoto University), 2003. http://hdl.handle.net/2433/148882.

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42

Bartlett, Edward J. "Structural and functional characterisation of the Nonhomologous End-Joining proteins of the archaeon Methanocella Paludicola." Thesis, University of Sussex, 2013. http://sro.sussex.ac.uk/id/eprint/47033/.

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Maintenance of the genome is essential for life to prosper. Regular insults to the genome are sustained by all cellular life and can foster genetic instability if left unrepaired. The most lethal genetic damage is a double strand break (DSB), the cleavage of the phosphate backbone on both strands of the DNA double helix. Two main pathways exist which provide mechanisms for coping with DSBs; precise repair utilising the identical sister chromatid as a template to recreate the broken segment (homologous recombination; HR), and direct fusion of the broken ends in the absence of an intact template (nonhomologous end joining; NHEJ). NHEJ was first characterised in eukaryotes, and an analogous system has been found to exist in bacteria during the past decade. The bacterial NHEJ pathway is composed of four key proteins; the DNA end binding Ku homodimer, a DNA Ligase, a DNA polymerase and a phosphoesterase (PE). The first results chapter of this thesis details the identification of an orthologous set of proteins in the archaeon Methanocella paludicola, and their subsequent isolation and characterisation. The second results chapter expands on the individual activities of the proteins by combining them, and asserting the ability of archaeal NHEJ to join discontinuous ends in vitro. The role of the PE has been unclear in the bacterial system, but in vitro assays described here suggest that the enzyme plays a role in processing NHEJ intermediates formed by the NHEJ polymerase. The PE is found to optimise repair intermediates for ligation, and to reverse potentially genotoxic DNA strand displacements. The final results chapter investigates the structural aspects of the archaeal NHEJ enzymes. Together these studies establish a functional NHEJ system in an archaeon for the first time, and expand our knowledge of the bacterial system by proposing a standard model of archaeo--‐prokaryotic NHEJ.

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43

Matsumi, Rie. "Studies on membrane-bound peptidases and a sugar transporter in the hyperthermophilic archaeon Thermococcus kodakaraensis." 京都大学 (Kyoto University), 2008. http://hdl.handle.net/2433/57291.

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44

Nomura, Norimichi. "Studies on structure and function of the rRNA introns in the hyperthermophilic archaeon Aeropyrum pernix." Kyoto University, 1998. http://hdl.handle.net/2433/157115.

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本文データは平成22年度国立国会図書館の学位論文(博士)のデジタル化実施により作成された画像ファイルを基にpdf変換したものである
Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第7393号
農博第977号
新制||農||760(附属図書館)
学位論文||H10||N3139(農学部図書室)
UT51-98-G322
京都大学大学院農学研究科水産学専攻
(主査)教授内田有恆, 教授坂口守彦, 教授大山莞爾
学位規則第4条第1項該当

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45

CONSTANTINESCO, FLORENCE. "Etudes de la biosynthese de nucleosides modifies dans les arnt d'un archaeon hyperthermophile pyrococcus furiosus." Paris 11, 1999. http://www.theses.fr/1999PA112183.

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La maturation du transcrit primaire des arnt implique toute une serie de modifications chimiques au niveau de certaines bases et/ou riboses. Mon travail de these traite de l'etude de la biosynthese de plusieurs nucleotides modifies au sein des arnt d'une archaebacterie hyperthermophile, pyrococcus furiosus dont la temperature optimale de croissance est de 100\c. En utilisant des extraits cellulaires de p. Furiosus et des precurseurs d'arnt obtenus par transcription in vitro de genes synthetiques d'arnt, nous avons mis en evidence l'activite in vitro de douze enzymes de modification. Nous avons demontre que de simples structures tige-boucle sont substrats pour la plupart des enzymes de modification agissant au sein de la boucle t- des arnt. Nous avons defini que la biosynthese de la 1-methyl inosine-57 implique deux etapes distinctes et ordonnees, la synthese de 1-methyl-adenosine-57 dependant de la s-adenosyl-l-methionine (sam), puis une desamination de la 1-methyl-adenosine en 1-methyl inosine. Nous avons clone et sequence le gene pftrm1. L'expression de pftrm1p, chez e. Coli confere aux cellules la propriete de catalyser in vivo la biosynthese de m 2 2g dans les arnt de la cellule hote, depourvue de cette activite enzymatique. His 6pftrm1p, fusionne a son extremite n-terminale a une queue polyhistidine catalyse la biosynthese in vitro de m 2 2g exclusivement a la position 26 des arnt-substrats via la formation de l'intermediaire m 2g26. His 6-pftrm1p est monomerique en solution et forme un complexe de stoechiometrie 1:1 avec un arnt-substrat. L'enzyme se dissocie de l'arnt entre les deux transferts de groupe methyle sur la guanosine-26. Nous avons determine les elements d'identite de l'arnt requis pour la biosynthese de m 2g26 et de m 2 2g26.

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46

Malotky, Erica Louise. "Functional Characterization of MoeA and MoeB Tungsten Cofactor Synthesis Proteins from the Hyperthermophilic Archaeon Pyrococcus furiosus." NCSU, 2002. http://www.lib.ncsu.edu/theses/available/etd-11202002-162819/.

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The hyperthermophilic archaeon, Pyrococcus furiosus depends on the element tungsten for growth since tungsten-containing enzymes such as aldehyde ferredoxin oxidoreductase (AOR) are key to its metabolism. Crystal structure analysis of the tungsten cofactor in AOR indicated that the tungsten cofactor exists as part of a tricyclic pterin moiety analogous to molybdopterin cofactor present in molybdoenzymes such as nitrate reductase. Molybdopterin cofactor synthesis has been well characterized in Escherichia coli with the identification of at least 14 genes that participate in this process. Analysis of the P. furiosus genome revealed that it has homologs to all cofactor synthesis genes except for modE, a transcriptional regulator of molybdopterin cofactor synthesis, and mogA, a putative molybdo-chelator. Two of the molybdenum cofactor biosynthesis genes, moeA and moeB, involved in activation of molybdenum and in donation of sulfur to the pterin ring structure, respectively, each have two homologs in P. furiosus (MoeA, 45%, MoeA2, 44%, MoeB, 50%, and MoeB2, 47% similar to E. coli MoeA and MoeB respectively). The MoeA and MoeB homologs were targeted for initial functional activity studies to determine if they participate in cofactor formation. The activity studies entailed complementing E. coli strains mutant in moeA or moeB with recombinant P. furiosus homologs in an in vitro system and assaying for restoration of the molydoenzyme nitrate reductase (NR) activity. Partial complementation of defects in E. coli moeA and moeB were observed for assays including P. furiosus MoeA2 and MoeB2 which supported 13.1 nmole NO2-?min-1?mg-1 (10µg MoeA2) and 19.6 nmole NO2-?min-1?mg-1 (100µg MoeB2) activity respectively. These specific activities represent 10.1% and 15.1% of wild type E.coli nitrate reductase activity (130 nmole NO2-?min-1?mg-1) Only negligible restoration of nitrate reductase activity was observed when P. furiosus MoeA or MoeB was included in the assay, with specific activities 0.16 nmole NO2-?min-1?mg-1 (1µg MoeA) and 0.74 NO2-?min-1?mg-1 (50µg MoeB). Partial complementation of the E. coli moeA mutant was also observed for in vitro trimethyl amine oxide (TMAO) reductase assays where 10 g MoeA2 supported a specific activity of 40.97 nmole TMAO reduced?min-1?mg-1 and 10 g MoeB2 supported a specific activity of 6.3 nmole TMAO reduced?min-1?mg-1 compared to 2,374 nmole TMAO reduced?min-1?mg-1 for the wild type E. coli. When TMAO assays were conducted in the presence of tungsten rather than molybdenum, the wild type E. coli had a specific activity of 1,297 nmole TMAO reduced-?min-1?mg-1. E. coli moeA mutant had an activity of 2.07 nmole TMAO reduced -?min-1?mg-1 when supplemented with 10 g MoeA2 and the E. coli moeB mutant supported 6.01 nmole TMAO reduced-?min-1?mg-1 when supplemented with 100 g MoeB2. The partial nature of the complementation seen in these studies is likely due in part to the use of sub optimal assay temperatures (37C), as required for E. coli NR, well below the optimum temperature of 95C seen for most P. furiosus enzymes. Nevertheless, these complementation assays demonstrate that P. furiosus MoeA2, and MoeB2 homologs likely function as MoeA and MoeB in tungsten cofactor synthesis in P. furiosus.

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47

Sullivan, Eric L. S. M. Massachusetts Institute of Technology. "Use of bgaH as a reporter gene for studying translation initiation in the archaeon Haloferax volcanii." Thesis, Massachusetts Institute of Technology, 2008. http://hdl.handle.net/1721.1/43232.

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Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Biology, 2008.
Includes bibliographical references (leaves 30-32).
The bgaH gene isolated from Haloferax lucentensis codes for P-galactosidase. To study the function of initiator tRNAs in translation initiation in Haloferax volcanii, the initiator AUG codon of the bgaH gene was mutated to UAG, UAA, UGA, and GUC. Four different H. volcanii initiator tRNA derived mutants with complementary anticodons were also made. When plasmids carrying the bgaH reporter and mutant initiator tRNAs were coexpressed in H. volcanii, the UGA and GUC decoding tRNAs were aminoacylated, but functional 0-galactosidase was produced only in the presence of the latter tRNA. This result confirms that translation can initiate with some alternative codons, but suggests that the amino acid attached to the tRNA also plays a role. It is unknown if leaderless transcripts will have similar requirements, therefore mutant bgaH reporters lacking 5' untranslated regions were also generated. I also describe modifications of the bgaH reporter for studying suppression of termination codons in H. volcanii. The serine codon at position 184 of the bgaH gene was mutated to the termination codons UAA and UAG. H. volcanii serine tRNA derived suppressor tRNAs with complementary anticodons were also generated. These suppressor tRNAs should allow a study of the requirements for suppression of UAG and UAA codons in H. volcanii, in particular the question of whether suppressors of the UAA codon can also suppress the UAG codon in archaea. H. volcanii WFD 11 used as the host does not have any endogenous 3-galactosidase.
(cont.) I have shown that extracts made from H. volcanii transformants can be used to assay for 3-galactosidase using either O-Nitrophenyl-p-galactoside or Beta-Glo reagent as a substrate. This latter assay couples the D-Luciferin product of cleavage of 6-O-P-galactopyranosyl-luciferin by P-galactosidase to the more precise and sensitive luciferase assay. Since little is known about translation in archaea, future work will involve modifying identity elements in the initiator tRNA to study their requirements in both initiation and elongation in archaea.
by Eric L. Sullivan.
S.M.

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48

Craig, Michael P. "Biochemical and Structural Analysis of the Thermostable Orotidine 5'-Monophosphate Decarboxylase from the Archaeon Sulfolobus Acidocaldarius." University of Cincinnati / OhioLINK, 2001. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1004733890.

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49

Fukuda, Wakao. "Studies on the metabolism of C3 and C4 compounds in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1." 京都大学 (Kyoto University), 2005. http://hdl.handle.net/2433/144401.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(工学)
甲第11943号
工博第2585号
新制||工||1362(附属図書館)
23732
UT51-2006-B122
京都大学大学院工学研究科合成・生物化学専攻
(主査)教授今中忠行, 教授青山安宏, 教授森泰生
学位規則第4条第1項該当

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50

Starkuviene, Vytaute. "Identification and characterization of thermostable uracil glycosylases from the archaeon Methanobacterium thermoautotrophicum and the bacterium Thermus thermophilus." [S.l.] : [s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=965254992.

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