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1.
Uzarraga salazar, Rafael.
Effet de l’oxygène sur le métabolisme énergétique d’Aquifex aeolicus, bactérie hyperthermophile, hydrogénotrophe et microaérophile : The French University and the Making of professionals : An Essay of Typology of the Academic Programs.
Degree: Docteur es, Microbiologie, 2012, Aix Marseille Université
URL: http://www.theses.fr/2012AIXM4811
► Cette thèse porte sur l'écophysiologie et la physiologie d'une bactérie hyperthermophile et microaérophile, Aquifex aeolicus, cultivée dans différentes conditions d'oxygénation. Au cours de ce travail,…
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▼ Cette thèse porte sur l'écophysiologie et la physiologie d'une bactérie hyperthermophile et microaérophile, Aquifex aeolicus, cultivée dans différentes conditions d'oxygénation. Au cours de ce travail, trois systèmes expérimentaux (jarres, microcosmes et fermenteur) ont été testés : (1) le nouveau système de jarres qui été mis au point est muni de microplaques de 24 puits couplé à un robot. Il permet d'étudier un grand nombre de facteurs trophiques ou de formulations de milieux de cultures tout en conservant une atmosphère de composition constante, (2) pour l'étude de facteurs trophiques gazeux, l'utilisation des microcosmes a été montrée peu adaptée, amenant même dans certains cas, à des interprétations erronées, et, 3) le fermenteur reste le meilleur outil pour étudier l'influence de la concentration en O2 dissous (pO2) sur le métabolisme d'A. aeolicus. A partir des cinétiques de croissance obtenues en fermenteur, il a été établi que la densité de biomasse est constante et que la vitesse de croissance est maximale pour une pO2 comprise, respectivement, entre 0.006 et 6 mg/L et, entre 1 et 2 mg/L. Pour des pO2 supérieures à 2 mg/L, il a été montré que l'oxygène a un effet toxique sur la croissance d'A. aeolicus. Pour des conditions optimales d'oxygénation (pO2=1.5 mg/L) et lorsque l'H2 (100 mL/min) limite la croissance, le catabolisme énergétique est alors dévié vers la consommation du thiosulfate. En effet, pour les débits d'H2 de 450 et 100 mL/min, d'une part 97 et 79 % de l'O2 sont respectivement réduits par l'hydrogène et d'autre part 3 et 21 % de l'O2 sont respectivement réduits par le thiosulfate.
This manuscript addresses the physiology and ecophysiology of the microaerophilic hyperthermophilic bacterium Aquifex aeolicus, grown under different oxygen-supply conditions. Three experimental systems, jar, microcosm and fermentor were tested in those experiments: (1) a newly-engineered jar system containing 24-well microplates coupled to an automated controller. This system allows to study a broad spectrum of trophic factors or culture media formulations while maintaining a constant atmospheric composition; (2) microcosm systems were, here, proved ill-adapted to studying gas-phase trophic factors, and in some cases even to leading to false interpretations; 3) the fermentor system remains the best tool to studying the influence of dissolved O2 concentration (pO2) on A. aeolicus metabolism. Based on in-fermentor growth kinetic curves, we established that biomass density was maximum and constant at a pO2 in the range 0.006 to 6 mg/L and growth rate was maximum at a pO2 of about 2 mg/L. At a pO2 over 2 mg/L, oxygen level had a toxic effect on A. aeolicus growth. Under optimal oxygen supply (pO2 = 1.5 mg/L) and when H2 (100 mL/min) is the growth-limiting factor, energy catabolism is diverted towards thiosulfate consumption: at H2 flow-rates of 450 and 100 mL/min, 97% and 79% of O2 is reduced by hydrogen while 3% and 21% of O2 is reduced by thiosulfate, respectively. Under over-oxygenation conditions (pO2 = 10.5 and…
Advisors/Committee Members: Auria, Richard (thesis director).
Subjects/Keywords: Aquifex aeolicus; Oxygène; Thiosulfate; Hydrogène; Métabolisme énergétique; Aquifex aeolicus; Oxygen; Thiosulfate; Hydrogen; Energy metabolism
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APA (6th Edition):
Uzarraga salazar, R. (2012). Effet de l’oxygène sur le métabolisme énergétique d’Aquifex aeolicus, bactérie hyperthermophile, hydrogénotrophe et microaérophile : The French University and the Making of professionals : An Essay of Typology of the Academic Programs. (Doctoral Dissertation). Aix Marseille Université. Retrieved from http://www.theses.fr/2012AIXM4811
Chicago Manual of Style (16th Edition):
Uzarraga salazar, Rafael. “Effet de l’oxygène sur le métabolisme énergétique d’Aquifex aeolicus, bactérie hyperthermophile, hydrogénotrophe et microaérophile : The French University and the Making of professionals : An Essay of Typology of the Academic Programs.” 2012. Doctoral Dissertation, Aix Marseille Université. Accessed January 17, 2021.
http://www.theses.fr/2012AIXM4811.
MLA Handbook (7th Edition):
Uzarraga salazar, Rafael. “Effet de l’oxygène sur le métabolisme énergétique d’Aquifex aeolicus, bactérie hyperthermophile, hydrogénotrophe et microaérophile : The French University and the Making of professionals : An Essay of Typology of the Academic Programs.” 2012. Web. 17 Jan 2021.
Vancouver:
Uzarraga salazar R. Effet de l’oxygène sur le métabolisme énergétique d’Aquifex aeolicus, bactérie hyperthermophile, hydrogénotrophe et microaérophile : The French University and the Making of professionals : An Essay of Typology of the Academic Programs. [Internet] [Doctoral dissertation]. Aix Marseille Université 2012. [cited 2021 Jan 17].
Available from: http://www.theses.fr/2012AIXM4811.
Council of Science Editors:
Uzarraga salazar R. Effet de l’oxygène sur le métabolisme énergétique d’Aquifex aeolicus, bactérie hyperthermophile, hydrogénotrophe et microaérophile : The French University and the Making of professionals : An Essay of Typology of the Academic Programs. [Doctoral Dissertation]. Aix Marseille Université 2012. Available from: http://www.theses.fr/2012AIXM4811
2.
Aussignargues, Clement.
Optimisation du métabolisme énergétique du soufre chez la bactérie hyperthermophile Aquifex aeolicus. : Prediction of the compliance of packaging materials using deformulation methods and partition coefficients modelling.
Degree: Docteur es, Microbiologie, 2012, Aix Marseille Université
URL: http://www.theses.fr/2012AIXM4709
► Le soufre est utilisé à des fins bioénergétiques par des micro-organismes tels que la bactérie hyperthermophile Aquifex aeolicus qui nécessite pour sa croissance de l'oxygène,…
(more)
▼ Le soufre est utilisé à des fins bioénergétiques par des micro-organismes tels que la bactérie hyperthermophile Aquifex aeolicus qui nécessite pour sa croissance de l'oxygène, de l'hydrogène et un composé soufré indispensable. Une soufre réductase réduisant des chaînes de soufre, une Sulfure Quinone Oxydoréductase (SQR) oxydant l'H2S et une Soufre Oxygénase Réductase (SOR) oxydant et réduisant simultanément des chaînes de soufre ont été caractérisées chez cette bactérie. L'organisation de certaines de ces enzymes dans des supercomplexes membranaires a également été démontrée.Nous avons montré qu'Aq_477, précédemment caractérisée comme une soufre transférase de la famille des rhodanèses, est capable (i) de « charger » des chaînes de soufre ; (ii) d'interagir avec deux partenaires (la soufre réductase et la SOR) ; (iii) de leur présenter ce substrat. Ceci conduit à une optimisation du métabolisme. Nous avons ainsi démontré l'implication directe d'Aq_477, rebaptisée SbdP pour Sulfur -binding -donating Protein, dans le métabolisme énergétique du soufre de la bactérie. Une analyse poussée du génome nous a permis de construire un nouveau modèle suggérant notamment un recyclage des composés soufrés entre différents systèmes enzymatiques. La recherche de l'existence d'un niveau d'organisation des complexes respiratoires supérieur aux supercomplexes chez Aquifex aeolicus nous a conduits à développer de nouvelles méthodes d'étude permettant de proposer plusieurs pistes de recherche. Enfin, nous avons montré l'existence d'un nanocompartiment protéique constitué de l'encapsuline Aq_1760, dans lequel vient s'ancrer la ferritine atypique à domaines en tandem Aq_331.
Sulfur can be used in energy metabolism by microorganisms as electron donor and acceptor. The hyperthermophilic bacterium Aquifex aeolicus, which need oxygen, hydrogen and an essential sulfur compound for its growth presents sulfur reduction and oxidation pathways linked to the energy synthesis. A sulfur reductase (reduction of sulfur chains), a Sulfide Quinone Oxidoreductase (SQR, oxidation of H2S) and a Sulfur Oxygenase Reductase (SOR, simultaneous oxidation and reduction of sulfur chains) have been characterized in this bacterium. It has also been shown that some of these enzymes are organized in membrane-bound supercomplexes.We have demonstrated that Aq_477, previously characterized as a sulfurtransferase belonging to the rhodanese superfamily, can load long sulfur chains and acts as a sulfur donor for its partners (sulfur reductase and SOR) which use these sulfur chains as substrate, thus optimizing the metabolism. These results show that Aq_477, renamed SbdP for Sulfur -binding -donating Protein, is involved in the sulfur energy metabolism of Aquifex aeolicus. The identification in the genome of some new proteins potentially involved in this metabolism permitted us to propose a new model which suggests a recycling of sulfur compounds between different enzymatic systems. We also looked for an organization level of respiratory complexes higher than…
Advisors/Committee Members: Giudici-Orticoni, Marie-Thérèse (thesis director).
Subjects/Keywords: Métabolisme énergétique du soufre; Transfert de soufre; Enzymes membranaires respiratoires; Aquifex aeolicus; Rhodanèse; Sulfur energy metabolism; Sulfur transfer; Respiratory enzymes; Aquifex aeolicus; Rhodanese
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Aussignargues, C. (2012). Optimisation du métabolisme énergétique du soufre chez la bactérie hyperthermophile Aquifex aeolicus. : Prediction of the compliance of packaging materials using deformulation methods and partition coefficients modelling. (Doctoral Dissertation). Aix Marseille Université. Retrieved from http://www.theses.fr/2012AIXM4709
Chicago Manual of Style (16th Edition):
Aussignargues, Clement. “Optimisation du métabolisme énergétique du soufre chez la bactérie hyperthermophile Aquifex aeolicus. : Prediction of the compliance of packaging materials using deformulation methods and partition coefficients modelling.” 2012. Doctoral Dissertation, Aix Marseille Université. Accessed January 17, 2021.
http://www.theses.fr/2012AIXM4709.
MLA Handbook (7th Edition):
Aussignargues, Clement. “Optimisation du métabolisme énergétique du soufre chez la bactérie hyperthermophile Aquifex aeolicus. : Prediction of the compliance of packaging materials using deformulation methods and partition coefficients modelling.” 2012. Web. 17 Jan 2021.
Vancouver:
Aussignargues C. Optimisation du métabolisme énergétique du soufre chez la bactérie hyperthermophile Aquifex aeolicus. : Prediction of the compliance of packaging materials using deformulation methods and partition coefficients modelling. [Internet] [Doctoral dissertation]. Aix Marseille Université 2012. [cited 2021 Jan 17].
Available from: http://www.theses.fr/2012AIXM4709.
Council of Science Editors:
Aussignargues C. Optimisation du métabolisme énergétique du soufre chez la bactérie hyperthermophile Aquifex aeolicus. : Prediction of the compliance of packaging materials using deformulation methods and partition coefficients modelling. [Doctoral Dissertation]. Aix Marseille Université 2012. Available from: http://www.theses.fr/2012AIXM4709

Dalhousie University
3.
Eveleigh, Robert.
Being Aquifex aeolicus: Untangling a hyperthermophile's
Checkered Past.
Degree: MS, Department of Computational Biology and
Bioinformatics, 2012, Dalhousie University
URL: http://hdl.handle.net/10222/14412
► Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show…
(more)
▼ Lateral gene transfer (LGT) is an important factor
contributing to the evolution of prokaryotic genomes. The Aquificae
are a hyperthermophilic bacterial group whose genes show
affiliations to many other lineages, including the
hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea.
Here I outline these scenarios and consider the fit of the
available data, including two recently sequenced genomes from
members of the Aquificae, to different sets of predictions.
Evidence from phylogenetic profiles and trees suggests that the
?-Proteobacteria have the strongest affinities with the three
Aquificae analyzed. However, this phylogenetic signal is by no
means the dominant one, with the Archaea, many lineages of
thermophilic bacteria, and members of genus Clostridium and class
?-Proteobacteria also showing strong connections to the Aquificae.
The phylogenetic affiliations of different functional subsystems
showed strong biases: as observed previously, most but not all
genes implicated in the core translational apparatus tended to
group Aquificae with Thermotogae, while a wide range of metabolic
systems strongly supported the Aquificae - ?-Proteobacteria link.
Given the breadth of support for this latter relationship, a
scenario of ?-proteobacterial ancestry coupled with frequent
exchange among thermophilic lineages is a plausible explanation for
the emergence of the Aquificae.
Advisors/Committee Members: Dr Andrew Roger (external-examiner), Dr. Christian Blouin (graduate-coordinator), Dr Andrew Roger (thesis-reader), Drs. Robert Beiko and John Archibald (thesis-supervisor), Not Applicable (ethics-approval), No (manuscripts), No (copyright-release).
Subjects/Keywords: Aquifex aeolicus; Thermotogae; phylogenomics; hyperthermophily; lateral gene transfer
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Eveleigh, R. (2012). Being Aquifex aeolicus: Untangling a hyperthermophile's
Checkered Past. (Masters Thesis). Dalhousie University. Retrieved from http://hdl.handle.net/10222/14412
Chicago Manual of Style (16th Edition):
Eveleigh, Robert. “Being Aquifex aeolicus: Untangling a hyperthermophile's
Checkered Past.” 2012. Masters Thesis, Dalhousie University. Accessed January 17, 2021.
http://hdl.handle.net/10222/14412.
MLA Handbook (7th Edition):
Eveleigh, Robert. “Being Aquifex aeolicus: Untangling a hyperthermophile's
Checkered Past.” 2012. Web. 17 Jan 2021.
Vancouver:
Eveleigh R. Being Aquifex aeolicus: Untangling a hyperthermophile's
Checkered Past. [Internet] [Masters thesis]. Dalhousie University; 2012. [cited 2021 Jan 17].
Available from: http://hdl.handle.net/10222/14412.
Council of Science Editors:
Eveleigh R. Being Aquifex aeolicus: Untangling a hyperthermophile's
Checkered Past. [Masters Thesis]. Dalhousie University; 2012. Available from: http://hdl.handle.net/10222/14412
4.
Fürtenbach, Karin.
Characterization of two Protein Disulfide Oxidoreductases from Thermophilic Organisms Pyrococcus furiosus and Aquifex aeolicus : Characterization of two Protein Disulfide Oxidoreductases.
Degree: Life Sciences, 2008, Södertörn University College
URL: http://urn.kb.se/resolve?urn=urn:nbn:se:sh:diva-1644
► Members of the thioredoxin superfamily of proteins catalyze disulfide bond reduction and oxidation using the active site C-X-X-C sequence. In hyperthermophilic organisms, cysteine side…
(more)
▼ Members of the thioredoxin superfamily of proteins catalyze disulfide bond reduction and oxidation using the active site C-X-X-C sequence. In hyperthermophilic organisms, cysteine side chains were expected in low abundance since they were not believed to endure the high temperatures under which they grow. Recently it has been found that disulfide bonds in hyperthermophiles are more frequent, the higher the growth temperature of the organism. This is perhaps used as an adaptation to high temperature in order to stabilize proteins under harsh conditions. A protein with sequence and structural similarities to mesophilic members of the thioredoxin superfamily, called protein disulfide oxidoreductases (PDO), has been found in the genomes of recently sequenced hyperthermophilic genomes. In this study PDOs from the hyperthermophiles Aquifex aeolicus (AaPDO) and Pyrococcus furiosus (PfPDO) have been investigated. The molecular weight is about 26 kDa and their structures are comprised of two homologous thioredoxin folds, referred to as the N-unit and the C-unit, each containing a C-X-X-C motif. The sequence identity between the two units and the two proteins is low, but they are still structurally very similar. The function of these proteins in vivo is unknown. As a first step in characterizing the activity of these proteins, the redox characteristics of these domains will be investigated. During this project, the genes for AaPDO and PfPDO have been cloned into overexpression vectors, expressed in E. coli and purified to homogeneity. To allow for individual study of the activities of two units, mutated proteins were prepared in which the cysteine residues of the N-unit (AaPDOnm and PfPDOnm) and of the C-unit (AaPDOcm and PfPDOcm) and purified. Circular dichroism spectra recorded of the wild type and mutants indicate that all purified proteins are folded and that the N- and C-unit active site mutants are structurally similar to the corresponding wild type proteins.
Subjects/Keywords: PDO; protein disulfide oxidoreductase; Pyrococcus furiosus; Aquifex aeolicus; disulfide; Molecular biology; Molekylärbiologi
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Fürtenbach, K. (2008). Characterization of two Protein Disulfide Oxidoreductases from Thermophilic Organisms Pyrococcus furiosus and Aquifex aeolicus : Characterization of two Protein Disulfide Oxidoreductases. (Thesis). Södertörn University College. Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:sh:diva-1644
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Fürtenbach, Karin. “Characterization of two Protein Disulfide Oxidoreductases from Thermophilic Organisms Pyrococcus furiosus and Aquifex aeolicus : Characterization of two Protein Disulfide Oxidoreductases.” 2008. Thesis, Södertörn University College. Accessed January 17, 2021.
http://urn.kb.se/resolve?urn=urn:nbn:se:sh:diva-1644.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Fürtenbach, Karin. “Characterization of two Protein Disulfide Oxidoreductases from Thermophilic Organisms Pyrococcus furiosus and Aquifex aeolicus : Characterization of two Protein Disulfide Oxidoreductases.” 2008. Web. 17 Jan 2021.
Vancouver:
Fürtenbach K. Characterization of two Protein Disulfide Oxidoreductases from Thermophilic Organisms Pyrococcus furiosus and Aquifex aeolicus : Characterization of two Protein Disulfide Oxidoreductases. [Internet] [Thesis]. Södertörn University College; 2008. [cited 2021 Jan 17].
Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:sh:diva-1644.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Fürtenbach K. Characterization of two Protein Disulfide Oxidoreductases from Thermophilic Organisms Pyrococcus furiosus and Aquifex aeolicus : Characterization of two Protein Disulfide Oxidoreductases. [Thesis]. Södertörn University College; 2008. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:sh:diva-1644
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Temple University
5.
Shi, Zhongjie.
Biochemical properties and substrate reactivities of Aquifex Aeolicus Ribonuclease III.
Degree: PhD, 2012, Temple University
URL: http://digital.library.temple.edu/u?/p245801coll10,213666
► Chemistry
Ribonuclease III is a highly-conserved bacterial enzyme that cleaves double-stranded (ds) RNA structures, and participates in diverse RNA maturation and decay pathways. Essential insight…
(more)
▼ Chemistry
Ribonuclease III is a highly-conserved bacterial enzyme that cleaves double-stranded (ds) RNA structures, and participates in diverse RNA maturation and decay pathways. Essential insight on the RNase III mechanism of dsRNA cleavage has been provided by crystallographic studies of the enzyme from the hyperthermophilic bacterium, Aquifex aeolicus. However, those crystals involved complexes containing either cleaved RNA, or a mutant RNase III that is catalytically inactive. In addition, neither the biochemical properties of A. aeolicus (Aa)-RNase III, nor the reactivity epitopes of its cognate substrates are known. The goal of this project is to use Aa-RNase III, for which there is atomic-level structural information, to determine how RNase III recognizes its substrates and selects the target site. I first purified recombinant Aa-RNase III and defined the conditions that support its optimal in vitro catalytic activity. The catalytic activity of purified recombinant Aa-RNase III exhibits a temperature optimum of 70-85°C, a pH optimum of 8.0, and with either Mg2+ or Mn2+ supports efficient catalysis. Cognate substrates for Aa-RNase III were identified and their reactivity epitopes were characterized, including the specific bp sequence elements that determine processing reactivity and selectivity. Small RNA hairpins, based on the double-stranded structures associated with the Aquifex 16S and 23S rRNA precursors, are cleaved in vitro at sites that are consistent with production of the immediate precursors to the mature rRNAs. Third, the role of the dsRBD in scissile bond selection was examined by a mutational analysis of the conserved interactions of RNA binding motif 1 (RBM1) with the substrate proximal box (pb). The individual contributions towards substrate recognition were determined for conserved amino acid side chains in the RBM1. It also was shown that the dsRBD plays key dual roles in both binding energy and selectivity, through RBM1 responsiveness to proximal box bp sequence. The dsRBD is specifically responsive to an antideterminant (AD) bp in pb position 2. The relative structural rigidity of both dsRNA and dsRBD rationalizes the strong effect of an inhibitory bp at pb position 2: disruption of one RBM1 side chain interaction can effectively disrupt the other RBM1 side chain interactions. Finally, a cis-acting model was developed for subunit involvement in substrate recognition by RNase III. Structurally asymmetric mutant heterodimers of Escherichia coli (Ec)-RNase III were constructed, and asymmetric substrates were employed to reveal how RNase III can bind and deliver hairpin substrates to the active site cleft in a pathway that requires specific binding configurations of both enzyme and substrate.
Temple University – Theses
Advisors/Committee Members: Nicholson, Allen W., Schafmeister, Christian, Zdilla, Michael J., Waring, Richard B..
Subjects/Keywords: Biochemistry; Aquifex aeolicus; dsRNA-binding domain; nuclease domain; proximal box; Ribonuclease III; RNA binding motif
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Shi, Z. (2012). Biochemical properties and substrate reactivities of Aquifex Aeolicus Ribonuclease III. (Doctoral Dissertation). Temple University. Retrieved from http://digital.library.temple.edu/u?/p245801coll10,213666
Chicago Manual of Style (16th Edition):
Shi, Zhongjie. “Biochemical properties and substrate reactivities of Aquifex Aeolicus Ribonuclease III.” 2012. Doctoral Dissertation, Temple University. Accessed January 17, 2021.
http://digital.library.temple.edu/u?/p245801coll10,213666.
MLA Handbook (7th Edition):
Shi, Zhongjie. “Biochemical properties and substrate reactivities of Aquifex Aeolicus Ribonuclease III.” 2012. Web. 17 Jan 2021.
Vancouver:
Shi Z. Biochemical properties and substrate reactivities of Aquifex Aeolicus Ribonuclease III. [Internet] [Doctoral dissertation]. Temple University; 2012. [cited 2021 Jan 17].
Available from: http://digital.library.temple.edu/u?/p245801coll10,213666.
Council of Science Editors:
Shi Z. Biochemical properties and substrate reactivities of Aquifex Aeolicus Ribonuclease III. [Doctoral Dissertation]. Temple University; 2012. Available from: http://digital.library.temple.edu/u?/p245801coll10,213666

University of California – Berkeley
6.
Vidangos, Natasha Keith.
Structural and biochemical studies of sigma54 transcriptional activation in Aquifex aeolicus.
Degree: Chemistry, 2010, University of California – Berkeley
URL: http://www.escholarship.org/uc/item/62h3j5cj
► This thesis addresses a diversity of questions regarding the structural details of sigma54 transcriptional activation, and the function of sigma54 activation in the hyperthermophile Aquifex…
(more)
▼ This thesis addresses a diversity of questions regarding the structural details of sigma54 transcriptional activation, and the function of sigma54 activation in the hyperthermophile Aquifex aeolicus. In order to place each topic in its appropriate context, a general introduction is provided in the first chapter, and supplemented with additional, more detailed introductions in each subsequent chapter. The second chapter reflects the central project of this thesis, the determination of the structure of the DNA-binding domain of an NtrC-like sigma54 transcriptional activator protein in Aquifex aeolicus, in complex with its high-affinity DNA binding site. Although this project was attempted by NMR, its structure was ultimately solved by X-ray crystallography. This structure, which shows slight DNA-bending, is compared to the recent structure of the homologous Fis protein in complex with DNA. In the third chapter, I describe a cross-comparison of DNA-binding domains from Aquifex aeolicus, including new structures of the DNA-binding domains of NtrC1 and NtrC2, and comparisons to NtrC4, ZraR and NtrC from Salmonella enterica serovar typhimurium, and Fis from Escherichia coli. These structures of DNA-binding domains from a single family enable a detailed comparison of structural changes that tune protein function. A trend is noted, in which larger dimerization interfaces in the DNA-binding domains appear to correlate with smaller dimerization interfaces in the other domains of the protein. The additional structure of the full-length NtrC1 protein is presented, but the DNA-binding domains were missing from the density, providing evidence for the flexibility of the linker between the central and DNA-binding domains. Together with structural information about the CD linker regions at the N-termini of the DNA-binding domains, I conclude that the CD linker regions are generally unstructured in the inactive state, functioning as tethers to bring the RC domains of NtrC into appropriate local concentrations for activity. In the fourth chapter, I depart from sigma54 transcriptional activators, and discuss NMR studies on the sigma54 factor. The Darst lab at Rockefeller University has produced a crystal structure of the full-length intact sigma54 factor in complex with DNA. However, poor data quality prevents regions of the molecule from being traced unambiguously through the density. By applying new methods in NMR including TROSY spectroscopy and specific isotopic labeling, I attempted to resolve small regions of structure in this ambiguous region. However, these studies were complicated by protein aggregation. The fifth and final chapter takes a step back from structural perspective and compiles and discusses our current understanding of sigma54 regulatory networks in Aquifex aeolicus. This analysis of genes with bioinformatics and biochemical techniques led me to discover that NtrC3, an unstudied sigma54 transcriptional activator,…
Subjects/Keywords: Biophysics; Biochemistry; Aquifex aeolicus; NMR; NtrC; protein structure; x-ray crystallography
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Vidangos, N. K. (2010). Structural and biochemical studies of sigma54 transcriptional activation in Aquifex aeolicus. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/62h3j5cj
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Vidangos, Natasha Keith. “Structural and biochemical studies of sigma54 transcriptional activation in Aquifex aeolicus.” 2010. Thesis, University of California – Berkeley. Accessed January 17, 2021.
http://www.escholarship.org/uc/item/62h3j5cj.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Vidangos, Natasha Keith. “Structural and biochemical studies of sigma54 transcriptional activation in Aquifex aeolicus.” 2010. Web. 17 Jan 2021.
Vancouver:
Vidangos NK. Structural and biochemical studies of sigma54 transcriptional activation in Aquifex aeolicus. [Internet] [Thesis]. University of California – Berkeley; 2010. [cited 2021 Jan 17].
Available from: http://www.escholarship.org/uc/item/62h3j5cj.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Vidangos NK. Structural and biochemical studies of sigma54 transcriptional activation in Aquifex aeolicus. [Thesis]. University of California – Berkeley; 2010. Available from: http://www.escholarship.org/uc/item/62h3j5cj
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Virginia Commonwealth University
7.
Uzzell, Jamar.
STRUCTURAL BASIS FOR THERMAL STABILITY OF THERMOPHILIC TRMD PROTEINS.
Degree: MS, Biochemistry, 2011, Virginia Commonwealth University
URL: https://doi.org/10.25772/6DKP-1H28
;
https://scholarscompass.vcu.edu/etd/2539
► Thermal stability of theG37 tRNA methyltransferase proteins from Thermotoga maritima and Aquifex aeolicus have been compared using Differential Scanning Calorimetry. It was shown that the…
(more)
▼ Thermal stability of theG37 tRNA methyltransferase proteins from Thermotoga maritima and
Aquifex aeolicus have been compared using Differential Scanning Calorimetry. It was shown that the Thermotoga protein is remarkably stable and is denatured at temperatures in excess of 100 degrees Centigrade. The
Aquifex aeolicus protein was less stable, denaturing broadly at temperatures between 55 °C and 100 °C. In contrast, the mesophilic E. coli protein was completely denatured at 55 °C.
Enzymatic activity of the proteins was measured at various temperatures. Both the Thermotoga and
Aquifex enzymes are active at ambient temperatures, and display a significant
decrease in activity when the temperature is raised above 50 °C. This may relate to subtle changes in protein structure causing an effect on the tRNA based assay.
Both enzymes contain inter subunit disulfide bonds which might contribute to thermal stability. Assays of the enzymes in the presence of high concentrations of Dithiothreitol (DTT) did not significantly reduce activity at higher temperatures, but did stimulate activity at lower temperatures.
Site directed mutagenesis of non -conserved protein sequences within Thermotoga maritima were initiated in order to determine what structures might confer heat stability on the protein. Alanine mutagenesis of lysine residues 103,104 led to reduced catalytic activity, but did increased activity at higher temperatures. Aspartate is the most common residue at the relative position 166 in the variable loop of most TrmD genes. It has been shown that in E. coli this is essential for catalytic activity and possibly the residue which carries out N1 deprotonation on residue G37 in tRNA. In Thermotoga glutamate is present at this position. Alanine mutagenesis of this residue did not eliminate activity suggesting another nearby residue may function in this capacity in the Thermotoga TrmD protein.
Advisors/Committee Members: Walter M. Holmes.
Subjects/Keywords: TrmD; Thermophilies; Thermophilic; Aquifex aeolicus; Thermotoga maritima; DSC; Differential Scanning Calorimetry; Biochemistry, Biophysics, and Structural Biology; Life Sciences
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APA (6th Edition):
Uzzell, J. (2011). STRUCTURAL BASIS FOR THERMAL STABILITY OF THERMOPHILIC TRMD PROTEINS. (Thesis). Virginia Commonwealth University. Retrieved from https://doi.org/10.25772/6DKP-1H28 ; https://scholarscompass.vcu.edu/etd/2539
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Uzzell, Jamar. “STRUCTURAL BASIS FOR THERMAL STABILITY OF THERMOPHILIC TRMD PROTEINS.” 2011. Thesis, Virginia Commonwealth University. Accessed January 17, 2021.
https://doi.org/10.25772/6DKP-1H28 ; https://scholarscompass.vcu.edu/etd/2539.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Uzzell, Jamar. “STRUCTURAL BASIS FOR THERMAL STABILITY OF THERMOPHILIC TRMD PROTEINS.” 2011. Web. 17 Jan 2021.
Vancouver:
Uzzell J. STRUCTURAL BASIS FOR THERMAL STABILITY OF THERMOPHILIC TRMD PROTEINS. [Internet] [Thesis]. Virginia Commonwealth University; 2011. [cited 2021 Jan 17].
Available from: https://doi.org/10.25772/6DKP-1H28 ; https://scholarscompass.vcu.edu/etd/2539.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Uzzell J. STRUCTURAL BASIS FOR THERMAL STABILITY OF THERMOPHILIC TRMD PROTEINS. [Thesis]. Virginia Commonwealth University; 2011. Available from: https://doi.org/10.25772/6DKP-1H28 ; https://scholarscompass.vcu.edu/etd/2539
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
.