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Dalhousie University
1.
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 (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 24, 2021.
http://hdl.handle.net/10222/14412.
MLA Handbook (7th Edition):
Eveleigh, Robert. “Being Aquifex aeolicus: Untangling a hyperthermophile's
Checkered Past.” 2012. Web. 24 Jan 2021.
Vancouver:
Eveleigh R. Being Aquifex aeolicus: Untangling a hyperthermophile's
Checkered Past. [Internet] [Masters thesis]. Dalhousie University; 2012. [cited 2021 Jan 24].
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
University of California – Berkeley
2.
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 (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 24, 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. 24 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 24].
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
Temple University
3.
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 ·
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CSE |
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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 24, 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. 24 Jan 2021.
Vancouver:
Shi Z. Biochemical properties and substrate reactivities of Aquifex Aeolicus Ribonuclease III. [Internet] [Doctoral dissertation]. Temple University; 2012. [cited 2021 Jan 24].
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
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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Record Details
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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 24, 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. 24 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 24].
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
. 
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