Theses and Dissertations
This collection includes both ASU Theses and Dissertations, submitted by graduate students, and the Barrett, Honors College theses submitted by undergraduate students.
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- Genre: Masters Thesis
Description
Rhodoferax antarcticus strain ANT.BR, a purple nonsulfur bacterium isolated from a microbial mat in Ross Island, Antarctica, is the first described anoxygenic phototrophic bacterium that is adapted to cold habitats and is the first beta-proteobacterium to undergo complete genome sequencing. R. antarcticus has unique absorption spectra and there are no obvious intracytoplasmic membranes in cells grown phototrophically, even under low light intensity. Analysis of the finished genome sequence reveals a single chromosome (3,809,266 bp) and a large plasmid (198,615 bp) that together harbor 4,262 putative genes. The genome contains two types of Rubiscos, Form IAq and Form II, which are known to exhibit quite different kinetic properties in other bacteria. The presence of multiple Rubisco forms could give R. antarcticus high metabolic flexibility in diverse environments. Annotation of the complete genome sequence along with previous experimental results predict the presence of structural genes for three types of light-harvesting (LH) complexes, LH I (B875), LH II (B800/850), and LH III (B800/820). There is evidence that expression of genes for the LH II complex might be inhibited when R. antarcticus is under low temperature and/or low light intensity. These interesting condition-dependent light-harvesting apparatuses and the control of their expression are very valuable for the further understanding of photosynthesis in cold environments. Finally, R. antarcticus exhibits a highly motile lifestyle. The genome content and organization of all putative polar flagella genes are characterized and discussed.
ContributorsZhao, Tingting, M.S (Author) / Touchman, Jeffrey (Thesis advisor) / Rosenberg, Michael (Committee member) / Redding, Kevin (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2011
Description
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is widely accepted as the world's most abundant enzyme and represents the primary entry point for inorganic carbon into the biosphere. Rubisco's slow carboxylation rate of ribulose-1,5-bisphosphate (RuBP) and its susceptibility to inhibition has led some to term it the "bottle neck" of photosynthesis. In order to ensure that Rubisco remains uninhibited, plants require the catalytic chaperone Rubisco activase. Activase is a member of the AAA+ superfamily, ATPases associated with various cellular activities, and uses ATP hydrolysis as the driving force behind a conformational movement that returns activity to inhibited Rubisco active sites. A high resolution activase structure will be an essential tool for examining Rubisco/activase interactions as well as understanding the activase self-association phenomenon. Rubisco activase has long eluded crystallization, likely due to its infamous self-association (polydispersity). Therefore, a limited proteolysis approach was taken to identify soluble activase subdomains as potential crystallization targets. This process involves using proteolytic enzymes to cleave a protein into a few pieces and has previously proven successful in identifying crystallizable protein fragments. Limited proteolysis, utilizing two different proteolytic enzymes (alpha-chymotrypsin and trypsin), identified two tobacco activase products. The fragments that were identified appear to represent most of what is considered to be the AAA+ C-terminal all alpha-domain and some of the AAA+ N-terminal alpha beta alpha-domain. Identified fragments were cloned using the pET151/dTOPO. The project then moved towards cloning and recombinant protein expression in E. coli. NtAbeta(248-383) and NtAbeta(253-354) were successfully cloned, expressed, purified, and characterized through various biophysical techniques. A thermofluor assay of NtAbeta(248-383) revealed a melting temperature of about 30°C, indicating lower thermal stability compared with full-length activase at 43°C. Size exclusion chromatography suggested that NtAbeta(248-383) is monomeric. Circular dichroism was used to identify the secondary structure; a plurality of alpha-helices. NtAbeta(248-383) and NtAbeta(253-354) were subjected to crystallization trials.
ContributorsConrad, Alan (Author) / Wachter, Rebekka (Thesis advisor) / Moore, Thomas (Committee member) / Redding, Kevin (Committee member) / Arizona State University (Publisher)
Created2012
Description
All known life requires three main metabolic components to grow: an energy source, an electron source, and a carbon source. For energy, an organism can use light or chemical reactions. For electrons, an organism can use metals or organic molecules. For carbon, an organism can use organic or inorganic carbon. Life has adapted to use any mixture of the endpoints for each of the three metabolic components. Understanding how these components are incorporated in a living bacterium on Earth in modern times is relatively straight forward. This becomes much more complicated when trying to determine what metabolisms may have been used in ancient times on Earth or potential novel metabolisms that exist on other planets. One way to examine these possibilities is by creating genetically modified mutant bacteria that have novel metabolisms or proposed ancient metabolisms to study. This thesis is the beginning of a broader study to understand novel metabolisms using Heliobacteria modesticaldum. H. modesticaldum was grown under different environmental conditions to isolate the impacts of energy, electron, and carbon sources on carbon and nitrogen isotope fractionation. Additionally, the wild type and a novel mutant H. modesticaldum were compared to measure the effects of specific enzymes on carbon and nitrogen isotope fractionation. By forcing the bacterium to adapt to different conditions, variation in carbon and nitrogen content and isotopic signature are detected. Specifically, by forcing the bacterium to fix nitrogen as opposed to nitrogen incorporation, the isotopic signature of the bacterium had a noticeable change. Themutant H. modesticaldum also had a different isotopic signature than the wild type. Without the enzyme citrate synthase, H. modesticaldum had to adapt its carbon metabolic cycle, creating a measurable carbon isotope fractionation. The results described here offer new insight into the effects of metabolism on carbon and nitrogen fractionation of ancient or novel organisms.
ContributorsElms, Nicholas (Author) / Hartnett, Hilairy E (Thesis advisor) / Redding, Kevin (Committee member) / Trembath-Reichert, Elizabeth (Committee member) / Anbar, Ariel D (Committee member) / Arizona State University (Publisher)
Created2021