Biochemistry, Biophysics, and Structural Biology Commons^™

Novel Protein Secretion And Chitin Utilization Machinery Of Flavobacterium Johnsoniae, Sampada Suresh Kharade

Theses and Dissertations

Flavobacterium johnsoniae, a member of phylum Bacteroidetes, is a gliding bacterium that digests insoluble chitin. A novel protein secretion system, the Type IX secretion system (T9SS), secretes the motility adhesins SprB and RemA and is also required for chitin utilization. In order to understand F. johnsoniae chitin utilization and the role of the T9SS, Fjoh_4555 (chiA) was targeted for analysis. Disruption of chiA resulted in cells that failed to digest chitin and complementation restored this ability. Antisera raised against ChiA were used to characterize its secretion. ChiA was secreted in soluble form by wild-type cells but remained cell-associated in T9SS …

Oligomerization Of The Sterile-2 G-Protein Coupled Receptor In Yeast Cells In The Presence And Absence Of Alpha-Factor Pheromone Using Fluorescence Spectroscopy And Forster Resonance Energy Transfer Analysis, Joel David Paprocki

Theses and Dissertations

G-protein-coupled receptors (GPCRs) are the largest family of receptors that respond to a wide variety of extracellular stimuli, including molecular ligands such as odorants, neurotransmitters, and hormones, as well as physical agents sigh as light and pressure. The stimulation event results in initiating conformational changes in the structure of the receptor, which further results in the release of the heterotrimeric G-protein; the latter has a variety of functions within signaling pathways in cellular biology. The GPCR explored in this investigation is the Sterile 2 α-factor receptor (Ste2), whose natural function is that of a yeast mating pheromone receptor. Its natural …

Interaction Of Rhizobium Sp. Strain Irbg74 With A Legume (Sesbania Cannabina) And A Cereal (Oryza Sativa), Shubhajit Mitra

Theses and Dissertations

Rhizobium sp. IRBG74 (IRBG74) develops a classical nitrogen-fixing symbiosis with the legume Sesbania cannabina and also promotes the growth of rice (Oryza sativa), but not much is known about the rhizobial determinants important for these interactions. We hypothesize that Rhizobium sp. IRBG74 utilizes similar mechanisms to endophytically colonize both legume and cereal hosts. In this study, we analyzed the colonization of rice and S. cannabina using a strain of IRBG74 marked with β-glucuronidase (GUS) and Green Fluorescent Protein (GFP). IRBG74 infected both of the host plants through crack entry under submerged conditions, but showed root hair mediated infection under aerobic …

Gene Regulatory Pathways Driving Central Nervous System Regeneration In Zebrafish, Ishwariya Venkatesh

Theses and Dissertations

Damage to the central nervous system (CNS) circuitry of adult mammals results in permanent disability. In contrast, the ability to regenerate damaged CNS nerves and achieve functional recovery occurs naturally in fish. The ability of fish to successfully regrow damaged CNS nerves is in part a consequence of their ability to re-express key neuronal growth-associated genes/proteins in response to CNS injury. On such protein is Growth-Associated Protein-43 (Gap43), a protein which is highly enriched in axonal growth cones during CNS development and regeneration. Experiments conducted in mammals have demonstrated that ectopic expression of GAP-43 improves axonal re-growth after injury. Using …

Cellular Zinc Trafficking: The Zinc Proteome And Its Reactions With Cadmium, Mohammad Ali Namdarghanbari

Theses and Dissertations

Metals play a crucial role in living systems. Iron, zinc, copper, molybdenum, and manganese are involved in many essential biological activities. Among transition metals, zinc after iron is the most abundant transition metal in the human body and the most abundant in the brain. It exists in more than 3000 proteins, which comprise about 10% of the human proteome. Zn2+ dyshomeostasis is associated with chronic diseases such as metabolic syndrome, diabetes and related complications, bone loss, growth retardation in young children, and neurological and behavioral problems. Despite a good knowledge obtained for metabolism of some metal ions such as copper, …

Development Of Peripheral Innervation In The Frog Xenopus Laevis, Mitali A. Gandhi

Theses and Dissertations

The skin in Xenopus laevis is innervated by two different sets of mechanosensory neurons at different times during development. Rohon Beard (RB) neurons start differentiating during gastrulation, innervate the embryonic skin and mediate sensory function during hatching. Dorsal Root Ganglion (DRG) neurons start differentiating after neural crest migration, innervate adult epidermal targets and mediate mechanosensory function during larval and adult stages and eventually replace RB neurons. The change in sensory neurons occurs during the transformation of skin, sensory structures, and behavior from their embryonic to their larval forms. We hypothesized that developmental changes in either the sensory end organs or …

Mechanism Of The Hydroxylation Reactions Catalyzed By 4-Hydroxyphenylpyruvate Dioxygenase And Hydroxymandelate Synthase, Dhara D. Shah

Theses and Dissertations

4-Hydroxyphenylpyruvate dioxygenase (HPPD) and Hydroxymandelate synthase (HMS) carry out highly similar complex dioxygenation reactions using the substrates, 4-hydroxyphenylpyruvate (HPP) and dioxygen. HPPD catalyzes decarboxylation, aromatic hydroxylation and substituent migration (NIH shift) in a single catalytic cycle to form homogentisate (HG), whereas HMS catalyzes decarboxylation and aliphatic hydroxylation to give hydroxymandelate (HMA). Wild-type HPPD, HPPD variants and HMS variants produce both native and non-native products. Based on this observation, we have employed a product analysis method with HPP deuterium substitutions (ring or benzylic) that reveal kinetic isotope effects from intermediate partitioning ratios. In this study we offer evidence for the 1) …

Enzyme Activity, Maturation And Regulation Of Anaerobic Reductases In Shewanella Oneidensis Mr-1, Kenneth L. Brockman

Theses and Dissertations

Shewanella oneidensis MR-1 is a metal-reducing bacterium capable of using a wide range of terminal electron acceptors. These include oxygen, metal oxides and organic compounds such as dimethyl sulfoxide (DMSO) and fumarate. In addition, several nitrogen and sulfur based compounds can be used as terminal electron acceptors, including sulfite, for which the terminal reductase was recently identified as an octaheme c-type cytochrome that contains an atypical heme binding site. In this study, several additional components involved in sulfite reduction were identified. These include SirCD that form a membrane-bound electron-transferring complex with SirA, SirBI that appear to be involved in protein …

The Role Of Antimicrobial Compounds In The Life Cycle Of The Symbiotic Bacterium, Xenorhabdus Nematophila, Swati Singh

Theses and Dissertations

The bacterium Xenorhabdus nematophila maintains a mutualistic relationship with the entomopathogenic nematode Steinernema carpocapsae and is also pathogenic towards insect larvae. X. nematophila possesses a large number of gene clusters potentially involved in antimicrobial production. Several antibiotics, including xenocoumacin (Xcn) produced at high levels in broth cultures, have been characterized. In this study I established that during nematode invasion of the insect body cavity (hemocoel) gut microbiota enter the hemocoel representing potential competitors for X. nematophila. As infection progressed some transient species, such as Staphylococcus saprophyticus disappeared early in infection, while other persistent species such as Enterococcus faecalis proliferated. S. …

Small Rna, Cyclic-Di-Gmp And Phenolic Compounds Regulate The Type Iii Secretion System In Bacterial Phytopathogens, Devanshi Khokhani

Theses and Dissertations

Type III Secretion System (T3SS) is an essential virulence factor in many Gram-negative bacterial pathogens. Expression of T3SS consumes large amount of energy. Hence it is tightly regulated by bacteria through several mechanisms. In this work we screened a library of phenolic compounds and found several compounds that

dramatically downregulate T3SS in Erwinia amylovora 273. Additionally, the role of small RNA (sRNA) chaperone, Hfq, and a secondary messenger, cyclic-di-GMP in T3SS regulation in Dickeya dadantii 3937 was also examined. Chapter 1 provides a brief overview of the history and virulence mechanisms of two phytopathogens - Erwinia amylovora 273 and Dickeya …