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Normal epithelial and triple-negative breast cancer cells show the same invasion potential in rigid spatial confinementFicorella, Carlotta, Martinez Vazquez, Rebeca, Heine, Paul, Lepera, Eugenia, Cao, Jing, Warmt, Enrico, Osellame, Roberto, Käs, Josef A. 26 April 2023 (has links)
The extra-cellular microenvironment has a fundamental role in tumor growth and progression,
strongly affecting the migration strategies adopted by single cancer cells during metastatic invasion. In
this study, we use a novel microfluidic device to investigate the ability of mesenchymal and epithelial
breast tumor cells to fluidize and migrate through narrowing microstructures upon chemoattractant
stimulation. We compare the migration behavior of two mesenchymal breast cancer cell lines and one
epithelial cell line, and find that the epithelial cells are able to migrate through the narrowest
microconstrictions as the more invasive mesenchymal cells. In addition, we demonstrate that
migration of epithelial cells through a highly compressive environment can occur in absence of a
chemoattractive stimulus, thus evidencing that they are just as prone to react to mechanical cues as
invasive cells
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The little engine that could: Characterization of noncanonical components in the speed-variable flagellar motor of the symbiotic soil bacterium Sinorhizobium melilotiSobe, Richard Charles 07 June 2022 (has links)
The bacterial flagellum is a fascinating corkscrew-shaped macromolecular rotary machine used primarily to propel bacterial cells through their environment via the conversion of chemical potential energy into rotational power and thrust. Flagella are the principal targets of complex chemotaxis systems, which allow microbes to navigate their habitats to locate favorable conditions and avoid harmful ones by continuous sampling of environmental compounds and cues. Flagella serve as surface and temperature sensors, mediators of host cell adherence by bacterial pathogens and symbionts alike, and important virulence factors for disease-causing microbes. They play several essential roles in accelerating the foundational stages of biofilm formation, during which bacteria build highly intricate microbial communities with increased resistance to predation and environmental assaults. Flagellum-mediated chemotaxis has broad and impactful implications in fields of bioremediation, targeted drug delivery, bacterial-mediated cancer therapy and diagnostics, and cross-kingdom horizontal gene transfer.
While the core structural and functional components of flagella have been well characterized in the closely related enteric bacteria, Escherichia coli and Salmonella typhimurium, major departures from this paradigm have been identified in other diverse species that merit further investigation. Many bacteria employ additional reinforcement modules to surround and stabilize their more powerful flagellar motors and provide increased contact points in the inner membrane, the peptidoglycan sacculus, and, in Gram-negative bacteria, the outer membrane. Additionally, the soil-dwelling bacterium Sinorhizobium meliloti exhibits marked distinctions in the regulation, structure, and function of its navigation systems. S. meliloti is a nitrogen-fixing symbiont of the agronomically valuable leguminous plant, Medicago sativa Lucerne, and uses its coupled chemotaxis and flagellar motility systems to search for host plant roots to colonize. Following root colonization, the bacterium converts to a nitrogen-fixing factory for the plant and the combined influences of this symbiosis can quadruple the yields of the host.
This dissertation is aimed at delivering a thorough representative overview of the processes facilitating bacterial flagellum-mediated chemotaxis and motility. Chapter 1 describes the interplay between chemotaxis and flagellar motility pathways as well as the structure, function, and regulation of these systems in several model bacteria. Particular emphasis is placed on the comparison of flagellar systems from the soil-dwelling legume symbiont, Sinorhizobium meliloti with other model systems, and a brief introduction is provided for its primary counterpart, the agronomically valuable legume, Medicago sativa, more commonly referred to as alfalfa.
Chapter 2 embodies the first report of a flagellar system to require two copies of a protein known as FliL for its function. FliL is found in all bacterial flagellar systems reported to date but is only essential for some to drive motility. The more conserved copy of the protein has retained the title of FliL and several experiments to assay the proficiency of flagellar motor function revealed that in the absence of FliL swimming is essentially abolished as is the presence of flagella on the cell body. Flagellar motor activity and swimming proficiency of mutants lacking the FliL-paralog MotF was nearly as abysmal as those without FliL but flagellation was essentially normal indicating distinct roles for the two proteins. FliL is implicated in initial stator recruitment to the motor while MotF was found to serve as a power or speed modulator. A model to accommodate and explain the roles of these proteins in the flagellar motor of S. meliloti is provided.
Chapter 3 links a never-before characterized flagellar protein, currently named Orf23, to a role in promoting maximum swimming velocity and perhaps stator alignment with the rotor in a peptidoglycan-dependent manner. The loss of LdtR, a transcriptional regulator of peptidoglycan-modification genes, caused defects in swimming motility that are restored only by removal of Orf23 or by replacing a nonpolar glycine with a polar serine in the periphery of stator units. Bioinformatics analyses, immunoblotting, and membrane topology reporter assays revealed that Orf23 is likely embedded in the inner membrane and that the remainder of the protein extends into the periplasm. Building on findings from Chapter 2, Orf23 is anticipated to influence stator positioning through interactions with MotF, FliL, and/or stator units directly. The chapter is concluded with the description of future experiments aimed to more thoroughly characterize Orf23.
Altogether, this work increases the depth and breadth of knowledge regarding the composition and function of the speed-variable bacterial flagellar motor. We have identified several components required for stator incorporation and function, as well as an accessory component that improves stator performance. A wise society will draw inspiration from these fascinating and powerful machines to inform new technologies to achieve modern goals including targeted drug delivery, bioremediation, and perhaps one day our own exploration. / Doctor of Philosophy / Bacteria are small autonomous single-celled organisms capable of existing and thriving in highly diverse environments. Motility is achieved by these organisms in various ways, but the most common approach is to produce one or more corkscrew-shaped propeller systems known as flagella that are constructed upon and anchored within the wall of the bacterial cell. Rotation of these propellers relies on power converters known as stators to transform the flow of ions down self-produced gradients into useful rotational energy. This process can be likened to the way that the stored energy of water behind a dam can be harnessed and used to power hydroelectric generators. While the core components of flagellar motors are well conserved and understood among distantly related bacteria, billions of years of evolution and refinement of additional structures have allowed bacteria to accommodate swimming in diverse habitats with e.g. low nutrient availability or high viscosity.
Here we describe the discovery and characterization of additional components in the flagellar motor system of the soil-dwelling bacterium Sinorhizobium meliloti to navigate soil environments. We report the first identification of a flagellar motor that requires two copies of a pervasive flagellar motor protein known as FliL and have named the more distinct version of the protein MotF. We found that FliL is required for the power converter components to install into the motor and that MotF is necessary to activate them. Next, we identify another motor component, Orf23, that is dispensible for motility but appears to be required to achieve maximum swimming velocity and may serve to shift the motor into a "higher gear". We find that disruption of a regulator of cell wall modification systems leads to defects in motility that are only restored when Orf23 is removed or when the power converter is modified. Ideas are proposed for how FliL, MotF, and Orf23 are integrated into the motor and may contribute to stator function.
An advanced understanding of the mechanisms governing flagellar motor structure and function will provide avenues for the improvement of bacteria-based agricultural improvements, development of optimized bacteria-mediated drug delivery systems, bioremediation techniques, and more.
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Development of an Injectable Hydrogel Platform to Capture and Eradicate Glioblastoma Cells with Chemical and Physical StimuliKhan, Zerin Mahzabin 15 May 2023 (has links)
Glioblastoma multiforme (GBM) is the most aggressive type of primary brain tumor. Even after patients undergo maximum and safe surgical resection followed by adjuvant chemotherapy and radiation therapy, residual GBM cells form secondary tumors which lead to poor survival times and prognoses for patients. This tumor recurrence can be attributed to the inherent GBM heterogeneity that makes it difficult to eradicate the therapy-resistant and tumorigenic subpopulation of GBM cells with stem cell-like properties, referred to as glioma stem cells (GSCs). Additionally, the migratory nature of GBM/GSCs enable them to invade into the healthy brain parenchyma beyond the resection cavity to generate new tumors. In an effort to address these challenges of GBM recurrence, this research aimed to develop a biomaterials-based approach to attract, capture, and eradicate GBM cells and GSCs with chemical and physical stimuli. Specifically, it is proposed that after surgical removal of the primary GBM tumor mass, an injectable hydrogel can be dispensed into the resection cavity for crosslinking in situ. A combination of chemical and physical cues can then induce the migration of the residual GBM/GSCs into the injectable hydrogel to localize and concentrate the malignant cells prior to non-invasively abating them. In order to develop this proposed treatment, this dissertation focused on 1) characterizing and optimizing the thiol-Michael addition injectable hydrogel, 2) attracting and entrapping GBM/GSCs into the hydrogel with CXCL12-mediated chemotaxis, and 3) assessing the feasibility of utilizing histotripsy to mechanically and non-invasively ablate cells entrapped in the hydrogel. The results revealed that hydrogel formulations comprising 0.175 M NaHCO3(aq) and 50 wt% water content were the most optimal for physical, chemical, and biological compatibility with the GBM microenvironment on the basis of their swelling characteristics, sufficiently crosslinked polymer networks, degradation rates, viscoelastic properties, and interactions with normal human astrocytes. Loading the hydrogel with 5 µg/mL of CXCL12 was optimal for the slow, sustained release of the chemokine payload. A dual layer hydrogel platform demonstrated in vitro that the resulting chemotactic gradient induced the invasion of GBM cells and GSCs from the extracellular matrix and into the synthetic hydrogel with ameboid migration and myosin IIA activation. This injectable hydrogel also demonstrated direct therapeutic benefits by passively eradicating entrapped GBM cells through matrix diffusion limitations as well as decreasing the GBM malignancy and GSC stemness upon cancer cell-hydrogel interactions. Research findings revealed the hydrogels can be synthesized under clinically relevant conditions mimicking GBM resection in vitro, and hydrogels were distinguishable with ultrasound imaging. Furthermore, the synthetic hydrogel was acoustically active to generate a stable cavitation bubble cloud with histotripsy treatment for ablation of entrapped red blood cells with well-defined, uniform lesion areas. Overall, the results from this research demonstrate this injectable hydrogel is a promising platform to attract and entrap malignant GBM/GSCs for subsequent eradication with chemical and physical stimuli. Further development of this platform, such as by integrating electric cues for electrotaxis-directed cell migration, may help to improve the cancer cell trapping capabilities and thereby mitigate GBM tumor recurrences in patients. / Doctor of Philosophy / Glioblastoma multiforme (GBM) is the deadliest type of primary brain cancer. Upon GBM diagnosis, patients first undergo surgery to remove the tumor from the brain. After waiting several weeks for the wound healing process due to surgery, patients are administered chemotherapy with drugs and radiation therapy to eradicate any remaining GBM cells. Even after undergoing these combinatorial treatments, the cancer returns and leads to median survival times of only 15 months in 90% of patients. Complete GBM eradication is difficult, since the cancer cells can migrate into healthy brain tissue beyond the original tumor site. Additionally, GBM is highly heterogenous and composed of different cell types that can resist chemotherapy and radiation therapy, which lead to secondary tumors and cancer relapse. To address these challenges, this dissertation aimed to develop a polymer-based material (specifically a hydrogel) that can attract, entrap, and localize the GBM cells into the material to subsequently eradicate them with chemical and physical signals. This hydrogel platform would have important clinical implications, as it can potentially be dispensed into the empty cavity after surgical removal of the tumor in the brain. The hydrogel can then be harnessed to attract residual GBM cells for directed migration into the hydrogel to concentrate and localize the cancer cells for their subsequent destruction with a non-invasive technology. In order to develop this proposed treatment, this dissertation investigated the following three aims: 1) to study and optimize the injectable hydrogel for chemical, physical, and biological compatibility with the GBM therapy; 2) to utilize chemical signals to attract and entrap the GBM cells into the hydrogel; and 3) to apply focused ultrasound with high amplitude, short duration negative pressure pulses to mechanically fractionate and destroy the cells entrapped in the hydrogel. The results revealed that the hydrogel comprising 0.175 M NaHCO3(aq) and 50 wt% water content was the most optimal formulation. CXCL12 chemokine proteins loaded into the hydrogel at 5 µg/mL released slowly from the hydrogel to generate a chemical gradient and thereby attract GBM cells to promote their invasion into the hydrogel matrix. The hydrogel was demonstrated to respond well to focused ultrasound treatment, which was capable of mechanically fractionating and destroying red blood cells in the hydrogel uniformly. Overall, the results from this research provide support that this hydrogel platform can attract, entrap, and eradicate GBM cells with chemical and physical stimuli. Hence, further improvement of this platform and implementation of this novel GBM treatment may in the future help minimize GBM cancer relapse in patients who undergo conventional therapies, thereby extending their survival times.
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Self-propelled particles with inhomogeneous activityVuijk, Hidde Derk 08 December 2022 (has links)
Movement is an essential feature of life. It allows organisms to move towards a more favorable environment and to search for food. There are many biological systems that fall under the category active matter, from molecular motors walking on microtubules inside cells to flocks of birds. What these systems have in common is that each of its constituents converts energy into directed motion, that is, they propel themselves forward. Besides the many biological examples, there is also synthetic active matter, these are self-propelled particles made in a laboratory. These are typically colloidal sized particles that can propel themselves forward by self-phoresis. In this work the focus is on the low Reynolds number regime, meaning that the typical size of the constituents is less than a few micrometers. The models that are used to describe such active matter are can be viewed as nonequilibrium extensions to Brownian motion (the thermal motion of small particles dissolved in a fluid).
In many systems the self-propulsion speed (activity) is not homogeneous in space: the particles swim faster in some areas than in others. The main topic of this dissertation is how a single active particle, or a few active particles tied together by a potential, behave in such systems. It is known that a single active particle without any steering mechanism spends most time in the regions where it moves slowly, or in other words, they spend most time in regions where they are less active.
However, here it is shown that, even though they spend most time in the less active regions, dynamical properties, such as the probability to move towards the more active regions is higher than moving towards the less active regions.
Furthermore, when the active particles are connected to a passive Brownian 'cargo' particle, chained together to form a colloidal sized polymer, or fixed to another active particle, the resulting active dimers or polymers either accumulate in the high activity regions or the low activity regions, depending on the friction of the cargo particle, the number of monomers in the polymer, or the relative orientation of active particles.
Lastly, when the activity is both time- and space-dependent, a steady drift of active particles can be induced, without any coupling between the self-propulsion direction and the gradient in the activity. This phenomenon can be used to position the particles depending on their size.:1. Brownian Motion
2. Active Matter
3. Modeling Active Matter
4. Introduction: Inhomogeneous activity
5. Pseudochemotaxis
6. Cargo-Carrying Particles
7. Active Colloidal Molecules
8. Time-Varying Activity Fields
Appendix: Hydrodynamics
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Cell Biological and Microfabrication Approaches Towards the Understanding of Transmigration and Nonmuscle Myosin II AssemblyBreckenridge, Mark T. 07 October 2010 (has links)
No description available.
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Analysis Of The Polymorphonuclear Leukocyte Formylpeptide Receptor in Aggressive PeriodontitisManey, Pooja 27 August 2009 (has links)
No description available.
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Effect of Extrinsic and Intrinsic Factors on Cancer InvasionEsmaeili Pourfarhangi, Kamyar January 2019 (has links)
Metastasis is the leading cause of death among cancer patients. The metastatic cascade, during which cancer cells from the primary tumor reach a distant organ and form multiple secondary tumors, consists of a series of events starting with cancer cells invasion through the surrounding tissue of the primary tumor. Invading cells may perform proteolytic degradation of the surrounding extracellular matrix (ECM) and directed migration in order to disseminate through the tissue. Both of the mentioned processes are profoundly affected by several parameters originating from the tumor microenvironment (extrinsic) and tumor cells themselves (intrinsic). However, due to the complexity of the invasion process and heterogeneity of the tumor tissue, the exact effect of many of these parameters are yet to be elucidated. ECM proteolysis is widely performed by cancer cells to facilitate the invasion process through the dense and highly cross-linked tumor tissue. It has been shown in vivo that the proteolytic activity of the cancer cells correlates with the cross-linking level of their surrounding ECM. Therefore, the first part of this thesis seeks to understand how ECM cross-linking regulates cancer cells proteolytic activity. This chapter first quantitatively characterizes the correlation between ECM cross-linking and the dynamics of cancer cells proteolytic activity and then identifies ß1-integrin subunit as a master regulator of this process. Once cancer cells degrade their immediate ECM, they directionally migrate through it. Bundles of aligned collagen fibers and gradients of soluble growth factors are two well-known cues of directed migration that are abundantly present in tumor tissues stimulating contact guidance and chemotaxis, respectively. While such cues direct the cells towards a specific direction, they are also known to stimulate cell cycle progression. Moreover, due to the complexity of the tumor tissue, cells may be exposed to both cues simultaneously, and this co-stimulation may happen in the same or different directions. Hence, in the next two chapters of this thesis, the effect of cell cycle progression and contact guidance-chemotaxis dual-cue environments on directional migration of invading cells are assessed. First, we show that cell cycle progression affects contact guidance and not random motility of the cells. Next, we show how exposure of cancer cells to contact guidance-chemotaxis dual-cue environments can improve distinctive aspects of cancer invasion depending on the spatial conformation of the two cues. In this dissertation, we strive to achieve the defined milestones by developing novel mathematical and experimental models of cancer invasion as well as utilizing fluorescent time-lapse microscopy and automated image and signal processing techniques. The results of this study improve our knowledge about the role of the studied extrinsic and intrinsic cues in cancer invasion. / Bioengineering / Accompanied by fourteen .avi files.
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Elucidating three novel mechanisms of Pseudomonas syringae pathogenicityClarke, Christopher R. 12 March 2012 (has links)
Pseudomonas syringae is an important bacterial plant pathogen that, as a species, is known to cause disease on hundreds of different plant species. However, any individual pathovar of P. syringae typically only causes disease on one or a few plant species, which constitute the host range of the pathovar. Plants are generally resistant to most pathogens primarily because the plant innate immune system is capable of recognizing conserved microbial-associated molecular patterns (MAMPs). Adapted pathovars of P. syringae secrete effector proteins through a Type Three Secretion System (T3SS) to suppress the immune response elicited by their MAMPs. However, secretion of effectors can also trigger a strong plant immune response if the plant harbors resistance proteins capable of recognizing the secreted effectors. Successful pathovars, therefore, must secrete a combination of effectors capable of suppressing MAMP/Pattern-Triggered Immunity (PTI) without eliciting Effector-Triggered Immunity. Here we identify several novel strategies employed by P. syringae to overcome the plant immune system and cause disease. First, we demonstrate that, in place of the canonical T3SS used by all known pathogens of P. syringae, several apparently nonpathogenic isolates of P. syringae employ a novel T3SS that is functional but not necessary for colonization of plants. Despite being closely related to pathogenic isolates of P. syringae, the isolates employing the noncanonical T3SS do not cause disease on any tested plants and instead appear to act more as commensal organisms. Second, we advance the understanding of PTI by identifying a second region of bacterial flagellin that triggers PTI in addition to the archetypical MAMP flg22, which is recognized by the archetypical plant receptor FLS2. This new elicitor, termed flgII-28, is also detected by FLS2 and appears to be under selection in very closely related lineages of P. syringae. Alleles of flagellin present in one recently expanded and agriculturally problematic lineage of P. syringae appear to trigger less PTI on their host plant, tomato, than the ancestral allele suggesting that avoidance of PTI through allelic diversity in MAMPs is an effective alternative strategy to suppression of PTI through delivery of effectors. Finally, we start to elucidate a role for chemotaxis (chemical-directed movement) in P. syringae pathogenicity. Not only is chemotaxis required for pathogenicity of P. syringae on plants, but it also appears to contribute to delimiting the host range of several P. syringae pathovars. These results highlight that additional aspects of P. syringae pathogenicity, such as chemotaxis, can directly contribute to defining the host range of individual P. syringae pathovars. The current paradigm of P. syringae pathogenicity posits that MAMPS and the repertoire of effector proteins are the primary determinant of the host range of any P. syringae pathovar; in contrast these results inspire a more nuanced view of pathogenicity that considers multiple aspects of the infection process. / Ph. D.
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Novel Perspectives on the Utilization of Chemotactic Salmonella Typhimurium VNP20009 as an Anticancer AgentBroadway, Katherine Marie 22 August 2018 (has links)
Attenuated bacterial strains have been investigated on the premise of selective tumor colonization and drug delivery potential for decades. Salmonella Typhimurium VNP20009 was derived from the parental strain 14028 through genetic modification and tumor targeting ability, being well studied for anticancer effects in mice. In 2001 Phase 1 Clinical Trials, patients diagnosed with melanoma were introduced with VNP20009, resulting in safe delivery of the strain and targeting to the tumor, however no anticancer effects were observed. Recently, it was discovered that VNP20009 contains a SNP in cheY, which encodes the chemotaxis response regulator of flagellar motor function, rendering the strain deficient in chemotaxis. Replacement of cheY with the 14028 wild-type copy resulted in a 70% restoration of phenotype in traditional chemotaxis capillary assays compared to the parental strain. We attempted to optimize the chemotactic potential of VNP20009 but were unable without reversing the attenuated state of VNP20009.
Due to the role of chemotaxis in bacterial tumor colonization and eradication remaining unclear, we aimed to compare VNP20009 and VNP20009 cheY+ primary tumor colonization and impact on metastasis in an aggressive 4T1 mouse mammary carcinoma model. Bacterial tumor colonization and metastatic potential of the cancerous cells to the lungs appear bacterial chemotaxis independent. Moreover, mice bearing tumors exposed to Salmonella exhibited increased morbidity that was associated with significant liver disease. Our results suggest that in our timeline VNP20009 may not be safe or efficacious when used in the context of immunocompetent animals with aggressive, metastatic breast cancer. In a novel approach, we aimed to understand the bacterial-cancer cell relationship within the tumor microenvironment, with an emphasis on gene expression changes occurring within the eukaryotic transcriptome. We employed the B16-F10 mouse melanoma model because VNP20009 is known to colonize and eradicate these tumors in mice. First, we optimized a timeline for Salmonella treatment of mouse melanoma, finding a dramatic delay in tumor growth between 2 and 7 days due to the presence of Salmonella. Additionally, we observed upregulation of the IFN-gamma signaling pathway within tumor tissue upon exposure to Salmonella after 7 days. In future studies, we aim to analyze the bacterial transcriptome in the tumor microenvironment to gain unique understanding and contribute to knowledge supporting bacterial-mediated cancer therapies. / Ph. D. / Bacteria have become our allies in the fight against cancer. Strains of Salmonella, normally thought of as a cause of gastrointestinal discomfort, are able to target cancer in the body and effectively shrink tumors in several animal models. Specifically, a strain of Salmonella Typhimurium called VNP20009, has shown great promise as an anticancer agent. Research on VNP20009 culminated in a Phase 1 Clinical Trial in which safe delivery of the strain and targeting to the tumor were achieved, however no anticancer effects were observed. We hypothesized further targeting of Salmonella could be achieved using chemotaxis, the coordination of flagellar driven movement with sensing environmental chemical gradients, akin to the nose of the bacterium. We discovered strain VNP20009 to be defective in chemotaxis, due to a genetic mutation that occurred during the strain’s construction. We were able to restore chemotaxis of the strain, at least partially, and discovered we could not further optimize chemotaxis without compromising the safety profile of VNP20009. We tested the effect of chemotaxis on tumor colonization in a mouse breast cancer model and found that the bacteria had an additive effect in causing liver disease and morbidity of the mice. We finally examined genome-wide gene expression changes occurring in the tumor microenvironment, as a response to anticancer agent VNP20009 colonization in a mouse melanoma model of cancer. Overall, this work contributes significantly to the understanding of VNP20009 chemotaxis and its tumor targeting abilities.
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Similarities and variations of the enterobacterial chemotaxis paradigm in Sinorhizobium melilotiAgbekudzi, Alfred 21 December 2023 (has links)
Sinorhizobium meliloti is a nitrogen-fixing endosymbiont of the legume Medicago sativa commonly known as alfalfa. It uses flagellar rotation and chemotaxis to seek roots of host plants to inhabit. This symbiosis serves as a great model system for studying biological nitrogen fixation and plant-microbe interactions. Since alfalfa brings enormous economic value to the USA, investments into the knowledge of the chemotaxis process that initiates symbiosis have the ability to mitigate deterioration of the environment and significantly increase food supply. The chemotaxis system in the enteric bacteria Escherichia coli is well studied and has been a great resource to understanding the process in other bacterial systems including our model organism S. meliloti.
This dissertation compares and contrasts the chemotaxis features in E. coli and S. meliloti and investigates their molecular functions. Based on the understanding gained so far, we attempt to offer plausible explanations for the underlying mechanisms of the S. meliloti chemotaxis pathway. Chapter 1 describes why biological nitrogen fixation is important for agriculture and the health of our environment. This chapter also sheds light on the symbiotic relationship between alfalfa and S. meliloti, which culminates in the formation of nitrogen fixing nodules. We expound on the chemotaxis systems in E. coli and other bacteria including S. meliloti and Bacillus subtilis.
In chapter 2, we compare the distribution of C-terminal pentapeptide-bearing receptors and the adaptation proteins that they tether in E. coli and S. meliloti. The stoichiometry data show that the ratio of pentapeptide-bearing chemoreceptors to chemotaxis protein (Che)R and CheB molecules are approximately 500- and 160-fold higher in S. meliloti than in E. coli, respectively. Since not all chemoreceptors in chemotactic bacteria have and utilize the pentapeptide moiety, we investigated the S. meliloti system and observed a strong interaction between CheR, activated CheB and the isolated pentapeptides via in-vitro binding studies. On the contrary, unmodified CheB showed weak binding to the pentapeptide. Through in-vivo studies, we highlighted the physiological necessity of the pentapeptide for chemotaxis. S. meliloti strains with substitutions of the conserved tryptophan residue to alanine in one or all four pentapeptide-bearing Methyl-accepting Chemotaxis Proteins (MCPs) resulted in diminished or loss of chemotaxis to glycine betaine, lysine, and acetate, ligands sensed by pentapeptide-bearing McpX and pentapeptide-lacking McpU and McpV, respectively. The flexible linker connecting the pentapeptide to the MCPs together with the pentapeptide itself were shown to be functional on pentapeptide-lacking chemoreceptors and provided adaptational assistance to other chemoreceptors that lacked a functional pentapeptide. Based on these results, we concluded that S. meliloti employs a pentapeptide-dependent adaptation system with MCPs possessing a consensus pentapeptide motif (N/D)WE(E/N)F). Finally, we postulated that the higher abundance of CheR and CheB in S. meliloti compared to E. coli compensates for the lower number of pentapeptide-bearing chemoreceptors in the chemosensory array.
In chapter 3, we explored the putative phosphatase function of a novel protein, CheT, on phosphorylated S. meliloti response regulators. The kinase CheA phosphorylates both the sink response regulator, CheY1, and the flagellar motor interacting response regulator, CheY2. CheY1 competes with CheY2 for these phosphate groups, but we have discovered another layer of complexity to the story. Sequence comparison of S. meliloti CheT and the E. coli phosphatase CheZ shows little sequence homology. However, both proteins share a DXXXQ phosphatase motif. Phosphorylation assays performed using radiolabeled [γ-32P]-ATP revealed that CheT acts as a phosphatase of CheY1~P and accelerates dephosphorylation of CheY1~P by at least two-fold. Interestingly, we also discovered that CheT interacts with CheR, but this interaction did not affect the enzymatic activity of either protein under the examined conditions. Unexpectedly, a cheT deletion strain and strains carrying mutations in the phosphatase motif exhibit an increased swimming speed, a phenotype that does not conform with the model that the absence of CheT or its activity results in increased CheY2~P levels and reduced swimming speed. We concluded that a revised S. meliloti signal termination pathway should include CheT enhancing dephosphorylation of CheY1~P and sensory adaptation involving the yet unknown function of CheT on CheR.
While the adaptation system in S. meliloti is unexplored, this work provides first insights into fascinating deviations and similarities to the known paradigm. We have also delivered evidence that the S. meliloti signal termination system requires a dedicated phosphatase. The knowledge gained here takes us a step closer to enhance the S. meliloti chemotaxis pathway towards improved symbiosis with alfalfa and to reduce our dependence on environmentally deleterious synthetic fertilizers. / Doctor of Philosophy / Like all living things, bacteria inhabit a constantly changing environment, hence the need to take up and process this information. Bacterial cells have evolved sophisticated biological tools to tackle this challenge of detecting, responding and adapting to environmental signals like nutrients, toxins, temperature changes, light, metabolites, etc. Motile bacteria such as Escherichia coli, a gut resident microbe, and Sinorhizobium meliloti, a soil dwelling bacterium, direct their swimming behavior in response to chemical gradients within the milieu through a process termed chemotaxis. Generally, this vital process enables a bacterium to escape harmful chemicals and gravitate towards beneficial ones. However, S. meliloti specifically employs chemotaxis to locate the roots of its plant host (alfalfa) and to establish a symbiotic relationship through which the bacteria provide essential nitrogen for plant growth in exchange for nourishment. The biological tools employed by S. meliloti for chemotaxis include environmental sensing receptors called Methyl-accepting Chemotaxis Proteins (MCPs) and proteins inside the bacterial cell that transfer information from the sensors to long, helical rotating propeller structures, called flagella. Importantly, the efficiency of this process hinges on a timely termination of information flow and the ability to adapt to prevailing stimuli while maintaining sensitivity to increasing concentration gradients. This work investigates the function of the C-terminal five amino acid motif of MCPs known to be critical for adaptation in E. coli and the phosphatase activity of a novel protein, CheT, in signal termination of S. meliloti chemotaxis system.
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