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UNIVERSITY of CALIFORNIA SANTA CRUZ Tlpd Mediates Chemotactic UNIVERSITY OF CALIFORNIA SANTA CRUZ TlpD mediates chemotactic repellent responses to reactive oxygen species that are relevant to Helicboacter pylori gastric gland colonization A dissertation submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in MICROBIOLOGY AND ENVIRONMENTAL TOXICOLOGY by Kieran D. Collins December 2017 The Dissertation of Kieran D. Collins is approved: ____________________________________ Professor Karen Ottemann, chair ____________________________________ Professor Fitnat Yildiz ____________________________________ Professor Doug Kellogg _____________________________ Tyrus Miller Vice Provost and Dean of Graduate Studies Table of Contents Abstract ........................................................................................................................................................ ix Acknowledgements .................................................................................................................................. xi Internal sense of direction: Sensing and signaling from cytoplasmic chemoreceptors .......................................................................................................................................... 1 Summary ........................................................................................................................................ 1 Introduction .................................................................................................................................. 2 Chemoreceptors signal via interactions with the key signaling proteins CheW and CheA ......................................................................................................................................... 4 Signal transduction in chemoreceptors ............................................................................. 6 Adaptation in chemoreceptors .............................................................................................. 9 Higher order structures of cytoplasmic chemoreceptors ........................................ 11 Cytoplasmic chemoreceptors are prevalent in Bacteria and Archaea ................ 12 Ligand-binding domains found in cytoplasmic chemoreceptors .......................... 13 Subcellular localization of cytoplasmic chemoreceptors ......................................... 18 Cytoplasmic chemoreceptors with nearly exclusive localization at the pole with the transmembrane chemoreceptor arrays ........................................................ 19 Cytoplasmic chemoreceptors with both polar colocalization with transmembrane receptor clusters and diffuse cytoplasmic localization ........... 21 iii Cytoplasmic chemoreceptors that form clusters distinct from the transmembrane polar receptors ........................................................................................ 23 Cytoplasmic chemoreceptors with dynamic cytoplasmic localization ............... 24 Cytoplasmic chemoreceptors with unknown cytoplasmic localization ............. 26 Conclusions ................................................................................................................................ 27 Acknowledgements ................................................................................................................. 28 References .................................................................................................................................. 30 The Helicobacter pylori CZB cytoplasmic chemoreceptor TlpD forms an autonomous polar chemotaxis signaling complex that mediates a tactic response to oxidative stress ................................................................................................................................... 59 Abstract ........................................................................................................................................ 60 Introduction ............................................................................................................................... 61 Methods ....................................................................................................................................... 65 Results .......................................................................................................................................... 72 Discussion ................................................................................................................................... 80 Acknowledgements ................................................................................................................. 88 Figures .......................................................................................................................................... 89 Chemotaxis allows bacteria to overcome host-generated reactive oxygen species that constrain gland colonization ................................................................................................... 121 Abstract: .................................................................................................................................... 121 Introduction: ............................................................................................................................ 122 Results ........................................................................................................................................ 125 iv tlpD H. pylori show antral colonization defects in WT hosts ................................. 125 The loss of tlpD increases corpus gland load, while the loss of chemotaxis signaling increases gland loads throughout the stomach. ..................................... 125 The loss of tlpD or chemotaxis results in a reduction in gland occupancy throughout the stomach in WT hosts ............................................................................. 126 tlpD mutants show evidence of increased ROS exposure relative to WT H. pylori ........................................................................................................................................... 127 Gland colonization defects of tlpD are rescued in hosts deficient in H 2O2 production by gastric epithelial cells. ............................................................................ 128 Gland colonization defects of tlpD are rescued in hosts deficient in O 2- production by phagocytes. ................................................................................................. 130 Discussion ................................................................................................................................. 131 Acknowledgements ............................................................................................................... 134 Methods: .................................................................................................................................... 135 Figures ........................................................................................................................................ 139 References ................................................................................................................................ 147 Exploring possible mechanisms of TlpD ROS sensing ............................................................ 166 Introduction: ............................................................................................................................ 166 Results: ....................................................................................................................................... 171 Conclusions: ............................................................................................................................. 182 Methods: .................................................................................................................................... 188 References: ............................................................................................................................... 207 v Future directions .................................................................................................................................. 226 References: ............................................................................................................................... 227 vi Table of Figures Figure 1. Domain structure of transmembrane and soluble chemoreceptors. ..... 49 Figure 2. Schematic of chemotaxis signal transduction. ................................................ 50 Figure 3. Abundance of cytoplasmic chemoreceptors ................................................... 52 Figure 4. Most common domains found in soluble chemoreceptors. ....................... 54 Figure 5. Examples of the diverse subcellular locations of cytoplasmic chemoreceptors. .................................................................................................................. 55 Table 1. Domains identified in cytoplasmic chemoreceptors. .................................... 58 Table 2. Characteristics of well-studied cytoplasmic chemoreceptors. .................. 58 Fig. 1. TlpD is stably produced when the sole chemoreceptor and confers chemotactic function in a soft agar assay. ................................................................. 89 Fig. 2. TlpD localizes to the pole and coordinates a chemotaxis complex there .. 92 Fig. 3. TlpD associates with the membrane fractions via interactions with chemoreceptors and chemotaxis signaling proteins. ...........................................
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