Eukaryotic initiation factor 4E (eIF4E) is a key part of initiation and regulation of translation in human cells. Three members of human eIF4E proteins have been characterized: eIF4E1, eIF4E2 and eIF4E3. Cellular stress causes translation initiation inhibition followed by disassembly of the polysomes, those processes are accompanied by the assembly of cytoplasmic RNA granules, called stress granules (SG). Stress granules are dynamic structures whose composition may vary depending on the cell type and the stress stimulus. In this study, human cells were subjected to the following stress conditions: high temperature (HS), sodium arsenite (AS) or hypoxia. Using fluorescence microscopy, pairs of human translational initiation factors from the 4E protein family were visualized and their localization to SG was assessed with one GFP- 4E incorporated in the stable cell line and the other one detected endogenously. Here we show eIF4E1 being a part of all the SGs, both in HS and AS conditions. Next, the eIF4E1 and eIF4E3 proteins together form more SGs than proteins eIF4E1, respectively eIF4E3, with eIF4E2. And last, that the presence of the particular 4E protein has no effect on the composition of SGs. Furthermore, selected groups of proteins were assessed for their potential to localize to the SGs under HS...

No description available.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第20338号 / 工博第4275号 / 新制||工||1662(附属図書館) / 京都大学大学院工学研究科社会基盤工学専攻 / (主査)教授 石田 毅, 教授 林 為人, 准教授 奈良 禎太 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

Quorum sensing (QS) is a type of microbial communication used by bacteria to coordinate their behavior based on population density, regulating complex processes like biofilm formation and virulence, among other behaviors. Quorum quenching (QQ), on the other hand, disrupts this communication, usually by degradation of the QS signaling molecule. QQ offers a potential strategy for controlling bacterial behaviors linked to pathogenicity and biofouling. Despite significant advances in understanding and modeling the spatial-temporal behavior of QS, predictive modeling of QQ remains nascent, with a notable gap in the quantitative assessment of QQ's impact on QS. Here we show quantitative evaluation and characterization of the effect of QQ on QS in agar-based experiments, combined with an experimentally validated computational model. This research utilizes green fluorescence in E. coli MG 1655 as an indicator of QS activation, focusing on the degradation of Acyl-Homoserine Lactone (AHL), a key QS molecule in Gram-negative bacteria linked to pathogenicity, by the AiiA enzyme in engineered AiiA-producing Salmonella Typhimurium 14028. Our findings suggest that QQ more effectively influences QS in spatial configurations of the populations with larger interaction surfaces and shorter diffusion distances. Contrary to our initially held hypothesis, the primary effect of QQ is not a delay in QS onset but rather an attenuation of QS activity, with the area-under-the-curve of fluorescence serving as a quantitative metric. This study also introduces, to the best of our knowledge, one of the first instances of experimentally validated predictive modeling for QQ, applied to agar-based experimental setups. We posit that the quantitative experimental characterization and modeling framework presented in this research will enhance the understanding of bacterial community interactions. Enhanced comprehension of QQ and QS behaviors holds significant promise for advancing practical applications, particularly in mitigating or diminishing undesirable QS-associated activities. This is especially relevant in areas like biofouling, waste treatment, and the reduction of infections and progression of diseases in plants and animals, areas increasingly important as concerns about drug resistance in microbes and food security escalates. / Master of Science / One of the ways bacteria communicate with each other is called quorum sensing (QS), where they use chemical signals to organize and time group behavior, including forming communities encapsulated in protective layers, called biofilms, and engaging in virulent attacks against hosts. Quorum quenching (QQ) in bacteria, however, disrupts this communication system, usually by breaking down the chemical signals that bacteria use to send messages to each other. Even though QS has been studied extensively, determining how to predict and control QQ is still a nascent area of research. Here, we studied and characterized how QQ affects QS by doing experiments with bacteria populations in agar (a jelly-like substance) and applied a computational model to explain and ultimately predict the experimental observations. Engineered QS population (E. coli MG 1655) produced Acyl-Homoserine Lactone (AHL) signaling molecules, and engineered QQ bacteria (S. Tm 14028) used the Autoinducer Inactivation A (AiiA) enzyme to break down the AHL. According to our results, QQ doesn't delay the QS bacteria's group behaviors (in our case, green fluorescent signal production); it weakens the signal instead. Understanding QQ and QS better, especially through measurements and modeling, could lead to expanded methods of deterring harmful bacterial behavior, managing waste better, and stopping diseases in plants, animals, and humans, especially with the concerning rise of drug-resistant microbes and food security. One exciting possibility is using QQ to protect plants from bacterial infections. This could be a way to shield our crops without always relying on antibiotics.

No description available.

Endgültig fehlgefaltete oder anderweitig beschädigte Proteine des Endoplasmatischen Retikulums (ER) werden durch das Proteasom in einem Prozess abgebaut, der als Endoplasmatischer Retikulum Assoziierter Abbau (ERAD) bezeichnet wird. Der Hrd1-Komplex ist ein aus mehreren Komponenten bestehender Transmembran-Proteinkomplex, der die Ubiquitinierung und den Export von Proteinen aus dem ER vermittelt, welche dann im Zytosol abgebaut werden. Trotz erheblicher Anstrengungen in den letzten zwei Jahrzehnten führte die biochemische Charakterisierung seiner Architektur und seines Mechanismus zu inkonsistenten und sogar widersprüchlichen Ergebnissen, sodass kein Konsens darüber besteht, wie Hrd1 den Proteintransport realisiert. In diesem Projekt habe ich Fluoreszenz-Mehrfarben-Einzelmolekül-Mikroskopie verwendet, um eine neue Perspektive auf die Architektur, Bildung und Dynamik des Hrd1-Komplexes zu eröffnen. Im Projektverlauf habe ich zellbiologische, experimentelle und analytische Werkzeuge entwickelt, um die Hrd1-Oligomerisierung in vivo robust zu quantifizieren und zu charakterisieren. Durch die Kombination von Mehrfarben-Einzelmolekül-Mikroskopie mit chemischer Inhibierung, der Herunterregulierung anderer Komplexkomponenten und einem neuartigen, auf Bindungswettbewerb basierenden Assay konnte ich nachweisen, dass Hrd1 ein stabiles Homo-Tetramer bildet, das über seine zytosolische Domäne Hrd1480-529 geformt wird. Durch Strukturmodellierung über AlphaFold konnte ich nachweisen, dass sich diese Domäne unabhängig von anderen Komplexkomponenten oder der Aktivität von Hrd1 zu einer kanonischen „coiled-coil“ Domäne zusammensetzt. Während diese Arbeit neue spezifische biologische Einblicke in die Hrd1-Komplexbildung liefert, dient sie auch als allgemeine Blaupause dafür, wie Einzelpartikel-Tracking verwendet werden kann, um Fragen zu beantworten, die mit klassischer Biochemie in der Regel nur begrenzt untersucht werden können. / Terminally misfolded or otherwise damaged proteins of the Endoplasmic Reticulum (ER) are degraded by the proteasome in a process termed Endoplasmic Reticulum Associated Degradation (ERAD). The Hrd1 complex is a multicomponent transmembrane protein complex that mediates ubiquitination and export of proteins from the ER to be degraded in the cytosol. Despite substantial effort in the past two decades, the biochemical characterization of its architecture and mechanism produced inconsistent and even contradictory results, yielding no consensus on how it mediates protein transport. Its elusive nature is representative of the limitations of classical biochemical approaches, whose often harsh experimental conditions directly interfere with the objects they study. In this project I used fluorescence multi-color single molecule microscopy to offer a new perspective on the architecture, formation and dynamics of the Hrd1 complex. In this process I developed cell biological, experimental and analytical tools to robustly quantify and characterize Hrd1 oligomerization in vivo. Combining live-cell dual-color single-particle tracking with chemical inhibition, downregulation of complex components and a novel, binding-competition based tracking assay, I demonstrated that Hrd1 forms a stable homo-tetramer via its cytosolic domain Hrd1480-529. By structural modeling via AlphaFold, results of which were validated with both single-particle tracking and recombinant protein expression, I showed that this domain assembles into a canonical coiled-coil domain independently of other complex components or Hrd1's activity. While yielding specific novel biological insight into Hrd1 complex formation, it also serves as a general blueprint on how dual-color single particle tracking can be used to address questions that bring classical biochemistry to its limits.

A functional sense of smell is mediated by Olfactory Receptor proteins (ORs), which reside in olfactory sensory neurons (OSNs) in the epithelium of our nose. Only a singular OR allele out of roughly 2,400 other OR alleles is expressed in every OSN⁽¹˒ ²⁾. Singular expression of the active OR gene occurs in a unique transcriptional hub⁽³⁻⁵⁾. This hub contains one OR promoter and many interchromosomal enhancers that converge upon the hub from far nuclear distances⁽⁵˒ ⁶⁾. Once in the hub, the enhancers work in tandem with each other and with the transcription factors (TFs) Lhx2, EBF, and their cofactor, Ldb1⁽⁵˒ ⁷˒ ⁸⁾ The Greek islands contain a novel “composite” motif containing an Lhx2 and EBF binding site directly next to each other⁽⁸⁾. My work aims to understand how these proteins interact with each other and the composite motif to contribute to the accumulation of many enhancers around only a single promoter in the hub. Our findings illuminate how transcription factor interactions contribute to the hub's unique DNA architecture. To investigate the biochemical foundation of OR hubs, we used 𝑒. 𝑐𝑜𝑙𝑖 to grow and purify full-length and truncated forms of Lhx2, Ebf1, and Ldb1. We used the recombinant proteins with other biochemical methods to characterize the interactions between Lhx2, Ebf1, Ldb1, and different types of DNA found in the OR hub. We used EMSAs to quantify the binding affinity that Lhx2 and Ebf1 have for promoter versus enhancer DNA. Finally, we mixed the purified full-length proteins and used fluorescence microscopy to visualize their behavior in solution. This research combined with in vivo imaging in the Lomvardas lab provides a better understanding as to how molecular interactions 𝑖𝑛 𝑣𝑖𝑡𝑟𝑜 contribute to the hub’s architecture 𝑖𝑛 𝑣𝑖𝑣𝑜, and ultimately, stable OR expression. Our biochemical studies suggest that Lhx2 and Ebf1 can bind at the same time to a single composite motif yet they seem to bind independently of one another. We have used EMSAs to determine that Lhx2 binds much better to OR enhancer DNA compared to Ebf1 and that it might stabilize enhancer contacts. We have also found that Lhx2 and Ebf1 do not cooperatively bind to enhancers- indicating that affinity alone does not explain the accumulation of TFs to the OR hub. Our 𝑖𝑛 𝑣𝑖𝑡𝑟𝑜 imaging shows that Lhx2, Ebf1, and Ldb1 self-assemble into rigid nucleoprotein condensates driven by the composite motif of enhancer DNA. This imaging work also reveals that Lhx2 and Ldb1 are scaffolding proteins with low mobility which drive rigid condensate formation over enhancers. Ebf1 displays more plasticity and turnover into condensates indicating that it plays a more complex role as a recruited factor to these assemblies. We have coupled this data with 𝑖𝑛 𝑣𝑖𝑣𝑜 imaging of endogenous Lhx2, Ebf1, and Ldb1 to find that these factors display similar binding and dynamics 𝑖𝑛 𝑣𝑖𝑣𝑜. This data helps to provide a biophysical model of how OR hubs support multi-enhancer and protein-rich environments that are succinct from their surrounding environment. Our studies suggest that the OR hub forms a rigid phase separated compartment in the nucleus- driven by Lhx2 and Ldb1. This solid-like phase separation may contribute to how singular OR expression is achieved. Such long-range enhancer contacts must stay assembled long-term for continuous OR transcription. Therefore, traditional TF DNA binding dynamics would not explain the longevity of these contacts in the OR hub. This work challenges the traditional model of liquid phase separated nuclear compartments and may provide a broader understanding to how long range and inter-chromosomal compartments are maintained.

In view of the increasing global challenge of bacterial resistance, there exists an urgent need for the rationale development of antibacterial compounds with either novel or multiple mechanisms of action. Two chalcone-derivatives, F1 and F23, demonstrated MICs within the range of 16 to >512 μg/ml against two plant pathogens (P. caratovoram and C. michiganensis subsp. michiganensis) as well as important clinical bacterial species. Both compounds displayed an MIC of 32 μg/ml against quinolone-resistant S. aureus. Whilst possessing weak activities individually, each semi-synthetic agent displayed notable synergistic action with polymyxin B against S. aureus, C. violaceum, E. coli and Ps. aeruginosa, thereby recording FICs within the range of <0.093 to 2 that indicated the existence of synergism in some instance. These chalcone compounds applied with polymyxin B displayed a notable FICindex of <0.093 against the Neisseriaceae C. violaceum, and a potential noteworthy capacity to extend the spectrum of activity of the latter antibiotic to include Gram-positive S. aureus species. F1 inhibited staphylococcal replication in broth and the combination of either of both chalcone-derivatives with polymyxin B instituted a metabolic blockage in S. aureus and other bacterial species as determined through a modified MTT reduction assay. The combined agents inflicted major disruptions to the S. aureus cytoplasmic membrane bilayer as evidenced by the release of intracellular potassium as well as the influx of Sytox Green fluorescent stain. Notable levels of cell membrane potential dissipation, leakage of intracellular potassium ions and blockage of reducing enzymes activities occurred within the first 30 minutes, well in advance of significant loss in cell viability that was recorded usually after 4 – 8 hours, suggesting these activities were prerequisites to cell death. In erythrocyte lysis assay, the synergistic combinations of 128 μg/ml of either of both chalcone derivatives with 128 μg/ml polymyxin B displayed the lowest degree of haemolysis, followed by that occurring with 32 μg/ml of the chalcone-derivatives combined with 256 μg/ml of the polypeptide antibiotic. In conclusion, further structure activity modifications aimed at improving the aqueous solubility of these chalcone-derivatives as well as the antibacterial activity recorded for certain combination concentrations of polymyxin B with either of these semi-synthetic agents may be required before considerations are made for the possibility for potential external formulations. Such preparations may include antiseptic creams, lotions, ointments, as well as aerosols that can be applied with nebulizers in targeted delivery for such cases like cystic fibrosis.

The two main themes in this thesis are the implementation of interference methods with optically trapped particles for measurements of position and optical phase (optical interferometric metrology) and the optical manipulation of nanoparticles for studies in the assembly of nanostructures, nanoscale heating and nonlinear optics (nanophotonics). The first part of the thesis (chapter 1, 2) provides an introductory overview to optical trapping and describes the basic experimental instrument used in the thesis respectively. The second part of the thesis (chapters 3 to 5) investigates the use of optical interferometric patterns of the diffracting light fields from optically trapped microparticles for three types of measurements: calibrating particle positions in an optical trap, determining the stiffness of an optical trap and measuring the change in phase or coherence of a given light field. The third part of the thesis (chapters 6 to 8) studies the interactions between optical traps and nanoparticles in three separate experiments: the optical manipulation of dielectric enhanced semiconductor nanoparticles, heating of optically trapped gold nanoparticles and collective optical response from an ensemble of optically trapped dielectric nanoparticles.

The discovery of the prokaryotic cytoskeleton has revolutionized our thinking about spatial organisation in prokaryotes. However, the roles different bacterial cytoskeletal proteins play in the localisations of diverse biomolecules are controversial. Bacterial chemotaxis depends on signalling through large protein clusters and each cell must inherit a cluster on cytokinesis. In Escherichia coli the membrane chemosensory clusters are polar and new static clusters form at pre-cytokinetic sites, ensuring positioning at new poles after cytokinesis and suggesting a role for the bacterial FtsZ and MreB cytoskeletons. Rhodobacter sphaeroides has both polar, membrane-associated and cytoplasmic, chromosome-associated chemosensory clusters. This study sought to investigate the roles of FtsZ and MreB in the partitioning of the two chemosensory clusters in R. sphaeroides. The relative positioning between the two chemosensory systems, FtsZ and MreB in R. sphaeroides cells during the cell cycle was monitored using fluorescence microscopy. FtsZ forms polar spots after cytokinesis, which redistribute to the midcell forming nodes from which gradients of FtsZ extend circumferentially to form the Z-ring. The proposed node-precursor model might represent a common mechanism for the formation of cytokinetic rings. The MreB cytoskeleton continuously reorganizes between patchy and filamentous structures, and colocalises with FtsZ at midcell. Membrane chemosensory proteins form individual dynamic unit-clusters with mature clusters containing about 1000 CheW₃ proteins. These unit-clusters diffuse randomly within the membrane but have a higher propensity for curved regions like cell poles. Membrane clusters do not colocalise with FtsZ and MreB and appear excluded from the Z-ring vicinity. The bipolar localisation of membrane clusters is established after cell division via random diffusion and polar trapping of clusters. The cytoplasmic chemosensory clusters colocalise with FtsZ at midcell in new-born cells. Before cytokinesis one cluster moves to a daughter cell, followed by the second moving to the other cell. FtsZ and MreB do not participate in the positioning of cytoplasmic clusters. Therefore the two homologous chemosensory clusters use different mechanisms to ensure partitioning, and neither system utilizes FtsZ or MreB for positioning.