Insights into the activation mechanism of PopA, a cyclic di-GMP effector protein involved in cell cycle and development of "Caulobacter Crescentus"

In Caulobacter crescentus, a complex network integrating cyclic di-GMP and Phosphorylation-dependent signals controls the proteolysis of key regulatory proteins to drive cell cycle and polar morphogenesis. The c-di-GMP input is processed by the effector protein PopA. Upon binding of c-di-GMP, PopA is sequestered to the old cell pole where it recruits the replication and cell division inhibitors CtrA and KidO and mediates their destruction by the polar ClpXP protease prior to entry into S-phase. In addition to its role at the stalked cell pole, PopA localizes to the opposite cell pole in dependence of the general topology factor PodJ where it exerts a yet unknown function. Here we address the activation and polar sequestration mechanism of PopA guided by an existing activation model for the highly homologous c-di-GMP signaling protein PleD. PopA and PleD do not only share an identical domain organization (Rec1-Rec2-GGDEF), but also show similar spatio-temporal behavior during the cell cycle. While PleD is activated and targeted to the old cell pole via phosphorylation-induced dimerization, we show that PopA stalked pole function is phosphorylation-independent and requires c-di-GMP binding as a primary input signal for activation and polar localization. c-di-GMP binds to conserved primary and secondary I-sites within the PopA GGDEF domain and we show that intact binding sites are required for PopA positioning and function. This suggests that c-di-GMP-dependent crosslinking of adjacent GGDEF domains contributes to the localization of an active PopA dimer to the cell pole. Consistent with this, we demonstrate that the GGDEF domain encodes the polar localization signal(s), while the N-terminal receiver domains serve as interaction platform for downstream components that are actively recruited by PopA. Among these downstream factors is RcdA, a small mediator protein that interacts with the first PopA receiver domain and helps to recruit and degrade CtrA and KidO. In a screen for additional components of the PopA pathway we identify two novel proteins that directly interact with PopA, CC1462 and CC2616. CC1462 is a ClpXP substrate that requires PopA for polar positioning and subsequent degradation during swarmer-to-stalked cell transition. Although located in a flagellar gene cluster, deletion of CC1462 did not affect flagellar assembly and function. Its cellular role as well as the significance of its cell cycle-dependent degradation requires further studies. CC2616, the second PopA interaction partner, is not proteolytically processed and thus belongs to another class of PopA-dependent substrates. CC2616 is annotated as guanine deaminase, which is predicted to catalyze the conversion from guanine to xanthine thereby irreversibly removing guanine based nucleotides from a cellular pool. A CC2616 deletion leads to increased attachment and decreased motility, a phenocopy of strains with elevated c-di-GMP levels. It is not clear whether CC2616 indeed has deaminase activity or whether it has adopted a novel function. Taken together, this work provides insight into the activation mechanism of a c-di-GMP effector protein. We propose that PopA has evolved through gene duplication from its ancestor, the catalytic PleD response regulator but has lost catalytic activity of the diguanylate cyclase domain. Moreover, PopA has adopted an inverse intra-molecular information transfer originating through c-di-GMP binding at the C-terminal GGDEF domain, which in turn activates the N-terminal receiver stem to serve as platform for downstream partner recruitment

Multinary Chalcogenide Nanocrystals: Synthesis, Characterisation and Electronic Structure Modelling

Semiconductor chalcogenide nanocrystals have been in the limelight of material research since the 1990s. Diverse fields such as thermoelectrics, photovoltaics, photodetection or biomedical imaging benefit from the extensive library of nanomaterials and their particular physical and chemical properties. Containing a few 100s to 10'000s of atoms, these particles exhibit unique size-dependent properties due to quantum confinement. Initially focused on binary materials such as cadmium selenide and lead sulfide, synthesis protocols rapidly expanded to diverse types of nanocrystals containing multiple elements with composition, shape and surface control. Earth-abundant and low-toxic elements replace cadmium, lead and mercury for increased sustainability and heterogeneous structures such as inorganic shells further diversify achievable properties. Chalcogenide nanocrystals typically display a periodic arrangement of various positively charged metal cations and negatively charged anions (sulphur, selenium and tellurium), forming a crystal lattice. The lattice type depends on various factors such as composition and temperature. Within a solid solution, the relative atomic concentration changes while lattice symmetry is preserved. The crystal may contain an array of disorder and defects, which may significantly impact electronic, optical and thermal properties. While the structure is non-trivial to investigate due to the small crystallite size, advanced measurement and modelling techniques such as electron microscopy and X-ray spectroscopy reveal structure-property relations. Combining complementary methods enables detailed insight into the structure of homogeneous and heterogeneous particles as well as dynamic processes. The aim of this thesis is to extend the scope of nanocrystal synthesis, investigate composition dependent properties, as well as understand the nature of atomic ordering in the nanocrystal lattice and implications for measurable optical properties. Resulting precisely designed, uniform nanocrystals will enable the bottom-up fabrication of highly functional devices for a variety of applications. The synthesis development of multinary nanocrystals requires rigorous balancing of precursor reactivity. Relevant synthesis parameters were evaluated to produce stoichiometric silver-antimony-telluride (AgSbTe2) nanocrystals with small sizes and narrow size distributions. Composition control was achieved through adjusting the cation precursor ratio. A significantly larger solid solution range than known in bulk Ag-Sb-Te was enabled due to nanoscaling. This increased composition tunability may further enhance thermoelectric properties previously measured in AgSbTe2. The detailed study of synthesis parameters and resulting nanocrystal properties reveals elaborate details on synthesis dynamics. The elemental composition of copper-antimony-selenide nanocrystals depends on time, temperature and precursor concentrations. Studying these trends illuminates the growth mechanism and permits predictable synthesis of highly uniform, stoichiometric Cu3SbSe4 and off-stoichiometric nanocrystals. The defect tolerance is increased compared to bulk, leading to a larger composition range without phase separation. With tight-binding computational modelling the resulting trend is correlated with an increased presence of copper vacancies. This combined study of experiment and electronic structure modelling provides the basis for future development of Cu3SbSe4 for mid-infrared absorption and thermoelectric devices. Ordered Vacancy Compounds within the silver-indium-selenide solid solution (such as Ag3In5Se9) are promising materials for biomedical imaging and energy harvesting and exhibit a periodic arrangement of vacancies and different cations. Tight-binding statistics reveal superior optical properties for a homogeneous distribution of cations in the crystal lattice. Inorganic zinc selenide shell growth synthesis significantly increases photoluminescence. Maximum values are measured up to two days of room temperature storage after shell growth. This phenomenon is linked to slow cation rearrangement with simulations and time-dependent photoluminescence measurements. These results promise widespread possibilities for developing novel chalcogenide nanocrystals. The understanding and control of lattice ordering is crucial for device performance and should be diligently studied in relevant nanomaterials. An interdisciplinary approach integrating experimental and computational methods will fuel the development of tailored nanomaterials, enabling desperately sought for technological advances for a more sustainable society

Activation and polar sequestration of PopA, a c-di-GMP effector protein involved in Caulobacter crescentus cell cycle control

When Caulobacter crescentus enters S-phase the replication initiation inhibitor CtrA dynamically positions to the old cell pole to be degraded by the polar ClpXP protease. Polar delivery of CtrA requires PopA and the diguanylate cyclase PleD that positions to the same pole. Here we present evidence that PopA originated through gene duplication from its paralogue response regulator PleD and subsequent co-option as c-di-GMP effector protein. While the C-terminal catalytic domain (GGDEF) of PleD is activated by phosphorylation of the N-terminal receiver domain, functional adaptation has reversed signal transduction in PopA with the GGDEF domain adopting input function and the receiver domain serving as regulatory output. We show that the N-terminal receiver domain of PopA specifically interacts with RcdA, a component required for CtrA degradation. In contrast, the GGDEF domain serves to target PopA to the cell pole in response to c-di-GMP binding. In agreement with the divergent activation and targeting mechanisms, distinct markers sequester PleD and PopA to the old cell pole upon S-phase entry. Together these data indicate that PopA adopted a novel role as topology specificity factor to help recruit components of the CtrA degradation pathway to the protease specific old cell pole of C. crescentus

Synthesis of Small Ag-Sb-Te Nanocrystals with Composition Control

Ternary telluride nanocrystals have gained increasing interest as materials for thermoelectric, optoelectronic, and phase-change memory applications. Synthetic approaches for colloidal multicomponent tellurides, however, remain sparse. Here, we report a convenient, amide-promoted synthesis for Ag-Sb-Te nanocrystals with small sizes and narrow size distributions (e.g., nanocrystal diameters of 3.5 ± 0.8 nm). We focus on achieving composition control for Ag-Sb-Te nanocrystals by adjusting the ratio of cationic precursors and find a broad solid solution range for AgxSb1-xTe1.5-x nanocrystals (x is from 0.3 and 0.6), which extends beyond that measured in Ag-Sb-Te thin films. The ability to produce size- and composition-controlled Ag-Sb-Te nanocrystals is a first step in achieving bottom-up assembled Ag-Sb-Te semiconductors for device applications.ISSN:2050-7526ISSN:2050-753

Composition- And Size-Controlled I-V-VI Semiconductor Nanocrystals

ISSN:0897-475

Size- and composition-controlled intermetallic nanocrystals via amalgamation seeded growth

Intermetallic nanocrystals are a large family of emerging materials with extensive applications in many fields. Yet, a generalized synthetic method for intermetallic nanocrystals is lacking. Here, we report the development of a colloidal synthesis method based on amalgamation of monometallic nanocrystal seeds with low–melting point metals. We use this approach to achieve crystalline and compositionally uniform intermetallic nanocrystals of Au-Ga, Ag-Ga, Cu-Ga, Ni-Ga, Pd-Ga, Pd-In, and Pd-Zn compounds. We demonstrate both compositional tunability across the phase spaces (e.g., AuGa2, AuGa, Au7Ga2, and Ga-doped Au), size tunability (e.g., 14.0-, 7.6-, and 3.8-nm AuGa2), and size uniformity (e.g., 5.4% size deviations). This approach makes it possible to systematically achieve size- and composition-controlled intermetallic nanocrystals, opening up a multitude of possibilities for these materials.ISSN:2375-254

New Target Genes Controlled by the Bradyrhizobium japonicum Two-Component Regulatory System RegSR▿ †

RegSR-like proteins, members of the family of two-component regulatory systems, are present in a large number of proteobacteria in which they globally control gene expression mostly in a redox-responsive manner. The controlled target genes feature an enormous functional diversity. In Bradyrhizobium japonicum, the facultative root nodule symbiont of soybean, RegSR activate the transcription of the nitrogen fixation regulatory gene nifA, thus forming a RegSR-NifA cascade which is part of a complex regulatory network for gene regulation in response to changing oxygen concentrations. Whole-genome transcription profiling was performed here in order to assess the full regulatory scope of RegSR. The comparative analysis of wild-type and ΔregR cells grown under oxic and microoxic conditions revealed that expression of almost 250 genes is dependent on RegR, a result that underscores the important contribution of RegR to oxygen- or redox-regulated gene expression in B. japonicum. Furthermore, transcription profiling of ΔregR bacteroids compared with wild-type bacteroids revealed expression changes for about 1,200 genes in young and mature bacteroids. Incidentally, many of these were found to be induced in symbiosis when wild-type bacteroids were compared with free-living, culture-grown wild-type cells, and they appeared to encode diverse functions possibly related to symbiosis and nitrogen fixation. We demonstrated direct RegR-mediated control at promoter regions of several selected target genes by means of DNA binding experiments and in vitro transcription assays, which revealed six novel direct RegR target promoters

Synthesis and Electronic Structure of Mid-Infrared Absorbing Cu₃SbSe₄ and CuₓSbSe₄ Nanocrystals

Aliovalent I–V–VI semiconductor nanocrystals are promising candidates for thermoelectric and optoelectronic applications. Famatinite Cu₃SbSe₄ stands out due to its high absorption coefficient and narrow band gap in the mid-infrared spectral range. This paper combines experiment and theory to investigate the synthesis and electronic structure of colloidal CuₓSbSe₄ nanocrystals. We achieve predictive composition control of size-uniform CuₓSbSe₄(x = 1.9–3.4) nanocrystals. Density functional theory (DFT)-parametrized tight-binding simulations on nanocrystals show that the more the Cu-vacancies, the wider the band gap of CuₓSbSe₄ nanocrystals, a trend which we also confirm experimentally via FTIR spectroscopy. We show that Sb꜀ᵤ antisite defects can create mid-gap states, which may give rise to sub-bandgap absorption. This work provides a detailed study of CuₓSbSe₄ nanocrystals and highlights the potential opportunities as well as challenges for their application in infrared devices.ISSN:0897-475