Biochemical and Structural Studies on PrfA, the Transcriptional Regulator of Virulence in Listeria monocytogenes

Abstract

Listeria monocytogenes is a gram-positive soil saprophytic bacterium that is capable of causing fatal infection in humans. The main virulence regulator PrfA, a member of the Crp/FNR family of transcriptional regulators, activates the expression of essential proteins required for host cell invasion and cell-to-cell spread. The mechanism of PrfA activation and the identity of its small molecule coactivator have remained a mystery for more than 20 years, but it is hypothesized that PrfA shares mechanistic similarity to the E. coli cAMP binding protein, Crp. Crp activates gene expression by binding cAMP, increasing the DNA binding affinity of the protein and causing a significant DNA bend that facilitates RNA polymerase binding and downstream gene activation. Our data suggests PrfA activates virulence protein expression through a mechanism distinct from the canonical Crp activation mechanism that involves a combination of cysteine residue reduction and glutathione (GSH) binding.

Listeria lacking glutathione synthase (ΔgshF) is avirulent in mice; however virulence is rescued when the bacterium expresses the constitutively active PrfA mutant G145S. Interestingly, Listeria expressing a PrfA mutant in which its four cysteines are mutated to alanine (Quad PrfA), demonstrate a 30-fold decrease in virulence. The Quad and ΔgshF double mutant strains are avirulent. DNA-binding affinity, measured through fluorescence polarization assays, indicate reduction of the cysteine side chains is sufficient to allow PrfA to binds its physiological promoters Phly and PactA with low nanomolar affinity. Oxidized PrfA binds the promoters poorly.

Unexpectedly, Quad also binds promoter DNA with nanomolar affinity, suggesting that the cysteines play a role in transcription efficiency in addition to DNA binding. Both PrfA and Quad bind GSH at physiologically relevant and comparable affinities, however GSH did not affect DNA binding in either case. Thermal denaturation assays suggest that Quad and wild-type PrfA differ structurally upon binding GSH, which supports the in vivo difference in infection between the regulator and its mutant.

Structures of PrfA in complex with cognate DNA, determined through X-ray crystallography, further support the disparity between PrfA and Crp activation mechanisms as two structures of reduced PrfA bound to Phly (PrfA-Phly30 and PrfA-Phly24) suggest the DNA adopts a less bent DNA conformation when compared to Crp-cAMP- DNA. The structure of Quad-Phly30 confirms the DNA-binding data as the protein-DNA complex adopts the same overall conformation as PrfA-Phly.

From these results, we hypothesize a two-step activation mechanism wherein PrfA, oxidized upon cell entry and unable to bind DNA, is reduced upon its intracellular release and binds DNA, causing a slight bend in the promoter and small increase in transcription of PrfA-regulated genes. The structures of PrfA-Phly30 and PrfA-Phly24 likely visualize this intermediate complex. Increasing concentrations of GSH shift the protein to a (PrfA-GSH)-DNA complex which is fully active transcriptionally and is hypothesized to resemble closely the transcriptionally active structure of the cAMP-(Crp)-DNA complex. Thermal denaturation results suggest Quad PrfA is deficient in this second step, which explains the decrease in virulence and implicates the cysteine residues as critical for transcription efficiency. Further structural and biochemical studies are on-going to clarify this mechanism of activation.

Design, Fabrication, and Characterization of Carbon Nanotube Field Emission Devices for Advanced Applications

Carbon nanotubes (CNTs) have recently emerged as promising candidates for electron field emission (FE) cathodes in integrated FE devices. These nanostructured carbon materials possess exceptional properties and their synthesis can be thoroughly controlled. Their integration into advanced electronic devices, including not only FE cathodes, but sensors, energy storage devices, and circuit components, has seen rapid growth in recent years. The results of the studies presented here demonstrate that the CNT field emitter is an excellent candidate for next generation vacuum microelectronics and related electron emission devices in several advanced applications.

The work presented in this study addresses determining factors that currently confine the performance and application of CNT-FE devices. Characterization studies and improvements to the FE properties of CNTs, along with Micro-Electro-Mechanical Systems (MEMS) design and fabrication, were utilized in achieving these goals. Important performance limiting parameters, including emitter lifetime and failure from poor substrate adhesion, are examined. The compatibility and integration of CNT emitters with the governing MEMS substrate (i.e., polycrystalline silicon), and its impact on these performance limiting parameters, are reported. CNT growth mechanisms and kinetics were investigated and compared to silicon (100) to improve the design of CNT emitter integrated MEMS based electronic devices, specifically in vacuum microelectronic device (VMD) applications.

Improved growth allowed for design and development of novel cold-cathode FE devices utilizing CNT field emitters. A chemical ionization (CI) source based on a CNT-FE electron source was developed and evaluated in a commercial desktop mass spectrometer for explosives trace detection. This work demonstrated the first reported use of a CNT-based ion source capable of collecting CI mass spectra. The CNT-FE source demonstrated low power requirements, pulsing capabilities, and average lifetimes of over 320 hours when operated in constant emission mode under elevated pressures, without sacrificing performance. Additionally, a novel packaged ion source for miniature mass spectrometer applications using CNT emitters, a MEMS based Nier-type geometry, and a Low Temperature Cofired Ceramic (LTCC) 3D scaffold with integrated ion optics were developed and characterized. While previous research has shown other devices capable of collecting ion currents on chip, this LTCC packaged MEMS micro-ion source demonstrated improvements in energy and angular dispersion as well as the ability to direct the ions out of the packaged source and towards a mass analyzer. Simulations and experimental design, fabrication, and characterization were used to make these improvements.

Finally, novel CNT-FE devices were developed to investigate their potential to perform as active circuit elements in VMD circuits. Difficulty integrating devices at micron-scales has hindered the use of vacuum electronic devices in integrated circuits, despite the unique advantages they offer in select applications. Using a combination of particle trajectory simulation and experimental characterization, device performance in an integrated platform was investigated. Solutions to the difficulties in operating multiple devices in close proximity and enhancing electron transmission (i.e., reducing grid loss) are explored in detail. A systematic and iterative process was used to develop isolation structures that reduced crosstalk between neighboring devices from 15% on average, to nearly zero. Innovative geometries and a new operational mode reduced grid loss by nearly threefold, thereby improving transmission of the emitted cathode current to the anode from 25% in initial designs to 70% on average. These performance enhancements are important enablers for larger scale integration and for the realization of complex vacuum microelectronic circuits.

Collimation of a D-D Neutron Generator for Clinical Implementation of Neutron Stimulated Emission Computed Tomography: a Monte Carlo Study

This work is an investigation into collimator designs for a deuterium-deuterium (DD) neutron generator for an inexpensive and compact neutron imaging system that can be implemented in a hospital. The envisioned application is for a spectroscopic imaging technique called neutron stimulated emission computed tomography (NSECT).

Previous NSECT studies have been performed using a Van-de-Graaff accelerator at the Triangle Universities Nuclear Laboratory (TUNL) in Duke University. This facility has provided invaluable research into the development of NSECT. To transition the current imaging method into a clinically feasible system, there is a need for a high-intensity fast neutron source that can produce collimated beams. The DD neutron generator from Adelphi Technologies Inc. is being explored as a possible candidate to provide the uncollimated neutrons. This DD generator is a compact source that produces 2.5 MeV fast neutrons with intensities of 1012 n/s (4π). The neutron energy is sufficient to excite most isotopes of interest in the body with the exception of carbon and oxygen. However, a special collimator is needed to collimate the 4π neutron emission into a narrow beam. This work describes the development and evaluation of a series of collimator designs to collimate the DD generator for narrow beams suitable for NSECT imaging.

A neutron collimator made of high-density polyethylene (HDPE) and lead was modeled and simulated using the GEANT4 toolkit. The collimator was designed as a 52 x 52 x 52 cm3 HDPE block coupled with 1 cm lead shielding. Non-tapering (cylindrical) and tapering (conical) opening designs were modeled into the collimator to permit passage of neutrons. The shape, size, and geometry of the aperture were varied to assess the effects on the collimated neutron beam. Parameters varied were: inlet diameter (1-5 cm), outlet diameter (1-5 cm), aperture diameter (0.5-1.5 cm), and aperture placement (13-39 cm). For each combination of collimator parameters, the spatial and energy distributions of neutrons and gammas were tracked and analyzed to determine three performance parameters: neutron beam-width, primary neutron flux, and the output quality. To evaluate these parameters, the simulated neutron beams are then regenerated for a NSECT breast scan. Scan involved a realistic breast lesion implanted into an anthropomorphic female phantom.

This work indicates potential for collimating and shielding a DD neutron generator for use in a clinical NSECT system. The proposed collimator designs produced a well-collimated neutron beam that can be used for NSECT breast imaging. The aperture diameter showed a strong correlation to the beam-width, where the collimated neutron beam-width was about 10% larger than the physical aperture diameter. In addition, a collimator opening consisting of a tapering inlet and cylindrical outlet allowed greater neutron throughput when compared to a simple cylindrical opening. The tapering inlet design can allow additional neutron throughput when the neck is placed farther from the source. On the other hand, the tapering designs also decrease output quality (i.e. increase in stray neutrons outside the primary collimated beam). All collimators are cataloged in measures of beam-width, neutron flux, and output quality. For a particular NSECT application, an optimal choice should be based on the collimator specifications listed in this work.