CitA/CitB two-component system regulating citrate fermentation in Escherichia coli and its relation to the DcuS/DcuR system in vivo.

Citrate fermentation by Escherichia coli requires the function of the citrate/succinate antiporter CitT (citT gene) and of citrate lyase (citCDEFXG genes). Earlier experiments suggested that the two-component system CitA/CitB, consisting of the membrane-bound sensor kinase CitA and the response regulator CitB, stimulates the expression of the genes in the presence of citrate, similarly to CitA/CitB of Klebsiella pneumoniae. In this study, the expression of a chromosomal citC-lacZ gene fusion was shown to depend on CitA/CitB and citrate. CitA/CitB is related to the DcuS/DcuR two-component system which induces the expression of genes for fumarate respiration in response to C(4)-dicarboxylates and citrate. Unlike DcuS, CitA required none of the cognate transporters (CitT, DcuB, or DcuC) for function, and the deletion of the corresponding genes showed no effect on the expression of citC-lacZ. The citAB operon is preceded by a DcuR binding site. Phosphorylated DcuR bound specifically to the promoter region, and the deletion of dcuS or dcuR reduced the expression of citC. The data indicate the presence of a regulatory cascade consisting of DcuS/DcuR modulating citAB expression (and CitA/CitB levels) and CitA/CitB controlling the expression of the citCDEFXGT gene cluster in response to citrate. In vivo fluorescence resonance energy transfer (FRET) and the bacterial two-hybrid system (BACTH) showed interaction between the DcuS and CitA proteins. However, BACTH and expression studies demonstrated the lack of interaction and cross-regulation between CitA and DcuR or DcuS and CitB. Therefore, there is only linear phosphoryl transfer (DcuS→DcuR and CitA→CitB) without cross-regulation between DcuS/DcuR and CitA/CitB.

Single molecule probing of dynamics in supercooled polymers.

Fluorescence experiments with single BODIPY molecules embedded in a poly(methyl acrylate) matrix have been performed at various temperatures in the supercooled regime. By using pulsed excitation, fluorescence lifetime and linear dichroism time trajectories were accessible at the same time. Both observables have been analyzed without data binning. While the linear dichroism solely reflects single particle dynamics, the fluorescence lifetime observable depends on the molecular environment, so that the dynamics from the polymer host surrounding a chromophore contributes to this quantity. We observe that the lifetime correlation decays slightly faster than polarization correlation, indicating the occurrence of large angular reorientations. Additionally, dichroism time trajectories have been adducted to reveal directly the geometry of rotational dynamics. We identify small but also significantly larger rotational jumps being responsible for the overall molecular reorientation.

Statistical analysis of time resolved single molecule fluorescence data without time binning.

We depict two algorithms to calculate correlation functions from two different time resolved single molecule fluorescence experiments without the need of time binning. Our first procedure allows to calculate the reduced linear dichroism from polarization resolved fluorescence data. Since we process single photon counts instead of time binned data, considerably faster fluctuations of the dichroism can be analyzed than with conventional methods. With our second procedure time resolved fluorescence obtained with a time correlated single photon counting setup can be analyzed with respect to fluorescence lifetime fluctuations. Again this new algorithm processes single photon events making time binning of photon counts obsolete. Both methods presented are characterized by enhanced time resolution thus allowing to study fast fluctuations of either single molecular orientation or fluorescence life times, respectively.

Analysis of the exponential character of single molecule rotational correlation functions for large and small fluorescence collection angles.

Coarse-grained molecular dynamics simulations and single molecule fluorescence microscopy experiments have been performed in order to investigate the influence of the numerical aperture (NA) of the microscope objective on the exponential character of the rotational correlation functions of probes embedded in complex matrices. The results obtained by using either a dry lens (NA=0.95) or an oil objective (NA=1.4) show that, in the moderately (simulations) and deeply (experiment) supercooled melts, the rotational (linear dichroism) correlation functions of the single molecules (SMs) exhibit a nonexponential character. Furthermore, by fitting Kohlrausch-Williams-Watt functions to the correlation curves, the stretching parameters turn out to be very similar for both types of objectives. Our results demonstrate that the nonexponentiality is intrinsic to the complex rotational dynamics of the SM in the supercooled solid and point to the validity of the use of a high NA dry lens to perform such experiments.

Scanning near-field optical microscopy using semiconductor nanocrystals as a local fluorescence and fluorescence resonance energy transfer source.

Local fluorescence probes based on CdSe semiconductor nanocrystals were prepared and tested by recording scanning near-field optical microscopy (SNOM) images of calibration samples and fluorescence resonance energy transfer SNOM (FRET SNOM) images of acceptor dye molecules inhomogeneously deposited onto a glass substrate. Thousands of nanocrystals contribute to the signal when this probe is used as a local fluorescence source while only tens of those (the most apical) are involved in imaging for the FRET SNOM operation mode. The dip-coating method used to make the probe enables diminishing the number of active fluorescent nanocrystals easily. Prospects to realize FRET SNOM based on a single fluorescence centre using such an approach are briefly described.

Two-photon excitation microscopy of tryptophan-containing proteins.

We have examined the feasibility of observing single protein molecules by means of their intrinsic tryptophan emission after two-photon excitation. A respiratory protein from spiders, the 24-meric hemocyanin, containing 148 tryptophans, was studied in its native state under almost in vivo conditions. In this specific case, the intensity of the tryptophan emission signals the oxygen load, allowing one to investigate molecular cooperativity. As a system with even higher tryptophan content, we also investigated latex spheres covered with the protein avidin, resulting in 340 tryptophans per sphere. The ratio of the fluorescence quantum efficiency to the bleaching efficiency was found to vary between 2 and 180 after two-photon excitation for tryptophan free in buffer solution, in hemocyanin, and in avidin-coated spheres. In the case of hemocyanin, this ratio leads to about four photons detected before photobleaching. Although this number is quite small, the diffusion of individual protein molecules could be detected by fluorescence correlation spectroscopy. In avidin-coated spheres, the tryptophans exhibit a higher photostability, so that even imaging of single spheres becomes possible. As an unexpected result of the measurements, it was discovered that the population of the oxygenated state of hemocyanin can be changed by means of a one-photon process with the same laser source that monitors this population in a two-photon process.

Fluorescence Detection from Single Dendrimers with Multiple Chromophores.

The differences in the fluorescence behavior of a polyphenylene dendrimer with eight peryleneimides chromophores (1) and a single hexaphenylperyleneimide chromophore have been investigated at a single-molecule level through the combination of ultrasensitive fluorescence detection and microscopy.