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Translated by A. Charles Muller. Table of Contents. First translated during the summer of Revised


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Precise imaging of the cell surface of fluorescently labeled bacteria requires super-resolution methods because the size-scale of these cells is on the order of the diffraction limit. In this work, we present a photocontrollable small-molecule rhodamine spirolactam emitter suitable for non-toxic and specific labeling of the outer surface of cells for three-dimensional 3D super-resolution SR imaging. Conventional rhodamine spirolactams photoswitch to the emitting form with UV light; however, these wavelengths can damage cells.

Further, an N -hydroxysuccinimide-functionalized derivative enabled covalent labeling of amines on the surface of live Caulobacter crescentus cells. Resulting 3D SR reconstructions of the labeled cell surface reveal uniform and specific sampling with thousands of localizations per cell and excellent localization precision in x , y , and z. The distribution of cell stalk lengths a sub-diffraction-sized cellular structure was quantified for a mixed population of cells. Pulse-chase experiments identified sites of cell surface growth.

Covalent labeling with the optimized rhodamine spirolactam label provides a general strategy to study the surfaces of living cells with high specificity and resolution down to 10—20 nm. The exterior of a cell is a three-dimensional 3D biological structure that delineates a barrier for material to enter or exit the cell and defines the overall cell morphology. In order to temporally separate SMs on a densely labeled structure, the fluorescent label must have at least two states with different emissive properties.

Transitions between the photophysical states can be driven optically photoswitching, photoactivation or non-optically ligand binding, reduction. Photocontrollable fluorescent proteins FPs 7, 21, 22 are frequently used for SR imaging because targeting a specific biological structure is more straightforward than for small organic fluorophores, though new labeling technologies have been developed for the latter. Rhodamine spirolactams are one class of photocontrollable organic fluorophores.

Absorption of UV light by the closed isomer can break the bond between the lactam nitrogen and the xanthene ring, restoring conjugation in the xanthene ring and generating the fluorescent open isomer Scheme 1 , Figure S1. The time interval before thermal return to the closed isomer depends on the local environment, but it is on the order of milliseconds in polar solvents.

In this work, we increased the biocompatibility of rhodamine spirolactam derivatives by extending the switching wavelength to the visible region of the spectrum. This allowed the use of a low-intensity, continuous-wave nm laser to photoactivate. Fluorescence was read out using a green nm laser. An optimized molecule was used to covalently label the surface of live Caulobacter crescentus bacterial cells for 3D SR imaging.

This straightforward labeling procedure can easily be applied to other cell surfaces. We hypothesized that varying the chromophore on the lactam nitrogen could lower the energy required to photoactivate without substantially altering the photophysics of the fluorescent isomer.

Increased conjugation and positive charge on the lactam stilbazolium substituent 8 — 10 result in a larger red-shift. Derivatives 6 — 10 are relatively more red-shifted and contain more conjugation. The presence of charge also seems to help stabilize the closed isomer: 8 and 10 are more red-shifted than 6. Molecules of 8 doped into polymer could be photoactivated using nm light Figure S2.

Figure 1. A Overlaid absorption spectra of the closed isomer of derivatives 1 — 10 in acetonitrile:water. B Schematic of absorption integration past nm. Example spectrum is for molecule 8. C Normalized absorption greater than nm for the most red-shifted derivatives. Further functionalization of our neutral red-shifted derivatives in combination with a targeting tag could have allowed labeling of internal cellular proteins.

Instead, we chose the surface of bacterial cells as our SR target. This demonstration structure avoids issues with dye penetration, specific labeling, and wash-out. Additionally, many SR experiments studying FP-labeled protein super-structures in bacteria would be enhanced with the context of the cell surface. Cell surfaces are inherently 3D, but without additional engineering, SR microscopy only improves the lateral 2D resolution.

One 3D strategy manipulates the point spread function PSF of the microscope to encode additional axial z information in the shape of the PSF. Figure 2. A Transmission image of six C. C Individual frames of raw data showing single molecules SMs.

Since the double-helix phase mask is in place, each SM appears as two spots, with the angle between the spots encoding axial position.

D Corresponding fitted SMs. E Three-dimensional reconstructed image of the four cells in the pink dashed rectangle in panel A. Arrows in panels A and E guide the eye to the cell stalk, a sub-diffraction-sized structure.

See Supporting Information for more information about sample preparation, data acquisition, SM fitting, and super-resolution reconstructions. We labeled the surface amines on the Gram-negative bacterium C. The N -hydroxysuccinimide ester on 9 non-specifically labels amines, and the positive charge of 9 also inhibits its entry into the cell.

The cells continue to grow normally after labeling. Fluorescence is read out using a green laser nm, 1. The x , y , and z position of each SM is extracted by fitting Supporting Information. Thermal drift of the sample over the acquisition time is corrected using a fluorescent bead as a fiduciary marker.

The SR data reveal sub-diffraction-sized stalk structures pink arrows in Figure 2 E not visible with standard microscopy Figure 2 B. These stalk structures are characteristic of one of the developmental states of C. This bacterium is a model organism for asymmetric cell division because the two daughter cells differ in their appearance and behavior.

Dividing cells are non-motile and contain a stalk at one pole. The nascent daughter cell termed a swarmer cell does not divide, is motile, and contains a single flagellum at one pole. Figure 3. A Montage of different stalk lengths in representative cells. Cell 1 does not have a stalk. B Corresponding white light image of the cells shown in panel A. C Histogram of the measured stalk length.

Since this population of cells is in a mixture of developmental states and generations, a variety of stalk lengths can be observed Figure 3. The average stalk length is 1. Some cells exhibit exceptionally long stalks see cell 7 in Figure 3 A. Assuming only the surface of the stalk is labeled, the underlying structure should be a hollow tube. This is not captured in our data because of the finite localization precision, a fact that has been verified by simulation Figure S7.

The surface specificity of 9 is more evident in reconstructions of the cell body. Figure 4 A highlights a 75 nm slice of localizations yellow perpendicular to the cell axis. The apparent surface thickness is a convolution of the statistical resolution and the true thickness of the underlying structure. The localization precision of the experiment dominates the thickness measurement, suggesting that the underlying sampled structure is much thinner.

For the pre-divisional cell shown in Figure 4 D i , the radii noticeably dip at the interface between the two daughter cells. In comparison, non-dividing cells lack this dip example in Figure 4 D ii. Figure 4. A 3D SR reconstruction of surface localizations, with a 75 nm slice highlighted in yellow. Inset: white light image of cell.

B Yellow section from panel A viewed in the plane of the cell axis. C Histogram of the radial distances of each of the localizations localizations total to the center of the circle fitted to the points in panel B.

D i 2D histogram of radial distances as a function of the long cell axis for the pre-divisional cell shown in panel A. Localizations are binned using a sliding window of 75 nm that slides 25 nm for each data point. Note that this histogram does not have a dip in the center.

Prior work highlighted the C. This may be sufficient to provide cellular context, but covalent labeling with 9 provides improved surface labeling. Nile Red is neutral and may have complicated binding kinetics facilitating its interaction with various components of the cell surface, bilayers, and wall. In contrast, 9 is positively charged and therefore excluded from the cell interior.

It covalently reacts with and labels surface amines, and unreacted dye can be washed away before imaging. One of the striking differences between the two strategies is the greater sampling uniformity of 9 with our method compared to PAINT Figure S9.

Since the exterior of the cell is almost entirely covered in a semi-crystalline S-layer of RsaA, we hypothesized that the majority of 9 was covalently attached to this protein Figure S RsaA monomers are held tightly in the S-layer lattice, and we do not see evidence of SM diffusion in our raw data. The spatial organization of new RsaA incorporation is not fully understood. To view this, we performed pulse-chase labeling with 9.

Imaging the cells immediately after labeling shows random and even incorporation over the cell surface. If the cells are allowed to grow after the labeling and washing step, patches with no localizations appear in the reconstructions Figures S11 and S12 , indicating non-uniform insertion of new cell surface. We report a rhodamine spirolactam capable of photoactivation at visible wavelengths and 3D super-resolution imaging. A reactive ester version can be used to provide the context of the living cell surface to enhance other imaging experiments and as a method to study the growth of the bacterial S-layer.


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