Smart fluorophores", such as reversibly switchable fluorescent proteins (RSFPs), are crucial for advanced fluorescence imaging. However, only a limited number of such labels is available and many display reduced biological performance compared to more classical variants.We present the development of robustly photoswitchable variants of EGFP, named rsGreens, that display up to 30-fold higher fluorescence in E. coli colonies grown at 37°C and more than 4-fold higher fluorescence when expressed in HEK293T cells compared to their ancestor protein rsEGFP. This enhancement is not due to an intrinsic increase in the fluorescence brightness of the probes, but rather due to enhanced expression levels that allow many more probe molecules to be functional at any given time. We developed rsGreens displaying a range of photoswitching kinetics and show how these can be used for multi-modal diffraction-unlimited fluorescence imaging such as pcSOFI and RESOLFT, achieving a spatial resolution of ~70 nm. By determining the first ever crystal structures of a negative reversibly switchable FP derived from Aequorea victoria in both the "on"-and "off"-conformation we were able to confirm the presence of a cis-trans isomerization and provide further insights into the mechanisms underlying the photochromism. Our work demonstrates that genetically encoded "smart fluorophores" can be readily optimized for biological performance, and provides a practical strategy for developing maturation-and stability-enhanced photochromic fluorescent proteins.KEYWORDS: fluorescent proteins, reversible photoswitching, super-resolution fluorescence microscopy, SOFI, RESOLFT, crystal structure determination, rsEGFP, superfolder Fluorescent proteins (FPs) enable the minimally-invasive labeling of intracellular structures in live systems. 1 The discovery and development of "smart photoactive FPs", 2,3 with features such as irreversible photoactivation and photoconversion, or reversible photoswitching, allowed the development of diffraction-unlimited imaging techniques such as (f)PALM 4,5 ((fluorescence) photoactivated localization microscopy), RESOLFT 6 (reversible saturable optical fluorescence transitions) and (pc)SOFI 7,8 ((photochromic) stochastic optical fluctuation imaging). These techniques strongly rely on the performance of the fluorophores and considerable efforts have therefore been dedicated to create optimized "smart labels". 9 This is exemplified by the continuous optimization and diversification of the EosFP family, 10-15 or the development of Dronpa 16 mutants with different or added photophysical properties. [17][18][19][20][21][22] Probes that combine multiple "smart" behaviors have also been engineered. [23][24][25] On the whole, however, the general acceptance of the FP-based "smart labels" has not quite risen up to the high expectations set by the many applications they enable. In some cases this is due to concerns surrounding the biological compatibility of the labels, meaning that the label may interfere with the functioning of the syst...

Genetically-encoded biosensors based on a single fluorescent protein are widely used to visualize analyte levels or enzymatic activities in cells, though usually to monitor relative changes rather than absolute values. We report photochromism-enabled absolute quantification (PEAQ) biosensing, a method that leverages the photochromic properties of biosensors to provide an absolute measure of the analyte concentration or activity. We develop proof-of-concept photochromic variants of the popular GCaMP family of Ca2+ biosensors, and show that these can be used to resolve dynamic changes in the absolute Ca2+ concentration in live cells. We also develop intermittent quantification, a technique that combines absolute aquisitions with fast fluorescence acquisitions to deliver fast but fully quantitative measurements. We also show how the photochromism-based measurements can be expanded to situations where the absolute illumination intensities are unknown. In principle, PEAQ biosensing can be applied to other biosensors with photochromic properties, thereby expanding the possibilities for fully quantitative measurements in complex and dynamic systems.

Fluorophores with dynamic or controllable fluorescence emission have become essential tools for advanced imaging, such as superresolution imaging. These applications have driven the continuing development of photoactivatable or photoconvertible labels, including genetically encoded fluorescent proteins. These new probes work well but require the introduction of new labels that may interfere with the proper functioning of existing constructs and therefore require extensive functional characterization. In this work we show that the widely used red fluorescent protein mCherry can be brought to a purely chemically induced blue-fluorescent state by incubation with β-mercaptoethanol (βME). The molecules can be recovered to the red fluorescent state by washing out the βME or through irradiation with violet light, with up to 80% total recovery. We show that this can be used to perform single-molecule localization microscopy (SMLM) on cells expressing mCherry, which renders this approach applicable to a very wide range of existing constructs. We performed a detailed investigation of the mechanism underlying these dynamics, using X-ray crystallography, NMR spectroscopy, and ab initio quantummechanical calculations. We find that the βME-induced fluorescence quenching of mCherry occurs both via the direct addition of βME to the chromophore and through βME-mediated reduction of the chromophore. These results not only offer a strategy to expand SMLM imaging to a broad range of available biological models, but also present unique insights into the chemistry and functioning of a highly important class of fluorophores. fluorescent proteins | mCherry | localization microscopy | β-mercaptoethanol | photoactivation

Composed of a reversibly photoswitchable unit allosterically linked to a sensing module, reversibly photoswitchable sensors (rs-sensors) represent a new and attractive strategy to quantitatively read-out analyte concentrations. However, their kinetic response to illumination is complex, and much attention is required from the design to the application steps. Here, we exploit a generic kinetic model of rs-sensors which enables us to point to key thermokinetic parameters, such as dissociation constants and kinetic rates for exchange toward the analyte, and cross-sections for photoswitching. The application of the model allows to evaluate the robustness of the analyzed parameters and to introduce a methodology for their reliable use. Model and methodology have been experimentally tested on a newly reported calcium sensor based on a reversibly photoswitchable green fluorescent protein allosterically linked to a calcium-sensing module integrating calmodulin and an RS20 peptide.

Genetically-encoded biosensors based on a single fluorescent protein are widely used to visualize analyte levels or enzymatic activities in cells, though usually to monitor relative changes rather than absolute values. We report photochromism-enabled analyte quantification (PEAQ) biosensing, a method that leverages photochromic properties of biosensors to provide an absolute measure of the analyte concentration or activity. We develop photochromic variants of the popular GCaMP family of calcium ion biosensors, and show that these can be used to resolve dynamic changes in the absolute Ca2+ concentration in live cells. We also show how our method can be expanded to fast imaging with reduced illumination intensities or to situations where the absolute illumination intensities are unknown. In principle, PEAQ biosensing can be applied to other biosensors with photochromic properties, thereby expanding the possibilities for fully quantitative measurements in complex and dynamic systems.

Super-resolution optical fluctuation imaging (SOFI) delivers an enhanced spatial resolution in fluorescence imaging by analyzing spontaneous fluctuations in the fluorophore emission. SOFI images are usually obtained by calculating cross-cumulants between adjacent pixels on the detector, which provides the increased pixel densities required to sample the improved spatial resolution, but can result in pixelation artifacts. In this contribution, we describe a simple, model-free, and computationally efficient algorithm to correct such artifacts by matching the means and variances of the different cross-cumulants. We show that this strategy not only results in pixels that are essentially free of artifacts, but can also correct for detector imperfections such as the spurious correlations present in electron-multiplied CCD cameras.

Smart fluorophores'', such as reversibly switchable fluorescent proteins, are crucial for advanced fluorescence imaging. However, only a limited number of such labels is available, and many display reduced biological performance compared to more classical variants. We present the development of robustly photoswitchable variants of enhanced green fluorescent protein (EGFP), named rsGreens, that display up to 30-fold higher fluorescence in E. coli colonies grown at 37 C and more than 4-fold higher fluorescence when expressed in HEK293T cells compared to their ancestor protein rsEGFP. This enhancement is not due to an intrinsic increase in the fluorescence brightness of the probes, but rather due to enhanced expression levels that allow many more probe molecules to be functional at any given time. We developed rsGreens displaying a range of photoswitching kinetics and show how these can be used for multimodal diffraction-unlimited fluorescence imaging such as pcSOFI and RESOLFT, achieving a spatial resolution of~70 nm. By determining the first ever crystal structures of a negative reversibly switchable FP derived from Aequorea victoria in both the ''on''-and ''off''-conformation we were able to confirm the presence of a cis-trans isomerization and provide further insights into the mechanisms underlying the photochromism. Our work demonstrates that genetically encoded ''smart fluorophores'' can be readily optimized for biological performance and provides a practical strategy for developing maturation-and stability-enhanced photochromic fluorescent proteins.

No abstract