Improved fluorescent proteins for single-molecule research in molecular tracking and co-localization

Volumetric imaging of fast cellular dynamics with deep learning enhanced bioluminescence microscopy

Bioluminescence microscopy is an appealing alternative to fluorescence microscopy, because it does not depend on external illumination, and consequently does neither produce spurious background autofluorescence, nor perturb intrinsically photosensitive processes in living cells and animals. The low photon emission of known luciferases, however, demands long exposure times that are prohibitive for imaging fast biological dynamics. To increase the versatility of bioluminescence microscopy, we present an improved low-light microscope in combination with deep learning methods to image extremely photon-starved samples enabling subsecond exposures for timelapse and volumetric imaging. We apply our method to image subcellular dynamics in mouse embryonic stem cells, epithelial morphology during zebrafish development, and DAF-16 FoxO transcription factor shuttling from the cytoplasm to the nucleus under external stress. Finally, we concatenate neural networks for denoising and light-field deconvolution to resolve intracellular calcium dynamics in three dimensions of freely moving Caenorhabditis elegans.

FLIM-FRET Imaging of Caspase-3 Activity in Live Cells Using Pair of Red Fluorescent Proteins

We report a new technique to detect enzyme activity inside cells. The method based on Fluorescence Lifetime Imaging (FLIM) technology allows one to follow sensor cleavage by proteolytic enzyme caspase-3. Specifically, we use the FLIM FRET of living cells via the confocal fluorescence microscopy. A specially designed lentivector pLVT with the DNA fragment of TagRFP-23-KFP was applied for transduction of A549 cell lines. Computer simulations are carried out to estimate FRET efficiency and to analyze possible steric restrictions of the reaction between the substrate TagRFP-23-KFP and caspase-3 dimer. Successful use of the fuse protein TagRFP-23-KFP to register the caspase-3 activation based on average life-time measurements is demonstrated. We show that the average life-time distribution is dramatically changed for cells with the modified morphology that is typical for apoptosis. Namely, the short-lived component at 1.8-2.1 ns completely disappears and the long-lived component appears at 2.4-2.6 ns. The latter is a fingerprint of the TagRFP molecule released after cleavage of the TagRFP-23-KFP complex by caspase-3. Analysis of life-time distributions for population of cells allows us to discriminate apoptotic and surviving cells within single frame and to peform statistical analysis of drug efficiency. This system can be adjusted for HTS by using special readers oriented on measurements of fluorescence life-time.

Single-molecule tracking of carbohydrate-binding modules on cellulose using fluorescence microscopy

Single-molecule fluorescence detection is an invaluable technique for the study of molecular behavior in biological systems, both in vitro and in vivo. In this chapter, we focus on detailed protocols that utilize Total Internal Reflection Fluorescence Microscopy (TIRF-M) to visualize single molecules of carbohydrate-binding module (CBM) labeled with green fluorescent protein (GFP). The content describes step-by-step sample preparation and data acquisition, processing, and analysis. These methods can also be further used to study interactions between domains of cellulase molecules and between cellulases and cellulose.

Determination of photophysical parameters of red fluorescent protein mRFP1 under ultraviolet excitation by methods of laser fluorimetry

We investigate photophysical processes that take place in macromolecules of a fluorescent protein mRFP1 under UV excitation [when the energy transfer in a localized donor-acceptor (LDA) pair, which is presented in the molecules of the protein, becomes apparent]. We used a special approach based on the fluorescence laser spectroscopy technique. The energy transfer rates in LDA pairs and photophysical parameters of fluorophores (chromophores) of three spectral forms, which coexist in the ensemble of the macromolecules of this protein, were determined under pulse UV laser excitation.

Covalent quantum dot receptor linkage via the acyl carrier protein for single-molecule tracking, internalization, and trafficking studies

Here we describe a labeling technique for the covalent linkage of quantum dots to transmembrane receptors for single-molecule tracking. Our method combines the acyl carrier protein (ACP) technique with coenzyme A (CoA)—functionalized quantum dots to covalently attach quantum dots to ACP fusions of receptor proteins. The advantages of this approach include: (i) the use of a smaller attachment linker than in many other quantum dot—labeling systems; (ii) the ability to achieve a reliable 1:1 fluorophore-to-receptor labeling stoichiometry; (iii) the specificity of the method; and (iv) the covalent nature of the quantum dot linkage. We demonstrate the general suitability of this technique in single-molecule tracking, internalization, and trafficking studies by imaging two different transmembrane receptors in living cells.

Zinc finger-mediated live cell imaging in Arabidopsis roots

Following the elucidation of recognition codes, artificial zinc finger (ZF) domains can now be assembled to create custom-made DNA-binding proteins in which the alpha helix of each zinc finger mediates an interaction with 3 or 4 bp of DNA. A module of consecutive zinc finger domains, designated a polydactyl zinc finger (PZF) domain, is thus capable of binding an extended number of base pairs of DNA. Besides the multitude of utilities of PZF domains addressed in other chapters, we have shown that they can also be used for live cell imaging of repetitive DNA sequences in Arabidopsis, as well as in mouse cells by generating and expressing PZF:GFP fusion proteins (1). Here we provide a detailed protocol for the construction of such PZF:GFP reporter proteins using our established cloning vehicles, together with a protocol for their expression in plants in order to achieve in vivo labelling of repetitive DNA. Furthermore we provide an accurate quantification method for GFP signals using fluorescent beads (FluoSpheres). Single-molecule precision can be obtained using any confocal setup once the fluorescent beads have been calibrated against purified GFP. The methods can easily be adapted to meet the demands for other situations or for other experimental systems.

Ultramicroscopy reveals axonal transport impairments in cortical motor neurons at prion disease

The functional imaging of neuronal circuits of the central nervous system is crucial for phenotype screenings or investigations of defects in neurodegenerative disorders. Current techniques yield either low penetration depth, yield poor resolution, or are restricted by the age of the animals. Here, we present a novel ultramicroscopy protocol for fluorescence imaging and three-dimensional reconstruction in the central nervous system of adult mice. In combination with tracing as a functional assay for axonal transport, retrogradely labeled descending motor neurons were visualized with >4 mm penetration depth. The analysis of the motor cortex shortly before the onset of clinical prion disease revealed that >80% neurons have functional impairments in axonal transport. Our study provides evidence that prion disease is associated with severe axonal transport defects in the cortical motor neurons and suggests a novel mechanism for prion-mediated neurodegeneration.

High throughput FRET screening of the plasma membrane based on TIRFM

Monitoring protein function with high throughput at individual cell level is of high interest both for basic research and diagnostic applications. For this, following the changes in fluorescence resonance energy transfer (FRET) between a donor/acceptor pair, genetically encoded in the proteins of interest, is a frequently used tool. As proteins attached to or located in the plasma membrane represent a considerable fraction of total proteins, there is a need for high throughput imaging techniques suited for observation of proteins in the cell membrane only. A system is presented, which allows rapid imaging of large areas via total internal reflection fluorescence microscopy (TIRFM) conditions, using a focus-hold system, multiwavelength excitation and dual color detection. The developed imaging system enables screening of large numbers of cells under TIRFM illumination combined with FRET imaging, thereby providing the means to record, e.g., FRET-efficiency of a membrane-associated protein labeled with a donor-acceptor pair. The capability of the system to perform live-FRET scanning with TIRFM on stoichiometric FRET constructs, reaching throughput of up to 1,000 cells/s at the optical resolution limit is demonstrated. A comparison with confocal microscopy shows that TIRFM offers a 4.2-fold advantage in our conditions over confocal microscopy in detecting contributions from membrane-localized proteins.

Fluorescent proteins for single-molecule fluorescence applications

We present single-molecule fluorescence data of fluorescent proteins GFP, YFP, DsRed, and mCherry, a new derivative of DsRed. Ensemble and single-molecule fluorescence experiments proved mCherry as an ideally suited fluorophore for single-molecule applications, demonstrated by high photostability and rare fluorescence-intensity fluctuations. Although mCherry exhibits the lowest fluorescence quantum yield among the fluorescent proteins investigated, its superior photophysical characteristics suggest mCherry as an ideal alternative in single-molecule fluorescence experiments. Due to its spectral characteristics and short fluorescence lifetime of 1.46 ns, mCherry complements other existing fluorescent proteins and is recommended for tracking and localization of target molecules with high accuracy, fluorescence resonance energy transfer (FRET), fluorescence lifetime imaging microscopy (FLIM), or multicolor applications.

A new detection algorithm for image analysis of single, fluorescence-labeled proteins in living cells

A new algorithm is presented for the detection of single, fluorescence-labeled proteins in the analysis of images from living cells. It is especially suited for images with just a few (<1 per 10 microm2) fluorescence peaks from individual proteins with high background and noise (signal to background ratios as low as 2 and signal to noise as low as 10). The analysis uses the peaks over threshold method from extreme value theory and requires minimal assumptions on the underlying distributions. The significant advantage of the method over others is the rare occurrence to detect false positives. Some examples of simulated and real data are given as comparisons. The algorithm is implemented in MATLAB.

Dynamic interaction between Src and C-terminal Src kinase in integrin alphaIIbbeta3-mediated signaling to the cytoskeleton

Integrin-bound Src tyrosine kinase mediates alpha(IIb)beta(3) out-side-in signaling to the cytoskeleton required for platelet adhesion and thrombus formation. Src activation (signal initiation) by phosphorylation of Tyr-418 occurs at lamellipodia leading edges. However, little is known about Src inactivation mediated by C-terminal Src kinase (Csk) Tyr-529 phosphorylation. In an established platelet model cell line (A5-Chinese hamster ovary), we studied the inactivation of Src during alpha(IIb)beta(3)-mediated adhesion to fibrinogen with live cell fluorescence resonance energy transfer (FRET) microscopy. Imaging revealed highly dynamic Src-Csk interactions at the leading edges of active lamellipodia. The Src-Csk interaction followed a highly dynamic pattern. Every 2-3 min, Src-Csk complexes moved inward in the cell, reorganized, and formed stable focal adhesions. These accumulations were primarily seen during retraction of lamellipodia, whereas no interaction was observed during protrusions. Western blot analysis during the run time of FRET signaling revealed an increase in Csk-mediated SrcTyr-529 phosphorylation with a parallel decline of tyrosine 418 phosphorylation. Mutation analysis provided additional insights into the role of Src. Although inactivation of Csk (CskK222R) had no effect on cell adhesion and spreading efficiency, cells with constitutively active expressed Src (SrcY529F) exhibited hardly any adhesion and no spreading. The few adherent cells showed weak focal adhesions that were disorganized and oversized. The data clearly demonstrate the important role of tight Src control by Csk for functional cell adhesion and spreading. The novel experimental FRET approach reported here for the inactivation of Src can be readily applied to other integrin and signaling pathways, including closely related Src family kinase members.

Live cell imaging of repetitive DNA sequences via GFP-tagged polydactyl zinc finger proteins

Several techniques are available to study chromosomes or chromosomal domains in nuclei of chemically fixed or living cells. Current methods to detect DNA sequences in vivo are limited to trans interactions between a DNA sequence and a transcription factor from natural systems. Here, we expand live cell imaging tools using a novel approach based on zinc finger-DNA recognition codes. We constructed several polydactyl zinc finger (PZF) DNA-binding domains aimed to recognize specific DNA sequences in Arabidopsis and mouse and fused these with GFP. Plants and mouse cells expressing PZF:GFP proteins were subsequently analyzed by confocal microscopy. For Arabidopsis, we designed a PZF:GFP protein aimed to specifically recognize a 9-bp sequence within centromeric 180-bp repeat and monitored centromeres in living roots. Similarly, in mouse cells a PZF:GFP protein was targeted to a 9-bp sequence in the major satellite repeat. Both PZF:GFP proteins localized in chromocenters which represent heterochromatin domains containing centromere and other tandem repeats. The number of PZF:GFP molecules per centromere in Arabidopsis, quantified with near single-molecule precision, approximated the number of expected binding sites. Our data demonstrate that live cell imaging of specific DNA sequences can be achieved with artificial zinc finger proteins in different organisms.

Novel fluorescent proteins for high-content screening

The development of fast microscopic imaging devices has enabled the application of automated fluorescence microscopy to pharmaceutical high-throughput drug-discovery assays, referred to as high-content screening (HCS). Initially, green fluorescent protein and its derivatives from Aequorea Victoria, and later anthozoan fluorescent proteins (FPs) have become potent tools as live-cell markers in HCS assays. We illustrate the broad applicability of classic and novel FPs to drug-discovery assays, giving example applications of the use of FPs in multiplexed imaging as fluorescent timers, photosensitizers and pulse-chase labels, and for robotically integrated compound testing.

Protein biosensors based on the principle of fluorescence resonance energy transfer for monitoring cellular dynamics

Genetically-coded, fluorescence resonance energy transfer (FRET) biosensors are widely used to study molecular events from single cells to whole organisms. They are unique among biosensors because of their spontaneous fluorescence and targeting specificity to both organelles and tissues. In this review, we discuss the theoretical basis of FRET with a focus on key parameters responsible for designing FRET biosensors that have the highest sensitivity. Next, we discuss recent applications that are grouped into four common biosensor design patterns--intermolecular FRET, intramolecular FRET, FRET from substrate cleavage and FRET using multiple colour fluorescent proteins. Lastly, we discuss recent progress in creating fluorescent proteins suitable for FRET purposes. Together these advances in the development of FRET biosensors are beginning to unravel the interconnected and intricate signalling processes as they are occurring in living cells and organisms.