This protocol is a guide for visualizing dynamic actin and microtubules using an in vitro total internal fluorescence (TIRF) microscopy assay.
Traditionally, the actin and microtubule cytoskeletons have been studied as separate entities, restricted to specific cellular regions or processes, and regulated by different suites of binding proteins unique for each polymer. Many studies now demonstrate that the dynamics of both cytoskeletal polymers are intertwined and that this crosstalk is required for most cellular behaviors. A number of proteins involved in actin-microtubule interactions have already been identified (i.e., Tau, MACF, GAS, formins, and more) and are well characterized with regard to either actin or microtubules alone. However, relatively few studies showed assays of actin-microtubule coordination with dynamic versions of both polymers. This may occlude emergent linking mechanisms between actin and microtubules. Here, a total internal reflection fluorescence (TIRF) microscopy-based in vitro reconstitution technique permits the visualization of both actin and microtubule dynamics from the one biochemical reaction. This technique preserves the polymerization dynamics of either actin filament or microtubules individually or in the presence of the other polymer. Commercially available Tau protein is used to demonstrate how actin-microtubule behaviors change in the presence of a classic cytoskeletal crosslinking protein. This method can provide reliable functional and mechanistic insights into how individual regulatory proteins coordinate actin-microtubule dynamics at a resolution of single filaments or higher-order complexes.
Historically, actin and microtubules have been viewed as separate entities, each with their own set of regulatory proteins, dynamics behaviors, and distinct cellular locations. Abundant evidence now demonstrates that actin and microtubule polymers engage in functional crosstalk mechanisms that are essential to execute numerous cell processes including migration, mitotic spindle positioning, intracellular transport, and cell morphology1,2,3,4. The diverse coordinated behaviors that underlie these examples are dependent on an intricate balance of coupling factors, signals, and physical properties. However, the molecular details that underpin these mechanisms are still largely unknown because most studies focus on a single cytoskeletal polymer at a time1,2,5.
Actin and microtubules do not directly interact6,7,8. The coordinated dynamics of actin and microtubules seen in cells is mediated by additional factors. Many proteins thought to regulate actin-microtubule crosstalk have been identified and their activities are well characterized with regard to either cytoskeletal polymer alone1,2. Growing evidence suggests this single polymer approach has concealed the dual functions of some of the proteins/complexes that enable actin-microtubule coupling events7,8,9,10,11,12,13. Experiments where both polymers are present are rare and often define mechanisms with a single dynamic polymer and static stabilized version of the other6,8,9,10,11,14,15,16,17,18. Thus, methods are needed to investigate the emergent properties of actin-microtubule coordinating proteins that may only be fully understood in experimental systems that employ both dynamic polymers.
The combination of direct protein labeling approaches, genetically encoded affinity tags, and total internal reflection fluorescence (TIRF) microscopy has been applied with great success in biomimetic reconstitution systems19,20,21,22,23. Many bottom-up schemes do not contain all the factors that regulate proteins in cells. However, "biochemistry on a coverglass" technology has refined many mechanisms of actin and microtubule dynamics at high spatial and temporal scales, including the components required for polymer assembly or disassembly, and motor protein movement5,12,23,24,25,26,27. Here a minimal component single-filament approach to investigate actin-microtubule coupling in vitro is described. This protocol can be used with commercially available or highly pure purified proteins, fluorescently labeled proteins, perfusion chambers, and extended to more complicated schemes containing cell extracts or synthetic systems. Here, commercially available Tau protein is used to demonstrate how cytoskeletal dynamics change in the presence of an actin-microtubule coupling protein, but can be substituted for other putative actin-microtubule coordinating factors. The major advantage of this system over other approaches is the ability to simultaneously monitor the dynamics of multiple cytoskeletal polymers in one reaction. This protocol also provides users with examples and simple tools to quantify changes to cytoskeletal polymers. Thus, protocol users will produce reliable, quantitative, single-filament resolution data to describe mechanisms that underlie how diverse regulatory proteins coordinate actin-microtubule dynamics.
1. Washing the coverslips
NOTE: Wash (24 mm x 60 mm, #1.5) coverslips according to Smith et al., 201328.
2. Coating cleaned (24 mm x 60 mm, #1.5) coverslips with mPEG- and biotin-PEG-silane
NOTE: This protocol specifically uses a biotin-streptavidin system to position actin and microtubules within the TIRF imaging plane. Other coatings and systems may be used (e.g., antibodies, poly-L-lysine, NEM myosin, etc.).
3. Assembling imaging flow chambers
4. Conditioning of perfusion chambers
5. Microscope preparation
NOTE: Biochemical reactions containing dynamic actin filaments and microtubules are visualized/performed using an inverted Total Internal Reflection Fluorescence (TIRF) microscope equipped with 120-150 mW solid-state lasers, a temperature corrected 63x oil immersion TIRF objective, and an EMCCD camera. Proteins in this example are visualized at the following wavelengths: 488 nm (microtubules) and 647 nm (actin).
6. Preparation of protein reaction mixes
7. Image actin and microtubule dynamics
8. Process and analyze images using FIJI software31
With the conditions described above (Figure 1), actin and microtubule polymers should be visible (and dynamic) within 2 min of image acquisition (Figure 2). As with any biochemistry-based protocol, optimization may be required for different regulatory proteins or batches of protein. For these reasons, the TIRF angle and image exposures are set first with reactions containing each individual polymer. This confirms that stored proteins are functional and enough labeled protein is present for detection. While not always necessary (and not performed here), post-processing of movies (i.e., background subtraction, averaging, or Fourier transformations) can be used to enhance the image contrast (particularly of microtubules)5,25,33. The direct visualization of single actin filaments and microtubules afforded by this assay supports the quantitative determination of several dynamic measures for either cytoskeleton component alone or together, including polymerization parameters (i.e., nucleation or elongation rate), disassembly parameters (i.e., shrinkage rates or catastrophe events), and polymer coalignment/overlap (Figure 3). Further, these measures can be used as a starting point to decipher the binding or influence of regulatory ligands like Tau (Figure 3). Many measurements of single actin filaments or microtubules can be made from one TIRF movie. However, due to variations in coverslip coating, pipetting, and other factors, reliable measurements should also include multiple technical replicate reactions/movies.
Many facets of microtubule dynamics can be determined from example kymographs including the rate of microtubule elongation, as well as the frequency of catastrophe and rescue events (Figure 3A). Using kymographs to measure actin dynamics in this system is not as straightforward because actin filaments are more convoluted than microtubules. As a consequence, parameters of actin filament dynamics are measured by hand, which is time consuming and labor intensive. Nucleation counts are measured as the number of actin filaments present at a consistent timepoint for all conditions. These counts vary widely across TIRF imaging fields, but can be used with many replicates or to supplement observations from other polymerization assays. Nucleation counts may also be used for microtubules if trial conditions lack stabilized microtubule seeds. Actin filament elongation rates are measured as the length of filament over time from at least four movie frames. Rate values are conveyed per micromolar actin with a correction factor of 370 subunits to account for the number of actin monomers in a micron of filament (Figure 3B)32. Measurements to define the coordinated behaviors between actin and microtubules are less well defined. However, correlative analyses have been applied to measure the coincidence of both polymers including line scans (Figure 3C) or overlap software5,11,34.
Data Availability:
All datasets associated with this work have been deposited in Zenodo and are available with reasonable request at: 10.5281/zenodo.6368327.
Figure 1. Experimental schematics: flow chamber assembly to image acquisition. (A) Imaging chamber assembly. Top to bottom: IBIDI imaging chambers are taped along perfusion wells (denoted by arrow); the second (white) layer of tape backing (left on in the image shown to better orient users) is removed and Epoxy is applied at the edge of the perfusion chamber (arrow). Note: To more easily orient users where to place the epoxy, the white backing was left on in this image. The cleaned and coated coverslip is attached to the imaging chamber with the coating side facing the inside of the perfusion well. (B) Flow-chart illustrating the steps for conditioning imaging chambers for biotin-streptavidin linkages. (C) Examples of reactions used to acquire TIRF movies of dynamic microtubules and actin filaments. Please click here to view a larger version of this figure.
Figure 2. Image sequences of growing actin filaments and microtubules in the absence or presence of Tau. Time-lapse image montage from TIRF assays containing 0.5 µM actin (10% Alexa-647-actin and 0.09% biotin-actin labeled) and 15 µM free tubulin (4% HiLyte-488 labeled) in the absence (A) or presence (B) of 250 nM Tau. Time elapsed from reaction initiation (mixing Tube A and Tube B) is shown. Scale bars, 25 µm. Please click here to view a larger version of this figure.
Figure 3. Example measurements of microtubules and actin filament dynamics. (A) Average time projection of the tubulin channel efficiently visualizes total microtubule lengths for the line scans used to generate kymograph plots. Black dotted lines correspond to the two example kymographs of dynamic microtubules shown on the right. The growth (solid black lines) and disassembly phases (doted pink lines; two denoted with pink arrows) of microtubules are shown on each kymograph. Time scale bar, 3 min. Length scale bar, 10 µm. Reaction contains 0.5 µM actin (10% 647-label) and 15 µM free tubulin (4% 488-HiLyte label). Only the tubulin channel is shown.(B) Two example time-lapse image montages depicting single-actin filaments actively polymerizing. Elongation rates are calculated as the slope of plots of the length of actin filaments over time per micromolar actin. Thus, a correction factor of two must be applied to 0.5 µM actin reactions for comparison for rates typically determined at the 1 µM actin concentration. Examples from five filaments are shown to the right. Scale bars, 10 µm. Reaction contains 0.5 µM actin (10% 647-label) and 15 µM free tubulin (4% 488-HiLyte label). Only the actin channel is shown. (C) TIRF images of dynamic microtubules (MT) (green) and actin filaments (purple) polymerizing in the absence (left) or presence of 250 nM Tau (middle). Blue dotted lines and arrows mark where a line was drawn for the line scan plots corresponding to each condition (below each image). Overlap between microtubules and actin regions (shown as black) can be scored at a set time point per area (right). Scale bars, 25 µm. Reactions contain 0.5 µM actin (10% 647-label) and 15 µM free tubulin (4% 488-HiLyte label) with or without 250 nM Tau. Please click here to view a larger version of this figure.
The use of total internal reflection fluorescence (TIRF) microscopy to visualized purified proteins has been a fruitful and compelling approach to dissect unique mechanisms of cytoskeletal regulation5,23,24,25,26,27,35. Compared to traditional biochemical assays, TIRF reactions require very small volumes (50-100 µL), and quantitative measurements of cytoskeletal dynamics can be gleaned from an individual assay. Most studies of cytoskeletal dynamics focus on a single polymer system (i.e., actin filaments or microtubules), thus detailed measurements of the crosstalk or emergent behaviors between actin filaments and microtubules typically seen in cells have remained elusive and difficult to recapitulate in the test tube. To solve this problem, this protocol describes a single-filament TIRF microscopy system that enables the direct visualization of dynamic actin and microtubule polymers in the same biochemical reaction. Thus, this method goes beyond traditional assays that recapitulate the dynamic behavior of actin filaments or microtubules alone. This technique was also performed with Tau as an example of how several dynamic properties change in the presence of a cytoskeleton coupling factor. This protocol can be used with additional proteins known or suspected to coordinate actin or microtubule dynamics, including (but not limited to) MACF, GAS, formins, and more. Finally, provided example analyses can be used as a guide to quantify data acquired with this protocol.
"Seeing is believing" is a compelling reason to perform microscopy-based assays. However, caution is required in the execution and interpretation of TIRF microscopy experiments. One major challenge of cytoskeletal co-assembly assays is that many commonly used imaging conditions are not compatible each polymer. Microtubules and actin typically have different buffer, temperature, salt, nucleotide, and concentration requirements for polymerization. Actin, tubulin, regulatory proteins of interest, and the buffers utilized in this protocol are sensitive to freeze-thaw cycles. Therefore, careful handling of proteins and buffers is necessary to successfully execute this protocol. To alleviate many of these concerns, using freshly recycled tubulin (frozen for <6 weeks), and pre-clearing frozen/resuspended actins via ultracentrifugation is strongly recommended. These considerations also apply to the myriad of regulatory proteins to be assessed with this procedure, which may be sensitive to freeze-thaw cycles or the concentration of buffer salts5,11,36.
Unfortunately, no one-size-fits-all buffer without experimental tradeoffs exists. To appropriate more volume for proteins of lower concentration, ATP and GTP may be included in the 2x TIRF buffer solution (Figure 1C). However, because these nucleotides are extremely sensitive to freeze-thaw cycles, it is not recommended. The oxygen scavenging compounds used here (i.e., catalase and glucose-oxidase) are necessary to visualize proteins for long periods of time (minutes to hours), but are known to restrict microtubule polymerization at high concentrations5. Related to these buffer considerations, a limitation of this protocol is that some canonical microtubule-associated regulatory proteins may require more or less salt to recapitulate functions found in cells or assays using microtubules alone (without actin). Changing the nature or concentration of salt to address these concerns will likely influence rates of actin filament polymerization and/or parameters of microtubule dynamics. Measurements of multiple descriptive parameters (minimally, nucleation, elongation rates, and stability) (Figure 3) are required to confirm protocol success or to explicitly document the effects of specific buffers or regulatory proteins. For example, too much actin filament polymerization can obscure actin-microtubule coupling events within seconds. Consequently, fine-tuning experimental conditions by lowering the overall concentration of actin or including additional proteins to suppress actin nucleation (i.e., profilin) will extend the overall period that coordinated actin-microtubule activities can be viewed clearly. Controls addressing these prerequisites, and technical replicates (beyond multiple fields of view), are critical for users to generate reliable and reproducible results.
Cell-based studies provide limited opportunity to observe direct protein-protein relationships or the action of regulatory complexes. In contrast, some of the mechanisms gleaned from in vitro assays do not always reflect the exact behaviors of proteins seen in cells. This classic biochemist dilemma can be addressed in future applications of this technique with specific modifications. For example, adding functional fluorescently labeled coupling proteins expands this method from single-filament studies to single-molecule studies. Assays can be further modified to use cell extracts that may add the "missing" unknown key factors required to recapitulate cell-like phenomena. For example, TIRF-based assays employing yeast or Xenopus extracts have reconstituted contractile actomyosin rings37, mitotic spindles26,38, components of actin or microtubule assembly39,40, and even dynamics at the centrosome and kinetochores36,41,42,43. Moreover, such systems may pave the way toward artificial cell systems that have lipids or signaling factors present44,45,46.
The authors have nothing to disclose.
I am grateful to Marc Ridilla (Repair Biotechnologies) and Brian Haarer (SUNY Upstate) for helpful comments on this protocol. This work was supported by the National Institutes of Health (GM133485).
1% BSA (w/v) | Fisher Scientific | BP1600-100 | For this purpose (blocking TIRF chambers), BSA is resuspended in ddH20 and filtered through a 0.22 µm filter. |
1× BRB80 | Homemade | 80 mM PIPES, 1 mM MgCl2, 1 mM EGTA, pH 6.8 with KOH | |
10 mg/mL (1000 U) glucose oxidase | Sigma Aldrich Inc, St. Louis, MO | G2133-50KU | Combined with catalase, aliquot and store at -80 oC until use |
100 µM tubulin | Cytoskeleton Inc, Denver, CO | T240 | Homemade tubulins should be recycled before use to remove polymerization-incompetent tubulin (Hyman et al. (1992)29; Li and Moore (2020)30). Commercially available tubulins are often too dilute to recycle, but function well if resuspended according to manufacturer’s instructions and pre-cleared via ultracentrifugation (278,000 × g) for 60 min, before use. |
100 mM ATP | Gold Biotechnology Inc, Olivette, MO | A-081 | Resuspended in ddH20 (pH 7.5) and filter sterilized. |
100 mM GTP | Fisher Scientific | AC226250010 | Resuspended in 1× BRB80 (pH 6.8) and filter sterilized. |
120-150 mW solid-state lasers | Leica Microsystems | 11889151; 11889148 | |
2 mg/mL catalase | Sigma Aldrich Inc, St. Louis, MO | C40-100 | Combined with glucose oxidase, aliquot and store at -80 oC until use |
2× TIRF buffer | Homemade | 2× BRB80, 100 mM KCl, 20 mM DTT, 80 mM glucose, 0.5% (v/v) methylcellulose (4,000 cp); Note: 1 µL of 0.1M GTP and 1 µL of 0.1M ATP added separately to TIRF reactions to avoid repeated freeze-thaw cycles. | |
24 × 60 mm, #1.5 coverglass | Fisher Scientific, Waltham, MA | 22-266882 | Coverglass must be extensively washed before use (Smith et al. (2014)22) |
37 oC heatblock | |||
37 oC water bath | |||
5 mg/mL Streptavidin (600x stock) | Avantor, Philadelphia, PA | RLS000-01 | Resuspended in Tris-HCl (pH 8.8); dilute the aliquot to 1× in HEK buffer on day of use |
5 min Epoxy resin and hardener | Loctite, Rocky Hill, CT | 1365736 | Combined resin and hardener may take up to 30 min to cure. |
50% biotinylated-GpCpp microtubule seeds | Cytoskeleton Inc; Homemade | T333P | (optional) GppCpp or Taxol stabilized microtubule seeds can more efficiently mediate microtubule polymerization. Taxol and GppCpp stabilize microtubules in different ways that can affect the microtubule lattice structure and ability of certain regulatory proteins to bind to the stabilized portion of the microtubule. A method to make diverse kinds of microtubule seeds is outlined in Hyman et al. (1992). |
70 oC incubator | |||
Actin mix stock | Homemade; this protocol | A 12.5 µM actin mix comprised of labeled (fluorescent and biotinylated) and unlabeled actin for up to six reactions. 2 µL of stock is used in the final TIRF reaction. The final concentration of actin used in each reaction is 0.5 µM (10% Alexa-647; 0.09% biotin-labeled). | |
Appropriate buffer controls | Homemade | Combination of buffers from all proteins being assessed | |
Biotin-PEG-silane (MW 3,400) | Laysan Bio Inc | biotin-PEG-SIL-3400 | Dispensed into 2-5 mg aliquots, backfilled with nitrogen, parafilmed closed, and stored at -20 oC with desiccant until use |
Biotinylated actin | Cytoskeleton Inc; Homemade | AB07 | Biotin-actin is made by labeling on lysine residues and thus assumed to be at least 100% labeled, but varies with different lots/preparations. Optimal biotinylated actin concentrations must be empirically determined for particular uses/experimental designs. Higher concentrations permit more efficient tracking, but may impede polymerization or interactions with regulatory proteins. Here a small percentage (0.09% or 900 pM) biotinylated actin is present in the final TIRF reaction. |
Dishsoap | Dawn, Procter and Gamble, Cincinnati, OH | For unknown reasons, the blue version cleans coverslips more efficiently than other available colors. | |
Dry ice | |||
FIJI Software | www.https://imagej.net/software/fiji/downloads | Schneider et al. (2012)31. | |
Fluorescently labeled actin | Cytoskeleton Inc; Homemade | AR05 | Homemade fluorescently labeled actin is stored in G-buffer supplemented with 50% glycerol at -20 oC (Spudich et al. (1971)47; Liu et al. (2022)48). Fluorescently labeled actin is dialyzed against G-buffer and precleared via ultracentrifugation for 60 min at 278,000 × g before use. |
Fluorescently labeled tubulin | Cytoskeleton Inc | TL488M, TLA590M, TL670M | Resuspended in 20 µL 1× BRB80 (10 µM final concentration) and pre-cleared via ultracentrifugation (278,000 × g) for 60 min, before use. |
G-buffer | Homemade | 3 mM Tris-HCl (pH 8.0), 0.2 mM CaCl2, 0.5 mM DTT, 0.2 mM ATP | |
HEK Buffer | Homemade | 20 mM HEPES (pH 7.5), 1 mM EDTA (pH 8.0), 50 mM KCl | |
Ice | |||
Ice bucket | |||
Imaging chambers | IBIDI, Fitchburg, WI | 80666 | Order chambers with no bottom to utilize different coverslip coatings |
iXon Life 897 EMCCD camera | Andor, Belfast, Northern Ireland | 8114137 | |
LASX Premium microscope software | Leica Microsystems | 11640611 | |
Methylcellulose (4,000 cp) | Sigma Aldrich Inc | M0512 | |
Microscope base equipped with TIRF module | Leica Microsystems, Wetzlar, Germany | 11889146 | |
mPEG-silane (MW 2,000) | Laysan Bio Inc, Arab, AL | mPEG-SIL-2000 | Dispensed into 10-15 mg aliquots, backfilled with nitrogen, parafilmed closed, and stored at -20 oC with desiccant until use |
Objective heater and heated stage insert | OKO labs, Pozzioli, Italy | 8113569 | Set temperature controls to 35-37 oC. Use manufacturer suggestions for accurate calibration. |
Perfusion pump | Harvard Apparatus, Holliston, MA | 704504 | A syringe and tubing can be substituted. |
Petri Dish, 100 x 15 mm | Genesee Scientific, San Diego, CA | 32-107 | |
Plastic slide mailer container | Fisher Scientific | HS15986 | |
SA-S-1L-SecureSeal 0.12 mm thick | Grace Biolabs, Bend, OR | 620001 | Double-sided tape of precise manufactured dimensions is strongly recommended. |
Small styrofoam container | Abcam, Cambridge, UK | Reused from shipping | |
Small weigh boat | Fisher Scientific | 02-202-100 | |
Spectrophotometer | |||
Tau | Cytoskeleton Inc | TA01 | Three isoforms of Tau are present in the commercially available preparation of Tau. The concentration in this protocol was determined from the highest molecular weight band (14.3 µM, when resuspended per manufacturer’s recommendations with 50 µL of ddH20). |
Temperature corrected 63× Plan Apo 1.47 N.A. oil immersion TIRF objective | Leica Microsystems | 11506319 | |
Tubulin stock | Homemade; this protocol | A tubulin stock consisting of 7.2 µL recycled 100 µM unlabeled tubulin and 3 µL of 10 µM resuspended commercially available fluorescently labeled tubulin. One tubulin stock is used per reaction and thawed/stored on ice. The final concentration of free tubulin in each reaction is 15 µM (4% labeled). More than 15 µM tubulin will result in hyperstabilized (not dynamic) microtubules, whereas concentrations below 7.5 µM free tubulin do not polymerize well. Careful determination of protein concentration and handling is required. | |
Unlabeled actin (dark) | Cytoskeleton Inc; Homemade | AKL99 | Actin nucleates are almost always present in commercially available (lyophilized) or frozen actins and contribute to variability in quantitative measurements (Spudich et al. (1971)47; Liu et al. (2022)48). Rabbit muscle actin is stored in G-buffer at -80 oC and precleared via ultracentrifugation for 60 min at 278,000 × g before use. Several actin stock solutions are made throughout the day (making no more than enough for six reactions at a time is strongly recommended). |