Microtubule Tip Tracking by the Spindle and Kinetochore Protein Ska1 Requires Diverse Tubulin-Interacting Surfaces

Abstract

The macromolecular kinetochore functions to generate interactions between chromosomal DNA and spindle microtubules [1]. To facilitate chromosome movement and segregation, kinetochores must maintain associations with both growing and shrinking microtubule ends. It is critical to define the proteins and their properties that allow kinetochores to associate with dynamic microtubules. The kinetochore-localized human Ska1 complex binds to microtubules and tracks with depolymerizing microtubule ends [2]. We now demonstrate that the Ska1 complex also autonomously tracks with growing microtubule ends in vitro, a key property that would allow this complex to act at kinetochores to mediate persistent associations with dynamic microtubules. To define the basis for Ska1 complex interactions with dynamic microtubules, we investigated the tubulin-binding properties of the Ska1 microtubule binding domain. In addition to binding to the microtubule lattice and dolastatin-induced protofilament-like structures, we demonstrate that the Ska1 microtubule binding domain can associate with soluble tubulin heterodimers and promote assembly of oligomeric ring-like tubulin structures. We generated mutations on distinct surfaces of the Ska1 microtubule binding domain that disrupt binding to soluble tubulin but do not prevent microtubule binding. These mutants display compromised microtubule tracking activity in vitro and result in defective chromosome alignment and mitotic progression in cells using a CRISPR/Cas9-based replacement assay. Our work supports a model in which multiple surfaces of Ska1 interact with diverse tubulin substrates to associate with dynamic microtubule polymers and facilitate optimal chromosome segregation.

Keywords: chromosome segregation; kinetochore; microtubule; mitosis; tubulin.

Figure 1. The Ska1 microtubule binding domain associates with soluble tubulin dimer

A. Negative stain transmission electron microscopy image of the human Ska1 microtubule binding domain forming oligomeric assemblies around a microtubule. B. Cryo-EM image of the C. elegans SKA-1 microtubule binding domain forming oligomeric assemblies around microtubules. C. 2 views of the cryo-EM reconstruction of the C. elegans SKA-1 microtubule binding domain bound to a microtubule showing the presence of the microtubule lattice, an outer oligomeric ring likely composed of tubulin, and density connecting these rings likely corresponding to the SKA-1 microtubule binding domain. D. Sedimentation assay demonstrating that incubation of soluble tubulin heterodimer with Ska1 MTBD or Ska1 complex results in the formation of large assemblies. Coomassie-stained gel showing supernatant (S) and pellet (P) fractions from the indicated conditions. E. Negative stain transmission electron microscopy images of the assemblies formed following incubation of the C. elegans SKA-1 MTBD or human Ska1 MTBD with soluble tubulin. Rings formed by the incubation of dolastatin-10 with tubulin are shown as a comparison. Scale bars, 100 nm. Also see Figure S1B. F. Size exclusion chromatography traces and Coomassie-stained gels of the peak fractions for the indicated samples demonstrating co-elution of the Ska1 MTBD with RB3-SLD-tubulin. Fractions run on the gel are indicated by the orange, blue and pink bars.

Figure 2. The Ska1 microtubule binding domain uses multiple distinct surfaces to interact with tubulin

A. Left: Schematic of the human Ska1 complex highlighting the location of the Ska1 microtubule binding domain within the complex, and within the Ska1 protein. Right: Structure of the human Ska1 microtubule binding domain (4C9Y.pdb) [12] showing the locations of the indicated residues targeted for mutational analysis. B. Coomassie-stained gels showing the pellet fractions from representative co-sedimentation assays for the binding of the indicated Ska1 microtubule binding domain mutants to either microtubule polymers, dolastatin-induced rings, or soluble tubulin dimer. For microtubules and dolastatin-induced rings, quantifications indicate the percentage of MTBD bound to the substrate for 2 experiments, with the mean + SD shown. For tubulin, the quantification indicates the percentage of tubulin in the pellet for 7 independent experiments, with the mean + SD shown. See Figure S2A for the Coomassie-stained gels of the supernatant fractions. C. Coomassie-stained gels of the size exclusion chromatography fractions for binding of the Ska1 MTBD and mutants to an RB3-SLD-tubulin complex. The gel for wild type MTBD is duplicated from Figure 1F. RB3-SLD-tubulin peak fractions (see Figure 1F) are shown for each of the Ska1 MTBD mutants. Quantifications indicate the amount of Ska1 MTBD co-eluting with RB3-SLD relative to wild type for 2 experiments, with the mean + SD shown. All mutants show reduced or eliminated binding to RB3-SLD-tubulin. Also see Figure S2B. D. Table summarizing the binding data from this figure.

Figure 3. In vitro analysis of Ska1 interactions with dynamic microtubules

A. Schematic of the in vitro TIRF assay to visualize Ska1 complex associations with dynamic microtubules. B. Representative kymographs of GFP-Ska1 complexes on elongating and depolymerizing microtubules, as visualized with GFP fluorescence. Also see Movie S1. Vertical scale bar is 30 s, horizontal - 2 μm; microtubule plus ends point to the right. Enlarged images are shown for the green, yellow and blue boxed regions. The kymograph on the right of the depolymerization panel is an equivalently enlarged region from a distinct microtubule. All enlargements shown were chosen to highlight Ska1 complex diffusion near the elongating and depolymerizing ends, their encounter with ends, and brief tracking. For the enlargements, the vertical scale bar is 3 s, horizontal - 2 μm. C. Representative kymographs of the indicated GFP-Ska1 complexes on polymerizing microtubules. Tracking by wild type Ska1 appears as an almost continuous bright line because at this time scale, individual complexes cannot be discriminated. Microtubule plus ends point to the right. Percent of microtubules (mean ± SD) that display Ska1 complex tip-tracking is shown below each kymograph. Data are based on ≥ 38 microtubules for each protein. D. Representative kymographs of the indicated GFP-Ska1 complexes on depolymerizing microtubules. Also see Movie S2. Microtubule plus end points to the right. Percent of microtubules (mean ± SD) that display Ska1 complex tip-tracking is shown below each kymograph. Data are based on ≥ 29 microtubules for each protein. ** for the K183A K184A mutant indicates that this mutant shows a similar percentage of microtubules that display tracking, but the tracking signal is less robust relative to the wild type Ska1 complex. Vertical scale bar is 20 s, horizontal - 1 μm. Also see Figure S3.

Figure 4. Ska1 microtubule binding domain mutants disrupt proper mitotic progression

A. Immunofluorescence images of microtubules (DM1A), DNA (Hoechst), kinetochores (ACA), and GFP-Ska1 in the indicated conditions. The Ska1 inducible knockout (iKO) was induced with doxycycline for 4 days prior to imaging. The fluorescence is not scaled identically in each panel due to acquisition on different days. Scale bar, 10 μm. B. Fluorescent images of live cells stably expressing the indicated GFP-Ska1 constructs. Images are provided for a qualitative comparison of localization, but the GFP fluorescence is not scaled identically in each panel due to acquisition on different days. Scale bar, 10 μm. C. Quantification of mitotic phenotypes in control cells (uninduced Ska1 iKO), Ska1 iKO cells, and cells expressing the indicated GFP-tagged Ska1 constructs in the iKO background 4 days following induction of CRISPR-Cas9. n=100 cells/condition D. Quantification of mitotic duration (chromosome condensation to anaphase onset; mean +/− SD) in control cells and the indicated GFP-Ska1 cell lines 4 days following induction of CRISPR/Cas9. Control (n=22), Ska1 iKO (n=24), wild type (n=18), ΔMTBD (n=10), K183A K184A (n=9), K223A K226A (n=37), R155A (n=34), R236A (n=17). The mutants are statistically different from the wild type rescue condition and the Ska1 ΔMTBD mutant based on unpaired t tests (see Figure S4B). The asterisk for the Ska1 iKO indicates that most cells did not exit mitosis during the imaging such that this data under-represents the mitotic duration.