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. 2014 Jun 16;24(12):1295-1303.
doi: 10.1016/j.cub.2014.03.078. Epub 2014 May 15.

Genome-wide Analysis Reveals Novel and Discrete Functions for Tubulin Carboxy-Terminal Tails

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Free PMC article

Genome-wide Analysis Reveals Novel and Discrete Functions for Tubulin Carboxy-Terminal Tails

Jayne Aiken et al. Curr Biol. .
Free PMC article

Abstract

Background: Microtubules (MTs) support diverse transport and force generation processes in cells. Both α- and β-tubulin proteins possess carboxy-terminal tail regions (CTTs) that are negatively charged, intrinsically disordered, and project from the MT surface where they interact with motors and other proteins. Although CTTs are presumed to play important roles in MT networks, these roles have not been determined in vivo.

Results: We examined the function of CTTs in vivo by using a systematic collection of mutants in budding yeast. We find that CTTs are not essential; however, loss of either α- or β-CTT sensitizes cells to MT-destabilizing drugs. β-CTT, but not α-CTT, regulates MT dynamics by increasing frequencies of catastrophe and rescue events. In addition, β-CTT is critical for the assembly of the mitotic spindle and its elongation during anaphase. We use genome-wide genetic interaction screens to identify roles for α- and β-CTTs, including a specific role for β-CTT in supporting kinesin-5/Cin8. Our genetic screens also identified novel interactions with pathways not related to canonical MT functions.

Conclusions: We conclude that α- and β-CTTs play important and largely discrete roles in MT networks. β-CTT promotes MT dynamics. β-CTT also regulates force generation in the mitotic spindle by supporting kinesin-5/Cin8 and dampening dynein. Our genetic screens identify links between α- and β-CTT and additional cellular pathways and suggest novel functions.

Figures

Figure 1
Figure 1. α- and β-CTTs contribute to microtubule function
A) Structure and predicted range of motion for mammalian α- and β-CTTs. The CTT regions of yeast α-tubulin/Tub1 and yeast β-tubulin/Tub2 were modeled on the structure of mammalian α/β tubulin heterodimer [5]. The surface and lumen sides of the microtubule are indicated, as well as the plus and minus ends. Shaded volumes represent the 95% confidence interval of the sampled range of motion for α(blue) and β-CTTs (red), based on molecular dynamics simulations. Volumes of these regions are shown in Å3. Tub1 residue A442 and Tub2 residue V430 are labeled in yellow. B) Sequences of CTTs. The carboxy-terminal residues of the α-tubulins, Tub1 and Tub3, and the β-tubulin, Tub2. These regions were selected based on abundance of negatively-charged residues, high interspecies sequence heterogeneity (Figure S1), lack of resolution in structural studies [5], and correspondence to the major fragment produced by subtilisin digestion [6]. Residues highlighted in yellow correspond to residues highlighted in (A). C) CTT mutants are sensitive to benomyl. 10-fold dilution series of indicated strains were spotted to rich media (YPD; “control”) or rich media supplemented with benomyl (10μg/mL). Strains: wild type, yJM0596; tub1-QQQQF, yJM0418; tub1-EEF, yJM0118; tub1-446Δ, yJM0105; tub1-442Δ, yJM0116; tub1-442Δ tub3-442Δ, yJM0212; tub2-445Δ, yJM0583; tub2-438Δ, yJM0565; tub2-430Δ, yJM0282; tub1-442Δ tub2-430Δ, yJM0559; tub1-442Δ tub3-442Δ tub2-430Δ, yJM0581; CTT swap, yJM0551.
Figure 2
Figure 2. β-CTT regulates microtubule stability
A) β-CTT mutants are cold tolerant. Cells were grown to saturation at 30°C in rich media and a 10-fold dilution series of each was spotted to YPD; plates were grown at 16°C for 5 days. Strains are the same used in Figure 1C. B) α- and β-CTT mutants exhibit longer astral microtubules. Distributions of astral microtubule lengths, with bars indicating mean ±SD. Asterisks indicate statistical significance (p < 0.01) by t-test, compared to wild type. Strains: wild type, yJM0596; tub1-442Δ tub3-442Δ, yJM0212; tub2-430Δ, yJM0282; tub1-442Δ tub3-442Δ tub2-430Δ, yJM0581; CTT swap, yJM0551.
Figure 3
Figure 3. Bik1 recruitment and microtubule plus end dynamics
A) Representative images of wild-type and α-CTT mutant cells labeled with Bik1-3GFP (green) and Spc110-DsRed (red) shown as merge. Cells are classified as G1, pre-anaphase (pre-ana), and mitosis based on bud morphology and spindle morphology. Arrow marks Bik1-3GFP at an astral microtubule plus end. Scalebar = 2μm. B) Fluorescence intensity measurements of Bik1-3GFP foci at MT plus-ends, from G1, pre-anaphase, and mitotic classes. Plot depicts background-adjusted intensity measurements with bars indicating mean ±SD. Single asterisk indicates significant difference compared to wild type, by t-test (p < 0.05). Double asterisk, p < 0.01. C) Representative lifeplots of astral microtubule dynamics in wild type and β-CTT mutants. Astral microtubule length was measured over time by plotting the distance between plus-end associated Bik1-3GFP and the proximal spindle pole. See also Figure S3. Strains: wild type, yJM0424; tub1/3-442Δ, yJM0324; tub2-430Δ, yJM0541.
Figure 4
Figure 4. Mapping genetic interactions of CTT mutants
A) Venn diagram of negative interactions recovered from SGA screens with tub1-442Δ and tub2-430Δ. The tub1-442Δ screen identified 67 negative genetic interactions. The tub2-430Δ screen identified 248. Seven interacting genes were common to both screens. B) Biological process gene ontology terms enriched among negatively interacting genes in tub1-442Δ and tub2-430Δ screens. Blue bars represent genes identified only in the tub1-442Δ screen, red bars represent genes identified only in the tub2-430Δ screen and yellow bars represent genes identified in both screens. All terms are significantly enriched in the respective data set, relative to the S. cerevisiae reference set, determined by Fisher’s exact test (p < 0.05; see Supplemental Experimental Procedures). C) tub2-430Δ screen is enriched for genes related to MT-processes and spindle checkpoints. Spindle checkpoint genes are highlighted in purple. Dynein pathway genes and highlighted in green. Red nodes are genes identified exclusively by the tub2-430Δ screen, yellow node (BUB3) was also identified in the tub1-442Δ screen, and white node (CIN8) is predicted to be related to the network (see Supplemental Experimental Procedures). Black lines denote previously identified genetic interactions with cin8 mutants.
Figure 5
Figure 5. β-CTT is important for spindle assembly and elongation
A) Wild-type cell labeled with Spc110-tdTomato (red) and Dad1-GFP (green), shown as merge with DIC image. Scalebar = 2μm. B) Spindle assembly. G1-arrested cells were released into fresh media and samples were collected at 15min intervals, fixed, and imaged. Percentage of cells with bipolar spindles (Spc110 foci linked by Dad1 signal) was determined for each timepoint. Wild-type cells show a decrease in the percentage of bipolar spindle at 120 min as many cells have completed mitosis and disassembled their spindles. The value increases at 150 min as cells begin another S-phase. At least 96 cells were assayed for each timepoint. Error bars are standard error of proportion. Strains: wild type, yJM0694; tub2-430Δ, yJM0695; tub2-430Δ td-dyn1, yJM0696. C) Spindle length. Pole-to-pole distance was measured for each bipolar spindle, and an average was determined per timepoint. Wild-type cells show decreased mean length at 135 min as many cells have completed mitosis and begun the assembly of short spindles for a new S-phase. At least 20 cells were assayed for each timepoint. Error bars are 95% confidence interval. D) Spindle movement. Percentage of bipolar spindles with at least one pole in the daughter cell was determined for each timepoint. Values for wild-type and tub2-430Δ cells decrease as cells complete mitosis and disassemble spindles. At least 20 cells were assayed for each timepoint. Error bars are standard error of proportion. E) Wild-type cell labeled with Spc110-GFP. Scalebar =2μm. F) Spindle elongation kinetics. Pole-to-pole distance was measured over time from 3D images of synchronized cells expressing Spc110-GFP. Plots are aligned at the timepoint prior to sustained spindle elongation (t=0s). Lines depict the mean pole-to-pole distance for at least 15 cells per strain. Error bars are 95% confidence interval. Strains: wild type, yJM0165; tub1/3-442Δ, yJM0215; tub2-430Δ, yJM0330. G) Dynein is essential in the absence of β-CTT. Cells were grown to saturation at 25°C in rich media and a 10-fold dilution series of each was spotted YPD; plates were grown at either 25°C or 37°C for 2 days. Strains: wild type, yJM0596; td-dyn1, yJM0604; tub1-442Δ td-dyn1, yJM0625; tub2-430Δ td-dyn1, yJM0623; tub1::βCTT tub2::αCTT td-dyn1, yJM0626; tub2::αCTT td-dyn1, yJM0629; tub1::βCTT tub2-430Δ td-dyn1, yJM0633.
Figure 6
Figure 6. β-CTT promotes the activity of kinesin-5/Cin8
A) Preanaphase wild-type and tub2-430Δ cells labeled with Cin8-3GFP (green) and Spc110-tdTomato (magenta), shown as merge. Preanaphase spindles were defined based on spindle length (see Supplemental Experimental Procedures). Scalebar = 2μm. B) Distribution of Cin8-3GFP in preanaphase spindles. Values are mean ± SEM of 38 half spindles from 19 wild-type cells (black), 50 half spindles from 25 tub2-430Δ cells (red), and 28 half spindles from 14 tub2-430Δ tub1::β-CTT cells (green). Asterisk indicates significant difference compared to tub2-430Δ, by t-test (p < 0.05). Strains: wild type, yJM0987; tub2-430Δ, yJM1024 and 1025; tub2-430Δ tub1::β-CTT, yJM1002 and 1003. C) Early anaphase wild-type and tub2-430Δ cells labeled with Cin8-3GFP (green) and Spc110-tdTomato (magenta), shown as merge. Early anaphase spindles were defined based on spindle length (see Supplemental Experimental Procedures). Scalebar = 2μm. D) Distribution of Cin8-3GFP in early anaphase spindles. Values are mean ± SEM of 12 half spindles from 6 wild-type cells (black), 40 half spindles from 20 tub2-430Δ cells (red), and 20 half spindles from 10 tub2-430Δ tub1::β-CTT cells (green). E) Spindle assembly is not rescued by CIN8 overexpression. Synchronized cells were analyzed as described in Figure 5B. Percentage of cells with bipolar spindles (two Spc110 foci) was determined for each timepoint. CIN8 overxpression was induced 1hr prior to release from G1 arrest, and maintained after release. At least 131 cells were assayed for each timepoint. Error bars are standard error of proportion. Strains: wild type, yJM0165; tub2-430Δ, yJM0330; tub2-430Δ [PGAL-CIN8], yJM1050. F) Spindle elongation rate in the presence or absence of CIN8 overexpression. Cells were synchronized as described in B; however, galactose was added at release from G1 arrest. Pole-to-pole distance was measured over time from 3D images of synchronized cells expressing Spc110-GFP. Elongation events were defined as the initial elongation event for a cell beginning from pre-anaphase length and exhibiting increasing pole-pole distance for at least 80 seconds (16 frames with Pearson’s correlation coefficient >0.9). P-values were determined by t-test. Strains: wild type [PGAL-CIN8], yJM1046; others are identical to B.

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