Cells contain an extensive network of long filaments called microtubules, which are made of a protein called tubulin and are essential for a wide variety of processes such as enabling cells to divide and move. Microtubules also serve as tracks along which motor proteins transport molecules from one part of the cell to another.

In yeast cells, a motor protein called Kip2 transports its cargo to one end (known as the “plus end”) of the microtubules. This is the fastest-growing end of the microtubule, although it frequently switches between phases of growth and shrinkage. Previous research has shown that cells containing reduced amounts of Kip2 have much shorter filaments than normal cells. One suggested explanation of these results is that Kip2 controls microtubule growth by transporting a protein that regulates filament length to the plus end of the microtubule.

However, by adding purified Kip2 to microtubules Hibbel et al. have now shown that Kip2 on its own can increase the length of filaments. The microtubules also switch much less frequently between growth and shrinkage in the presence of Kip2. This is because Kip2 moves along filaments at a speed that is greater than the rate at which microtubules grow. This sets up a positive feedback loop that causes microtubule growth to accelerate, as more copies of Kip2 can bind to longer microtubules. Each of these motor proteins can then move to the plus end of the microtubule and help the filament to grow even longer.

Several challenges remain. What is the molecular mechanism by which Kip2 increases the rate at which tubulin subunits are added to the microtubule end: does Kip2 carry tubulin dimers to the end in a shuttle-type mechanism? How does Kip2 prevent other proteins from promoting shrinkage? What stops microtubules from growing when they reach the end of the cell?

The budding yeast kinesin Kip2 promotes microtubule growth in vivo. Deletion of this kinesin results in nuclear migration defects, and the phenotype is associated with shorter, less abundant cytoplasmic microtubules (Cottingham and Hoyt, 1997; Huyett et al., 1998; Miller et al., 1998; Caudron et al., 2008). Conversely, Kip2 overexpression results in hyper-elongated cytoplasmic microtubules (Carvalho et al., 2004). The stabilization of microtubules by Kip2 is thought to be indirect and a consequence of Kip2 transporting the growth regulator Bik1 (Clip170) to microtubule plus ends (Carvalho et al., 2004; Caudron et al., 2008).

To test whether Kip2 alone can promote microtubule growth, the activity of full-length, purified Kip2 was measured in dynamic microtubule assays using porcine tubulin in the presence of adenosine triphosphate (ATP) (Gell, et al., 2010; 2011) (Figure 1A). Within 10 min, Kip2 (Figure 1B,C), as well as Kip2-enhanced green fluorescent protein (eGFP) (Figure 1—figure supplement 1A), strongly increased the length of freshly polymerized microtubules (p<0.0001, Welch’s unpaired t-test, please refer to Table 1 for porcine microtubule parameter values). The effect of Kip2 on microtubule length was almost completely inhibited when ATP was replaced by the non-hydrolyzable ATP analog adenylyl imidodiphosphate (AMP-PNP) (Figure 1C, blue markers, p<0.0001), showing that growth promotion requires ATP hydrolysis. To quantify how Kip2 influences microtubule dynamics, we drew kymographs from the time-lapse images of the dynamic microtubule assay (Figure 1D). Kip2 increased the growth rate of microtubules (the slope of the growing microtubule in the kymograph) 2.9-fold (Figure 1E). In addition, Kip2 reduced the frequency of catastrophe (the transition between growth and shrinkage phases) approximately 10-fold (Figure 1F). Kip2 did not affect the shrinkage rate (Figure 1—figure supplement 1B), or the frequency of rescue (the transition between shrinkage and growth phases, Figure 1—figure supplement 1C). All dynamic data on porcine tubulin are contained in Table 1. Note that rescue is not expected to have a large effect on microtubule length in our assays. This is because at lower Kip2 concentrations (< 10 nM), the average distance shortened following catastrophe (the shrinkage rate divided by the rescue frequency) is greater than the average distance grown before catastrophe (the growth rate divided by the catastrophe frequency), so microtubules usually shrink all the way back to the seed (as expected by theory, Verde et al., 1992). On the other hand, at higher Kip2 concentrations, catastrophes are so rare that microtubules are expected to be very long before they catastrophe (>18 μm for [Kip2] ≥ 10 nM). Consistent with the small contribution of rescue, the measured increase in microtubule length accorded with the effects of Kip2 on the growth rate and the catastrophe frequency alone (Figure 1C, red line). The half-maximal stimulation of polymerization and inhibition of catastrophe occurred at ≈7 nM Kip2. Given that the cellular concentration of Kip2 is ≈25 nM (Ghaemmaghami et al., 2003), these results show that Kip2 affects microtubule dynamics in vitro at physiologically relevant concentrations.

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To exclude potentially confounding effects introduced by using fluorescently labeled porcine brain tubulin, as well as to confirm that Kip2, which is a yeast protein, has the same activity on its conspecific protein, we repeated the dynamic microtubule assays with unlabeled yeast tubulin (Widlund et al., 2012) and differential interference contrast (DIC) microscopy (Figure 1—figure supplement 2A, please refer to Table 2 for yeast microtubule parameter values). Consistent with our porcine tubulin results, Kip2 increased the yeast microtubule growth rate by 2.3-fold and inhibited catastrophe 20-fold (Figure 1—figure supplement 2B,C). The half-maximal stimulation of polymerization and inhibition of catastrophe for yeast tubulin occurred at ≈12 nM Kip2, similar to the concentration at which Kip2 regulates porcine brain microtubules. In summary, Kip2 is a microtubule polymerase and anti-catastrophe factor in vitro and does not require additional proteins such as Bik1 for these activities. We will defer discussing a potential role for Bik1 until the end of the manuscript.

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To gain insight into the mechanism of Kip2’s polymerase and anti-catastrophe activities, we determined how Kip2 affects microtubule assembly and disassembly kinetics. By measuring the rate of growth of porcine microtubules from guanylyl (α,β)methylene-diphosphonate (GMPCPP) seeds over a range of tubulin concentrations (Figure 1—figure supplement 3A), we found that Kip2 doubled the effective tubulin association rate constant (k_on, the rate that tubulin is stably incorporated into the microtubule lattice) to 1.5 μM^-1.s^-1 (at the plus end) from 0.7 μM^-1.s^-1 in the absence of Kip2. In addition to accelerating the net addition of subunits, Kip2 also facilitated microtubule nucleation on the seeds, with robust growth observed at tubulin concentrations as low as 4 μM, compared with 10 μM in the absence of Kip2 (Figure 1—figure supplement 3A). Thus, Kip2 acted like a nucleation factor in analogy to XMAP215 (Wieczorek et al., 2015). The increased growth rate in the presence of Kip2 is expected to have only a modest effect on catastrophe because doubling the rate of microtubule growth by doubling the tubulin concentration only decreases the catastrophe frequency about twofold (Gardner et al., 2011; Walker, et al., 1988). Our observation that the catastrophe frequency decreased 10-fold might be explained by our finding that 40 nM Kip2 decreased the rate of dissociation of GMPCPP-tubulin subunits from GMPCPP microtubules (k_off) approximately threefold (Figure 1—figure supplement 3B). If GMPCPP-tubulin acts as an analog for guanosine-5'-triphosphate (GTP)-tubulin (Hyman et al., 1992), then a decrease in k_off is expected to stabilize the GTP cap and therefore inhibit catastrophe (Bowne-Anderson et al., 2013; Coombes et al., 2103; Margolin et al., 2011). Thus, the increase in k_on and the decrease in k_off likely account for most of the decrease in the catastrophe frequency.

To determine how Kip2 targets the plus ends of microtubules, we characterized its biophysical properties in single-molecule motility assays (Figure 2A). Kymographs revealed that in 1 mM ATP, single Kip2-eGFP molecules associated with GMPCPP-stabilized porcine microtubules along the lattice and walked processively toward the plus end of the microtubule (Figure 2B, Figure 2—figure supplement 1A). The velocity was 5.0 ± 0.9 μm/min at 28°C (mean ± standard deviation [SD], n = 674 traces). The average run distance before dissociating was 4.1 ± 0.3 μm (mean ± SE, n = 217, Figure 2—figure supplement 1B). A similar velocity was observed by Roberts et al. (2014), though the run distance was shorter (1.2 μm). At the plus end, Kip2-GFP resided for 30 ± 26 s before dissociating (mean ± SD, n = 40, Figure 2D, Figure 2—figure supplement 1C), leading to an accumulation of up to 12 Kip2-eGFP molecules at the plus-end, based on the fluorescence intensity (Figure 2B). When the ATP was replaced by the non-hydrolyzable analog AMP-PNP, Kip2-eGFP tightly bound to the lattice and did not translocate (Figure 2C). Kip2-eGFP moved slower on dynamic microtubules (2.1 ± 0.89 μm/min), but this velocity is still greater than the microtubule’s growth speed, so Kip2-eGFP was able to catch up to the growing ends of dynamic microtubules and track them (Figure 2E). Based on these properties, we conclude that Kip2’s mechanism differs from that of the well-studied microtubule polymerase XMAP215. XMAP215 targets ends by diffusion and capture (Brouhard et al. 2008; Widlund et al. 2011), increases both k_on and k_off (Brouhard et al., 2008) and has little effect on catastrophe (Zanic, et al., 2013). Furthermore, Kip2’s ATPase activity is necessary for its activity, while XMAP215 is not an ATPase. Thus, Kip2 is a unique regulator of microtubule dynamics. Two models for growth promotion can be envisaged. Kip2 may increase growth rates by shuttling tubulin to the microtubule plus end, locally increasing the tubulin concentration. Alternatively, it could promote microtubule growth by acting as a processive polymerase while at the plus end, similar to XMAP215 (Brouhard et al., 2008). More work will be required to distinguish between these and other mechanisms.

To probe the mechanical properties of Kip2, we measured the stall force of single molecules using optical tweezers (Jannasch et al., 2013). Positional tracking of single Kip2-powered microspheres moving along GMPCPP-stabilized porcine microtubules as a function of time under constant load revealed a zero-force speed of 4.0 ± 0.5 μm/min at 24.5°C, similar to that measured in the total internal reflection fluorescence (TIRF) assays. Kip2 stalled at a force of 0.81 ± 0.04 pN (Figure 3A) and showed a nearly linear force-velocity relation with increased velocity as the assisting force was increased (Figure 3C). At high forces, the motor often slipped along the microtubule in the direction of the applied force without detaching (Figure 3B). The ability to switch from the slip state to the normal translocation mode is thought to increase processivity by linking together several shorter run lengths (Jannasch et al., 2013). Thus, Kip2 is a processive, low-force motor with long run lengths and end residence times. The low force supports the idea that individual Kip2 motors transport small cargos such as dynein, Bik1, and other molecules (Roberts et al., 2014) rather than organelles, although it is possible that multiple Kip2s could cooperate to move larger cargos. The strong localization to the microtubule plus end accords with Kip2 being a regulator of microtubule dynamics.

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The low force and high processivity of Kip2 are reminiscent of the microtubule depolymerase Kip3, in the kinesin-8 family (Jannasch et al., 2013; Varga et al., 2006). Kip3 is a length-dependent depolymerase that uses an antenna mechanism to preferentially localize to the plus ends of longer microtubules (Varga et al., 2009). We therefore tested whether the promotion of microtubule growth by Kip2 is length-dependent (Figure 4A,B). Without Kip2, microtubules grew at a length-independent, constant rate (black circles, p=0.06, Student’s t-test on a linear fit to the raw data). By contrast, at low (1–2 nM) and intermediate (5–10 nM) Kip2 concentrations, long microtubules grew faster than short microtubules (p<0.0001). At high Kip2 concentrations (20–40 nM), microtubules again grew at a constant, length-independent rate (green circles, p=0.36); however, at these high Kip2 concentrations, we expect all the length dependence to be in the first few microns, which is not well resolved in these experiments (see green fitted line). An analysis of yeast microtubule growth rates as a function of microtubule length yielded similar results (Figure 4—figure supplement 1A). Thus, Kip2 is a length-dependent microtubule polymerase.

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To test whether Kip2 also prevents catastrophe in a length-dependent manner, we measured porcine microtubule lengths at the moment of catastrophe. To compare the catastrophe frequency at short versus long microtubule lengths, we set a cut-off length at 4 μm, which equals the run length of Kip2. Using data from the dynamic microtubule assays (Figure 1), we measured the catastrophe length for short microtubules as the total distance that microtubules grew while their length (including seed) was shorter than 4 μm divided by the number of catastrophes that occurred at lengths < 4 μm. For long microtubules, we summed the distance that microtubules grew while longer than 4 μm (final length minus 4 μm) and divided by the number of catastrophes that occurred at lengths > 4 μm (Figure 4C, inset). In the absence of Kip2, the catastrophe length of longer microtubules was less than that of shorter microtubules (Figure 4C, 0 nM Kip2, p<0.05, Welch’s unpaired t-test). This reflects an increase in catastrophe frequency with length, as expected due to microtubule aging (Gardner et al., 2011). By contrast, at 5 nM Kip2, the catastrophe length of longer microtubules was greater than that of shorter microtubules (Figure 4C, p<0.0001). This indicates that the inhibition of catastrophe is length-dependent. Similar results were obtained for yeast microtubules at 10 nM Kip2 (Figure 4—figure supplement 1B, p<0.0001). Hence, in the absence of Kip2, the catastrophe frequency increased with increasing microtubule length, whereas in the presence of Kip2, the catastrophe frequency decreased with increasing microtubule length. Thus, both the increase in microtubule growth rate and the prevention of catastrophe by Kip2 increase with increasing microtubule length.

Summarizing our results, we have found that budding yeast kinesin Kip2 promotes microtubule growth in vitro in a length-dependent manner. Because the rate at which Kip2 translocates exceeds the speed of microtubule growth, Kip2 catches up with the growing end of the microtubule (Figure 2E) where it promotes growth and inhibits catastrophe. As a consequence, this length dependence leads to positive feedback: the longer the microtubule, the greater the number of motors that land on it (the microtubule acts as an antenna), the higher the number of motors that can reach the plus end, and the higher the growth rate and lower the catastrophe frequency. This, in turn, leads to longer microtubules, which attract more Kip2 and so on. Hence, we expect that once a microtubule is long enough, it will effectively “escape” catastrophe and keep growing almost indefinitely, switching from a catastrophe length of only a few microns in the absence of Kip2 to a length ≥ 40 μm at high Kip2 concentrations (Figure 4C, Table 1). In this sense, Kip2 “paves its own way”. Thus, by combining processivity with polymerase activity, Kip2 can perform an elementary ‘computation’ that switches short microtubules to long ones. This computation differs from that performed by kinesin-8, a length-dependent depolymerase, which stabilizes microtubule length through negative feedback (Gupta et al., 2006; Mayr et al., 2007; Stumpff et al., 2008; Su, et al., 2013;Widlund, et al., 2011 Varga et al., 2006; 2009).

We propose that this positive feedback mechanism may operate in vivo and account for the phenotype of Kip2 deletion, which is a reduction in the length and the number of cytoplasmic microtubules. First, in vivo the rate at which Kip2 translocates exceeds the rate of microtubule growth; the respective rates are 6.6 (Carvalho et al., 2004) and 2.3 μm/min (Caudron et al., 2008). Second, the run length of Kip2 (≈4 μm) exceeds the length of cytoplasmic microtubules (≈2 μm [Caudron et al., 2008]). Taken together, these two observations imply that almost every Kip2 that lands on a microtubule will reach the growing plus end. By promoting growth and inhibiting catastrophe, Kip2 can deliver cytoplasmic dynein (Roberts et al., 2014) to the distal cortex of the growing daughter bud before the microtubules catastrophe.

While the polymerase and anti-catastrophe activities can account for the deletion phenotype of Kip2, it is not obvious why microtubule hyperelongation when Kip2 is overexpressed should require Bik1 (Carvalho et al., 2004). We propose that Bik1 may be required to increase Kip2’s processivity in vivo. Feedback can only operate if the run length exceeds the microtubule length. In our in vitro assays, the Kip2 run length was ≈4 μm, whereas that measured by Roberts et al. (2014) was only ≈1 μm. We do not know why there was a difference, as the assay buffers were similar. Importantly, though, Roberts et al. (2014) found that Bik1 could increase Kip2’s run length 3–4 fold (in the presence of Bim1). Therefore, if the run length of Kip2 in vivo is short, then the requirement for Bik1 in the overexpression assays may be due to Bik1 acting as a processivity factor that increases the run length, thereby allowing more Kip2 to reach the end where it enhances microtubule growth.

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Author details

1. Anneke Hibbel

   1. Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
   2. Institute of Biochemistry, ETH Zurich, Zurich, Switzerland

   Contribution

   AH, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article, Contributed unpublished essential data or reagents

   Competing interests

   The authors declare that no competing interests exist.

2. Aliona Bogdanova

   Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

   Contribution

   AB, Acquisition of data, Drafting or revising the article, Contributed unpublished essential data or reagents

   Competing interests

   The authors declare that no competing interests exist.

3. Mohammed Mahamdeh

   Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, United States

   Contribution

   MM, Acquisition of data, Drafting or revising the article

   Competing interests

   The authors declare that no competing interests exist.

4. Anita Jannasch

   1. Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
   2. Zentrum für Molekularbiologie der Pflanzen, Eberhard-Karls-Universität, Tübingen, Germany

   Contribution

   AJ, Conception and design, Acquisition of data, Analysis and interpretation of data

   Competing interests

   The authors declare that no competing interests exist.

5. Marko Storch

   Department of Life Sciences, Imperial College London, London, United Kingdom

   Contribution

   MS, Conception and design, Acquisition of data, Drafting or revising the article

   Competing interests

   The authors declare that no competing interests exist.

6. Erik Schäffer

   Zentrum für Molekularbiologie der Pflanzen, Eberhard-Karls-Universität, Tübingen, Germany

   Contribution

   ES, Conception and design, Analysis and interpretation of data, Drafting or revising the article

   Competing interests

   The authors declare that no competing interests exist.

7. Dimitris Liakopoulos

   CRBM-CRNS, Montpellier, France

   Contribution

   DL, Conception and design, Analysis and interpretation of data, Drafting or revising the article

   Competing interests

   The authors declare that no competing interests exist.

8. Jonathon Howard

   Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, United States

   Contribution

   JH, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article

   For correspondence

   jonathon.howard@yale.edu

   Competing interests

   The authors declare that no competing interests exist.

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