Growing Microtubule Ends Research Articles

Insights into EB1 structure and the role of its C-terminal domain for discriminating microtubule tips from the lattice.

End-binding proteins (EBs) comprise a conserved family of microtubule plus end-tracking proteins. The concerted action of calponin homology (CH), linker, and C-terminal domains of EBs is important for their autonomous microtubule tip tracking, regulation of microtubule dynamics, and recruitment of numerous partners to microtubule ends. Here we report the detailed structural and biochemical analysis of mammalian EBs. Small-angle X-ray scattering, electron microscopy, and chemical cross-linking in combination with mass spectrometry indicate that EBs are elongated molecules with two interacting CH domains, an arrangement reminiscent of that seen in other microtubule- and actin-binding proteins. Removal of the negatively charged C-terminal tail did not affect the overall conformation of EBs; however, it increased the dwell times of EBs on the microtubule lattice in microtubule tip-tracking reconstitution experiments. An even more stable association with the microtubule lattice was observed when the entire negatively charged C-terminal domain of EBs was replaced by a neutral coiled-coil motif. In contrast, the interaction of EBs with growing microtubule tips was not significantly affected by these C-terminal domain mutations. Our data indicate that long-range electrostatic repulsive interactions between the C-terminus and the microtubule lattice drive the specificity of EBs for growing microtubule ends.

Microtubule‐associated protein EB3 regulates calcium signaling and facilitates increase in endothelial permeability

End binding proteins (EBs) are highly conserved microtubule plus‐end tracking accessory factors that bind to growing microtubule ends and suppress microtubule catastrophe events. We investigated the roles of EB1 and EB3 in regulating endothelial cytoskeletal dynamics and cell shape change, the primary determinants of the permeability of endothelial barrier. Protein depletion experiments showed that EB3, but not EB1, facilitates thrombin‐induced release of calcium from endoplasmic reticulum (ER), and thereby activates calcium entry from extracellular stores. We observed that EB3 interacts with inositol 1,4,5‐thriphosphate receptor type 3 (IP3R3) in lung microvasculature. Cell permeant variant of IP3R3 derivative peptide containing EB3 consensus motif reduced the interaction between EB3 and IP3R3 and mitigated increased endothelial permeability response associated with the cell shape changes. Furthermore, infusion of IP3R3 derivative peptide in ex vivo murine lung preparation attenuates the increase in lung vascular liquid permeability (Kf,c) in response to activation of the Protease‐Activated Receptor ‐1. Intravenous injection of this peptide prevents lung injury and reduces the lethality of polymicrobial sepsis in mice. These data indicate that EB3 regulates calcium signaling in endothelium and facilitates pulmonary vascular leak in disease states.

Regulation of localization and activity of the microtubule depolymerase MCAK

Mitotic Centromere Associated Kinesin (MCAK) is a potent microtubule depolymerizing and catastrophe-inducing factor, which uses the energy of ATP hydrolysis to destabilize microtubule ends. MCAK is localized to inner centromeres, kinetochores and spindle poles of mitotic cells, and is also present in the cytoplasm. Both in interphase and in mitosis, MCAK can specifically accumulate at the growing microtubule ends. Here we discuss the mechanisms, which modulate subcellular localization and activity of MCAK through the interaction with the End Binding (EB) proteins and phosphorylation.

GTPγS microtubules mimic the growing microtubule end structure recognized by end-binding proteins (EBs)

Microtubule plus-end-tracking proteins (+TIPs) localize to growing microtubule plus ends to regulate a multitude of essential microtubule functions. End-binding proteins (EBs) form the core of this network by recognizing a distinct structural feature transiently existing in an extended region at growing microtubule ends and by recruiting other +TIPs to this region. The nature of the conformational difference allowing EBs to discriminate between tubulins in this region and other potential tubulin binding sites farther away from the microtubule end is unknown. By combining in vitro reconstitution, multicolor total internal reflection fluorescence microscopy, and electron microscopy, we demonstrate here that a closed microtubule B lattice with incorporated GTPγS, a slowly hydrolyzable GTP analog, can mimic the natural EB protein binding site. Our findings indicate that the guanine nucleotide γ-phosphate binding site is crucial for determining the affinity of EBs for lattice-incorporated tubulin. This defines the molecular mechanism by which EBs recognize growing microtubule ends.

Electron tomography reveals a flared morphology on growing microtubule ends

Microtubules (MTs) exhibit dynamic instability, alternating between phases of growth and shortening, mostly at their uncapped plus ends. Based on results from cryo-electron microscopy it was proposed that growing MTs display mainly curved sheets and blunt ends; during depolymerisation curled 'ramshorns' predominate. Observations of MTs in mitotic cells have suggested that the situation in vivo differs from that in vitro, but so far, a clear comparison between in vivo and in vitro results has not been possible because MT end structures could not be correlated directly with the dynamic state of that particular MT. Here we combine light microscopy and electron tomography (ET) to show that growing MT plus ends in the fission yeast Schizosaccharomyces pombe display predominantly a flared morphology. This indicates that MT polymerisation in vivo and in vitro can follow different paths.

A Catalytic Role for Mod5 in the Formation of the Tea1 Cell Polarity Landmark

SummaryMany systems regulating cell polarity involve stable landmarks defined by internal cues [1–5]. In the rod-shaped fission yeast Schizosaccharomyces pombe, microtubules regulate polarized vegetative growth via a landmark involving the protein Tea1 [6–9]. Tea1 is delivered to cell tips as packets of molecules associated with growing microtubule ends [10] and anchored at the plasma membrane via a mechanism involving interaction with the membrane protein Mod5 [11, 12]. Tea1 and Mod5 are highly concentrated in clusters at cell tips in a mutually dependent manner, but how the Tea1-Mod5 interaction contributes mechanistically to generating a stable landmark is not understood. Here, we use live-cell imaging, FRAP, and computational modeling to dissect dynamics of the Tea1-Mod5 interaction. Surprisingly, we find that Tea1 and Mod5 exhibit distinctly different turnover rates at cell tips. Our data and modeling suggest that rather than acting simply as a Tea1 receptor or as a molecular “glue” to retain Tea1, Mod5 functions catalytically to stimulate incorporation of Tea1 into a stable tip-associated cluster network. The model also suggests an emergent self-focusing property of the Tea1-Mod5 cluster network, which can increase the fidelity of polarized growth.

In Vitro Reconstitution of the Functional Interplay between MCAK and EB3 at Microtubule Plus Ends

The kinesin-13 family member mitotic centromere-associated kinesin (MCAK) is a potent microtubule depolymerase. Paradoxically, in cells it accumulates at the growing, rather than the shortening, microtubule plus ends. This plus-end tracking behavior requires the interaction between MCAK and members of the end-binding protein (EB) family, but the effect of EBs on the microtubule-destabilizing activity of MCAK and the functional significance of MCAK accumulation at the growing microtubule tips have so far remained elusive. Here, we dissect the functional interplay between MCAK and EB3 by reconstituting EB3-dependent MCAK activity on dynamic microtubules in vitro. Whereas MCAK alone efficiently blocks microtubule assembly, the addition of EB3 restores robust microtubule growth, an effect that is not dependent on the binding of MCAK to EB3. At the same time, EB3 targets MCAK to growing microtubule ends by increasing its association rate with microtubule tips, a process that requires direct interaction between the two proteins. This EB3-dependent microtubule plus-end accumulation does not affect the velocity of microtubule growth or shortening but enhances the capacity of MCAK to induce catastrophes. The combination of MCAK and EB3 thus promotes rapid switching between microtubule growth and shortening, which can be important for remodeling of the microtubule cytoskeleton.

Phosphorylation Controls Autoinhibition of Cytoplasmic Linker Protein-170

Cytoplasmic linker protein (CLIP)-170 is a microtubule (MT) plus-end-tracking protein that regulates MT dynamics and links MT plus ends to different intracellular structures. We have shown previously that intramolecular association between the N and C termini results in autoinhibition of CLIP-170, thus altering its binding to MTs and the dynactin subunit p150(Glued) (J. Cell Biol. 2004: 166, 1003-1014). In this study, we demonstrate that conformational changes in CLIP-170 are regulated by phosphorylation that enhances the affinity between the N- and C-terminal domains. By using site-directed mutagenesis and phosphoproteomic analysis, we mapped the phosphorylation sites in the third serine-rich region of CLIP-170. A phosphorylation-deficient mutant of CLIP-170 displays an "open" conformation and a higher binding affinity for growing MT ends and p150(Glued) as compared with nonmutated protein, whereas a phosphomimetic mutant confined to the "folded back" conformation shows decreased MT association and does not interact with p150(Glued). We conclude that phosphorylation regulates CLIP-170 conformational changes resulting in its autoinhibition.

History-Dependent Catastrophes Regulate Axonal Microtubule Behavior

In Chinese hamster ovary cells, microtubules originate at the microtubule organizing center (MTOC) and grow persistently toward the cell edge, where they undergo catastrophe. In axons, microtubule dynamics must be regulated differently because microtubules grow parallel to the plasma membrane and there is no MTOC. GFP-tagged microtubule plus end tracking proteins (+TIPs) mark the ends of growing neuronal microtubules. Their fluorescent "comet-like" pattern reflects turnover of +TIP binding sites. Using GFP-tagged +TIPs and fluorescence-based segmentation and tracking tools, we show that axonal microtubules grow with a constant average velocity and that they undergo catastrophes at random positions, yet in a programmed fashion. Using protein depletion approaches, we find that the +TIPs CLIP-115 and CLIP-170 affect average microtubule growth rate and growth distance in neurons but not the duration of a microtubule growth event. In N1E-115 neuroblastoma cells, we find that EB1, the core +TIP, regulates microtubule growth rate, growth distance, and duration, consistent with in vitro data. Combined, our data suggest that CLIPs influence the axonal microtubule/tubulin ratio, whereas EB1 stimulates microtubule growth and structural transitions at microtubule ends, thereby regulating microtubule catastrophes and the turnover of +TIP binding sites.

Highly Variable Microtubule Assembly Dynamics Reflect Near-Kilohertz Kinetics: Evidence Against Traditional Linear Growth Theory

Microtubules are intracellular polymers that dynamically grow and shorten at their ends via the stochastic addition and loss of alpha-beta-tubulin heterodimers. The kinetics of tubulin assembly are central to the regulation of microtubule dynamics by microtubule-associated proteins and therapeutic drugs. Previously, rates of tubulin subunit exchange at the ends of growing microtubules have been estimated using a linear growth theory that assumes tubulin dissociation occurs at a constant rate regardless of the free tubulin concentration. However, by measuring the variance of microtubule assembly at the nanometer scale, we find that stochastic tubulin dynamics are an order of magnitude faster than previously estimated. This discrepancy is explained by molecular-level simulations showing that the tubulin dissociation rate during microtubule growth is not constant, but rather should increase with increasing tubulin concentration. This indirect effect is due to a concentration-dependent bias in simulated microtubule tip structure, as has been experimentally observed. Our analyses indicate that the published tubulin subunit addition and loss rates at growing microtubule ends in vitro have been consistently underestimated in the literature: the variance in the assembly rate in vitro is too high to be consistent with the previous low kinetic rate estimates, and we conclude that both tubulin addition and tubulin loss events occur on the millisecond time scale, far faster than the previously believed 10-1000 millisecond scale. More generally, we demonstrate that the fixed off rate originally used in the linear growth theory of Oosawa and assumed in most subsequent models, fails to describe the behavior of self-assembled polymers having both lateral and longitudinal bonding interactions between subunits.

Chapter 2 - Analysis of Microtubule Polymerization Dynamics in Live Cells

The spatiotemporal regulation of intracellular microtubule polymerization dynamics, by numerous microtubule-associated proteins and other mechanisms, is central to many cell processes. Here, we give an overview and practical guide on how to acquire and analyze time-lapse sequences of dynamic microtubules in live cells by either fluorescently labeling entire microtubules or by utilizing proteins that specifically associate only with growing microtubule ends and summarize the strengths and weaknesses of different approaches. We give practical recommendations for imaging conditions, and discuss important limitations of such analysis that are dictated by the maximum achievable spatial and temporal sampling frequencies.

EB1 Recognizes the Nucleotide State of Tubulin in the Microtubule Lattice

Plus-end-tracking proteins (+TIPs) are localized at the fast-growing, or plus end, of microtubules, and link microtubule ends to cellular structures. One of the best studied +TIPs is EB1, which forms comet-like structures at the tips of growing microtubules. The molecular mechanisms by which EB1 recognizes and tracks growing microtubule ends are largely unknown. However, one clue is that EB1 can bind directly to a microtubule end in the absence of other proteins. Here we use an in vitro assay for dynamic microtubule growth with two-color total-internal-reflection-fluorescence imaging to investigate binding of mammalian EB1 to both stabilized and dynamic microtubules. We find that under conditions of microtubule growth, EB1 not only tip tracks, as previously shown, but also preferentially recognizes the GMPCPP microtubule lattice as opposed to the GDP lattice. The interaction of EB1 with the GMPCPP microtubule lattice depends on the E-hook of tubulin, as well as the amount of salt in solution. The ability to distinguish different nucleotide states of tubulin in microtubule lattice may contribute to the end-tracking mechanism of EB1.

SnapShot: Microtubule Regulators II

Dynamic remodeling of the microtubule cytoskeleton is essential for many cell processes including division, migration and differentiation. Microtubules are dynamic polymers of α/β-tubulin dimers and switch stochastically between phases of growth (polymerization) and shortening (depolymerization). Transitions from growth to shortening are referred to as catastrophes, and transitions from shortening to growth are called rescues. Intracellular microtubule organization is controlled by the activity and distribution of nucleation sites, proteins that directly influence polymerization dynamics, proteins that cut or bundle existing microtubules, and proteins that indirectly stabilize microtubules. In cells, microtubule nucleation is mediated by the multi-subunit γ-Tubulin Ring Complex. Associated proteins such as Cep192 recruit the γ-TuRC to the centrosome or spindle poles. However, regulation of microtubule nucleation is incompletely understood. In differentiated cells, microtubule minus ends are often redistributed away from the centrosome. For example, ninein anchors minus ends to cell-cell junctions in polarized epithelial cells and to desmosomes in differentiated keratinocytes. Several different proteins influence microtubule polymerization dynamics by direct interactions with microtubule plus ends. EB-family proteins directly recognize biochemical or structural differences at the growing microtubule end, influence microtubule polymerization dynamics, and may act as adaptors that mediate the association of other proteins with growing microtubule plus ends. Proteins of the XMAP215 family are thought to enhance the microtubule polymerization rate by processively adding tubulin subunits to the growing end. In contrast, neuronal CRMP-2 enhances microtubule assembly by interacting with free tubulin dimers. Microtubule disassembly is promoted by two different mechanisms. Stathmin is a small protein that binds to tubulin dimers and lowers the pool of free tubulin available for polymerization, thus decreasing microtubule growth rate and increasing catastrophe frequency. In contrast, internal motor domain kinesins directly bind to microtubule ends and utilize ATP hydrolysis to catalytically depolymerize microtubules. Microtubule-severing proteins cut existing microtubules generating new minus and plus ends. The generation of short microtubule fragments by these proteins is important for reorganization of the microtubule cytoskeleton without complete microtubule disassembly. Because organization and dynamics of the microtubule cytoskeleton is crucial for many cellular functions, most direct regulators of microtubule nucleation, polymerization and disassembly are involved in multiple cell processes. In addition, the existence of plant-specific families of microtubule regulatory proteins such as SPIRAL emphasizes important differences in microtubule function and organization between plant and animal cells.

Microtubule plus-end tracking by CLIP-170 requires EB1

Microtubules are polarized polymers that exhibit dynamic instability, with alternating phases of elongation and shortening, particularly at the more dynamic plus-end. Microtubule plus-end tracking proteins (+TIPs) localize to and track with growing microtubule plus-ends in the cell. +TIPs regulate microtubule dynamics and mediate interactions with other cellular components. The molecular mechanisms responsible for the +TIP tracking activity are not well understood, however. We reconstituted the +TIP tracking of mammalian proteins EB1 and CLIP-170 in vitro at single-molecule resolution using time-lapse total internal reflection fluorescence microscopy. We found that EB1 is capable of dynamically tracking growing microtubule plus-ends. Our single-molecule studies demonstrate that EB1 exchanges rapidly at microtubule plus-ends with a dwell time of <1 s, indicating that single EB1 molecules go through multiple rounds of binding and dissociation during microtubule polymerization. CLIP-170 exhibits lattice diffusion and fails to selectively track microtubule ends in the absence of EB1; the addition of EB1 is both necessary and sufficient to mediate plus-end tracking by CLIP-170. Single-molecule analysis of the CLIP-170-EB1 complex also indicates a short dwell time at growing plus-ends, an observation inconsistent with the copolymerization of this complex with tubulin for plus-end-specific localization. GTP hydrolysis is required for +TIP tracking, because end-specificity is lost when tubulin is polymerized in the presence of guanosine 5'-[alpha,beta-methylene]triphosphate (GMPCPP). Together, our data provide insight into the mechanisms driving plus-end tracking by mammalian +TIPs and suggest that EB1 specifically recognizes the distinct lattice structure at the growing microtubule end.

Dynamic Microtubules Regulate Dendritic Spine Morphology and Synaptic Plasticity

Dendritic spines are the major sites of excitatory synaptic input, and their morphological changes have been linked to learning and memory processes. Here, we report that growing microtubule plus ends decorated by the microtubule tip-tracking protein EB3 enter spines and can modulate spine morphology. We describe p140Cap/SNIP, a regulator of Src tyrosine kinase, as an EB3 interacting partner that is predominantly localized to spines and enriched in the postsynaptic density. Inhibition of microtubule dynamics, or knockdown of either EB3 or p140Cap, modulates spine shape via regulation of the actin cytoskeleton. Fluorescence recovery after photobleaching revealed that EB3-binding is required for p140Cap accumulation within spines. In addition, we found that p140Cap interacts with Src substrate and F-actin-binding protein cortactin. We propose that EB3-labeled growing microtubule ends regulate the localization of p140Cap, control cortactin function, and modulate actin dynamics within dendritic spines, thus linking dynamic microtubules to spine changes and synaptic plasticity.

EBs clip CLIPs to growing microtubule ends

Proteins that track growing microtubule (MT) ends are important for many aspects of intracellular MT function, but the mechanism by which these +TIPs accumulate at MT ends has been the subject of a long-standing controversy. In this issue, Bieling et al. (Bieling, P., S. Kandels-Lewis, I.A. Telley, J. van Dijk, C. Janke, and T. Surrey. 2008. J. Cell Biol. 183:1223–1233) reconstitute plus end tracking of EB1 and CLIP-170 in vitro, which demonstrates that CLIP-170 plus end tracking is EB1-dependent and that both +TIPs rapidly exchange between a soluble and a plus end–associated pool. This strongly supports the hypothesis that plus end tracking depends on a biochemical property of growing MT ends, and that the characteristic +TIP comets result from the generation of new +TIP binding sites through MT polymerization in combination with the exponential decay of these binding sites.

CLIP-170 tracks growing microtubule ends by dynamically recognizing composite EB1/tubulin-binding sites

The microtubule cytoskeleton is crucial for the internal organization of eukaryotic cells. Several microtubule-associated proteins link microtubules to subcellular structures. A subclass of these proteins, the plus end–binding proteins (+TIPs), selectively binds to the growing plus ends of microtubules. Here, we reconstitute a vertebrate plus end tracking system composed of the most prominent +TIPs, end-binding protein 1 (EB1) and CLIP-170, in vitro and dissect their end-tracking mechanism. We find that EB1 autonomously recognizes specific binding sites present at growing microtubule ends. In contrast, CLIP-170 does not end-track by itself but requires EB1. CLIP-170 recognizes and turns over rapidly on composite binding sites constituted by end-accumulated EB1 and tyrosinated α-tubulin. In contrast to its fission yeast orthologue Tip1, dynamic end tracking of CLIP-170 does not require the activity of a molecular motor. Our results demonstrate evolutionary diversity of the plus end recognition mechanism of CLIP-170 family members, whereas the autonomous end-tracking mechanism of EB family members is conserved.

STIM1 tracks growing microtubule ends

STIM1 tracks growing microtubule ends

Reconstitution of a microtubule plus-end tracking system in vitro

The microtubule cytoskeleton is essential to cell morphogenesis. Growing microtubule plus ends have emerged as dynamic regulatory sites in which specialized proteins, called plus-end-binding proteins (+TIPs), bind and regulate the proper functioning of microtubules. However, the molecular mechanism of plus-end association by +TIPs and their ability to track the growing end are not well understood. Here we report the in vitro reconstitution of a minimal plus-end tracking system consisting of the three fission yeast proteins Mal3, Tip1 and the kinesin Tea2. Using time-lapse total internal reflection fluorescence microscopy, we show that the EB1 homologue Mal3 has an enhanced affinity for growing microtubule end structures as opposed to the microtubule lattice. This allows it to track growing microtubule ends autonomously by an end recognition mechanism. In addition, Mal3 acts as a factor that mediates loading of the processive motor Tea2 and its cargo, the Clip170 homologue Tip1, onto the microtubule lattice. The interaction of all three proteins is required for the selective tracking of growing microtubule plus ends by both Tea2 and Tip1. Our results dissect the collective interactions of the constituents of this plus-end tracking system and show how these interactions lead to the emergence of its dynamic behaviour. We expect that such in vitro reconstitutions will also be essential for the mechanistic dissection of other plus-end tracking systems.

MCAK associates with EB1

The microtubule (MT)-associated protein EB1 localizes to and promotes growth at MT plus ends. The MT depolymerizing kinesin MCAK has also been reported to track growing MT plus ends. Here, we confirm that human MCAK colocalizes with EB1 at growing MT ends when expressed as a GFP fusion protein in transfected cells. We show that MCAK associates with the C-terminus of EB1 and EB3 but much less efficiently with RP1. EB1 associates with the N-terminal localization and regulatory domain in MCAK but not with the motor domain of the protein. The interaction is competitive with the binding of other EB1 ligands and does not require MTs. Knockdown of EB1 expression using siRNA impaired the ability of GFP-MCAK to localize to MT tips in transfected cells. We propose that MCAK is targeted to growing MT ends by EB1, that MCAK is held in an inactive conformation when associated with EB1 and that this could provide the basis for a mechanism that facilitates rapid switching between phases of MT growth and depolymerization.