Structural mechanisms underlying nucleotide-dependent self-assembly of tubulin and its relatives

Nucleotide-dependent lateral and longitudinal interactions in microtubules

Microtubule (MT) stability is related to the hydrolysis of the guanosine triphosphate nucleotide (NT) bound to β-tubulin. However, the molecular mechanism by which the NT state influences the stability of the contacts in the MT lattice remains elusive. Here, we present large-scale atomistic simulations of different tubulin aggregates, including individual dimers, short protofilaments, a small lattice patch, and a piece of the MT lattice with two infinite protofilaments in both NT states. Together with a coarse-grained (CG) analysis of the fluctuations, these simulations highlight several regions of the protein where local changes are induced by the NT state or by the lateral and longitudinal contacts in the aggregates. Additionally, the CG analysis provides an indication of how the structural changes affect the bonds between the proteins. The results suggest a consistent picture of a possible molecular mechanism by which the NT state induces changes in the H1-S2 loop and more stable longitudinal bonds, both of which locate the H1-S2 and M-loop in more favorable positions to form lateral contacts.

Dissecting the cellular functions of plant microtubules using mutant tubulins

α- and β-tubulins, the building blocks of the microtubule (MT) polymer, are encoded by multiple genes that are largely functionally redundant in plants. Null tubulin mutants are thus phenotypically indistinguishable from the wild type, but miss-sense or deletion mutations of critical amino acid residues that are important for the assembly, stability, or dynamics of the polymer disrupt the proper organization and function of the resultant MT arrays. Mutant tubulins co-assemble with wild-type tubulins into mutant MTs with compromised functions, and thus mechanistically act as dominant-negative MT poisons. Cortical MT arrays in interphase plant cells are most sensitive to tubulin mutations, and are transformed into helical structures or random orientation, which produce twisted or radially swollen cells. Mutant plants resistant to MT-targeted herbicides may possess tubulin mutations at the binding sites of the herbicides. Tubulin mutants are valuable tools for investigating how individual MTs are organized into particular patterns in cortical arrays, and for defining the functional contribution of MTs to various MT-dependent or -assisted cellular processes in plant cells.

Structural model for tubulin recognition and deformation by kinesin-13 microtubule depolymerases

To elucidate the structural basis of the mechanism of microtubule depolymerization by kinesin-13s, we analyzed complexes of tubulin and the Drosophila melanogaster kinesin-13 KLP10A by electron microscopy (EM) and fluorescence polarization microscopy. We report a nanometer-resolution (1.1 nm) cryo-EM three-dimensional structure of the KLP10A head domain (KLP10AHD) bound to curved tubulin. We found that binding of KLP10AHD induces a distinct tubulin configuration with displacement (shear) between tubulin subunits in addition to curvature. In this configuration, the kinesin-binding site differs from that in straight tubulin, providing an explanation for the distinct interaction modes of kinesin-13s with the microtubule lattice or its ends. The KLP10AHD-tubulin interface comprises three areas of interaction, suggesting a crossbow-type tubulin-bending mechanism. These areas include the kinesin-13 family conserved KVD residues, and as predicted from the crossbow model, mutating these residues changes the orientation and mobility of KLP10AHDs interacting with the microtubule.

A TOG:αβ-tubulin complex structure reveals conformation-based mechanisms for a microtubule polymerase

Stu2p/XMAP215/Dis1 family proteins are evolutionarily conserved regulatory factors that use αβ-tubulin-interacting tumor overexpressed gene (TOG) domains to catalyze fast microtubule growth. Catalysis requires that these polymerases discriminate between unpolymerized and polymerized forms of αβ-tubulin, but the mechanism by which they do so has remained unclear. Here, we report the structure of the TOG1 domain from Stu2p bound to yeast αβ-tubulin. TOG1 binds αβ-tubulin in a way that excludes equivalent binding of a second TOG domain. Furthermore, TOG1 preferentially binds a curved conformation of αβ-tubulin that cannot be incorporated into microtubules, contacting α- and β-tubulin surfaces that do not participate in microtubule assembly. Conformation-selective interactions with αβ-tubulin explain how TOG-containing polymerases discriminate between unpolymerized and polymerized forms of αβ-tubulin and how they selectively recognize the growing end of the microtubule.

Mechanism of action of the cell-division inhibitor PC190723: modulation of FtsZ assembly cooperativity

The cooperative assembly of FtsZ, the prokaryotic homologue of tubulin, plays an essential role in cell division. FtsZ is a potential drug target, as illustrated by the small-molecule cell-cycle inhibitor and antibacterial agent PC190723 that targets FtsZ. We demonstrate that PC190723 negatively modulates Staphylococcus aureus FtsZ polymerization cooperativity as reflected in polymerization at lower concentrations without a defined critical concentration. The crystal structure of the S. aureus FtsZ-PC190723 complex shows a domain movement that would stabilize the FtsZ protofilament over the monomeric state, with the conformational change mediated from the GTP-binding site to the C-terminal domain via helix 7. Together, the results reveal the molecular mechanism of FtsZ modulation by PC190723 and a conformational switch to the high-affinity state that enables polymer assembly.

Cytoskeleton in mast cell signaling

Mast cell activation mediated by the high affinity receptor for IgE (FcεRI) is a key event in allergic response and inflammation. Other receptors on mast cells, as c-Kit for stem cell factor and G protein-coupled receptors (GPCRs) synergistically enhance the FcεRI-mediated release of inflammatory mediators. Activation of various signaling pathways in mast cells results in changes in cell morphology, adhesion to substrate, exocytosis, and migration. Reorganization of cytoskeleton is pivotal in all these processes. Cytoskeletal proteins also play an important role in initial stages of FcεRI and other surface receptors induced triggering. Highly dynamic microtubules formed by αβ-tubulin dimers as well as microfilaments build up from polymerized actin are affected in activated cells by kinases/phosphatases, Rho GTPases and changes in concentration of cytosolic Ca(2+). Also important are nucleation proteins; the γ-tubulin complexes in case of microtubules or Arp 2/3 complex with its nucleation promoting factors and formins in case of microfilaments. The dynamic nature of microtubules and microfilaments in activated cells depends on many associated/regulatory proteins. Changes in rigidity of activated mast cells reflect changes in intermediate filaments build up from vimentin. This review offers a critical appraisal of current knowledge on the role of cytoskeleton in mast cells signaling.

The state of the guanosine nucleotide allosterically affects the interfaces of tubulin in protofilament

The dynamics of microtubules is essential for many microtubule-dependent cellular functions such as the mitosis. It has been recognized for a long time that GTP hydrolysis in αβ-tubulin polymers plays a critical role in this dynamics. However, the effects of the changes in the nature of the guanosine nucleotide at the E-site in β-tubulin on microtubule structure and stability are still not well understood. In the present work, we performed all-atom molecular dynamics simulations of a αβα-tubulin heterotrimer harboring a guanosine nucleotide in three different states at the E-site: GTP, GDP-Pi and GDP. We found that changes in the nucleotide state is associated with significant conformational variations at the α-tubulin N- and β-tubulin M-loops which impact the interactions between tubulin protofilaments. The results also show that GTP hydrolysis reduces αβ-tubulin interdimer contacts in favor of intradimer interface. From an atomistic point view, we propose a role for α-tubulin glutamate residue 254 in catalytic magnesium coordination and identified a water molecule in the nucleotide binding pocket which is most probably required for nucleotide hydrolysis. Finally, the results are discussed with reference to the role of taxol in microtubule stability and the recent tubulin-sT2R crystal structures.

DDA3 stabilizes microtubules and suppresses neurite formation

We have previously shown that DDA3 - also known as proline/serine-rich coiled-coil protein 1 (PSRC1) - is a microtubule-associated protein that promotes cell growth by stimulating the β-catenin pathway. Here, we report that DDA3 can bundle and stabilize microtubules in vivo and in vitro. We found that overexpression of DDA3 increased the abundance of acetylated and tyrosinated microtubules. We employed PC12 and N2a cell lines, as well as cultured hippocampal neurons, and demonstrated that overexpression of DDA3 suppressed neurite/axon outgrowth, whereas its depletion accelerated neurite/axon formation and elongation. Knockdown of DDA3 reduced β3-tubulin levels in N2a cells, which contributed to the spontaneous neurite formation caused by DDA3 depletion. Consistent with its role in suppressing neuritogenesis, DDA3 was downregulated during induced neuronal differentiation. Moreover, expression of DDA3 was detected in the rat brain at embryonic (E) day E15 and in the cortical region at E17, the period of active neurogenesis. Levels of cortical DDA3 decreased at the beginning of E19, when active neuritogenesis is completed. Overall our results demonstrate that DDA3 is a so-far-unknown microtubule-stabilizing protein that is involved in regulating neurite formation and elongation.

Depolymerizing kinesins Kip3 and MCAK shape cellular microtubule architecture by differential control of catastrophe

Microtubules are dynamic filaments whose ends alternate between periods of slow growth and rapid shortening as they explore intracellular space and move organelles. A key question is how regulatory proteins modulate catastrophe, the conversion from growth to shortening. To study this process, we reconstituted microtubule dynamics in the absence and presence of the kinesin-8 Kip3 and the kinesin-13 MCAK. Surprisingly, we found that, even in the absence of the kinesins, the microtubule catastrophe frequency depends on the age of the microtubule, indicating that catastrophe is a multistep process. Kip3 slowed microtubule growth in a length-dependent manner and increased the rate of aging. In contrast, MCAK eliminated the aging process. Thus, both kinesins are catastrophe factors; Kip3 mediates fine control of microtubule length by narrowing the distribution of maximum lengths prior to catastrophe, whereas MCAK promotes rapid restructuring of the microtubule cytoskeleton by making catastrophe a first-order random process.

The mechanisms of microtubule catastrophe and rescue: implications from analysis of a dimer-scale computational model

ETOC: The behavior of a dimer-scale computational model predicts that short interprotofilament “cracks” (laterally unbonded regions between protofilaments) exist even at the tips of growing MTs and that rapid fluctuations in the depths of these cracks govern both catastrophe and rescue.

Microtubule (MT) dynamic instability is fundamental to many cell functions, but its mechanism remains poorly understood, in part because it is difficult to gain information about the dimer-scale events at the MT tip. To address this issue, we used a dimer-scale computational model of MT assembly that is consistent with tubulin structure and biochemistry, displays dynamic instability, and covers experimentally relevant spans of time. It allows us to correlate macroscopic behaviors (dynamic instability parameters) with microscopic structures (tip conformations) and examine protofilament structure as the tip spontaneously progresses through both catastrophe and rescue. The model's behavior suggests that several commonly held assumptions about MT dynamics should be reconsidered. Moreover, it predicts that short, interprotofilament “cracks” (laterally unbonded regions between protofilaments) exist even at the tips of growing MTs and that rapid fluctuations in the depths of these cracks influence both catastrophe and rescue. We conclude that experimentally observed microtubule behavior can best be explained by a “stochastic cap” model in which tubulin subunits hydrolyze GTP according to a first-order reaction after they are incorporated into the lattice; catastrophe and rescue result from stochastic fluctuations in the size, shape, and extent of lateral bonding of the cap.

Mechanochemical modeling of dynamic microtubule growth involving sheet-to-tube transition

Microtubule dynamics is largely influenced by nucleotide hydrolysis and the resultant tubulin configuration changes. The GTP cap model has been proposed to interpret the stabilizing mechanisms of microtubule growth from the view of hydrolysis effects. Besides, the growth of a microtubule involves the closure of a curved sheet at its growing end. The curvature conversion from the longitudinal direction to the circumferential direction also helps to stabilize the successive growth, and the curved sheet is referred to as the conformational cap. However, there still lacks theoretical investigation on the mechanical–chemical coupling growth process of microtubules. In this paper, we study the growth mechanisms of microtubules by using a coarse-grained molecular method. First, the closure process involving a sheet-to-tube transition is simulated. The results verify the stabilizing effect of the sheet structure and predict that the minimum conformational cap length that can stabilize the growth is two dimers. Then, we show that the conformational cap and the GTP cap can function independently and harmoniously, signifying the pivotal role of mechanical factors. Furthermore, based on our theoretical results, we describe a Tetris-like growth style of microtubules: the stochastic tubulin assembly is regulated by energy and harmonized with the seam zipping such that the sheet keeps a practically constant length during growth.

Design, overexpression, and purification of polymerization-blocked yeast αβ-tubulin mutants

Microtubule dynamics play essential roles in intracellular organization and cell division. They result from structural and biochemical properties of αβ-tubulin heterodimers and how these polymerizing subunits interact with themselves and with regulatory proteins. A broad understanding of the underlying mechanisms has been established, but fundamental questions remain unresolved. The lack of routine access to recombinant αβ-tubulin represents an obstacle to deeper insight into αβ-tubulin structure, biochemistry, and recognition. Indeed, the widespread reliance on animal brain αβ-tubulin means that very few in vitro studies have taken advantage of powerful and ordinarily routine techniques like site-directed mutagenesis. Here we report new methods for purifying wild-type or mutant yeast αβ-tubulin from inducibly overexpressing strains of Saccharomyces cerevisiae. Inducible overexpression is an improvement over existing approaches that rely on constitutive expression: it provides higher yields while also allowing otherwise lethal mutants to be purified. We also designed and purified polymerization-blocked αβ-tubulin mutants. These "blocked" forms of αβ-tubulin give a dominant lethal phenotype when expressed in cells; they cannot form microtubules in vitro and when present in mixtures inhibit the polymerization of wild-type αβ-tubulin. The effects of blocking mutations are very specific, because purified mutants exhibit normal hydrodynamic properties, bind GTP, and interact with a tubulin-binding domain. The ability to overexpress and purify wild-type αβ-tubulin, or mutants like the ones we report here, creates new opportunities for structural studies of αβ-tubulin and its complexes with regulatory proteins, and for biochemical and functional studies of microtubule dynamics and its regulation.

Coarse-grained mechanochemical model for simulating the dynamic behavior of microtubules

Modeling the structure and mechanics of microtubules, which play significant roles in various physiological functions of cells, has long been a fascinating issue. In this paper, a coarse-grained mechanochemical model is presented to study the mechanical-chemical coupling and dynamic attributes of microtubules. The interactions among tubulins are taken into account from the molecular basis. This model is used to characterize the conformations of sheet-ended microtubules, to analyze the distributions of interaction energy, and further to simulate the radial indentation process of a microtubule. This method also works for investigating the dynamic properties of microtubules, e.g., their assembly, growth, deformation, and structural evolution for different conditions. This study is helpful for understanding the structure-mechanics-function relationship of microtubules and lays a foundation for further investigation of their dynamic behavior.

New insights into microtubule elongation mechanisms

Microtubules are cytoskeletal structures in the cytoplasm of eukaryotic cells, and their highly dynamic properties are essential to perform a wide variety of vital functions in cells. Microtubule growth proceeds through the endwise addition of nucleotide-bound tubulin molecules. It has largely been assumed that only tubulin dimers can incorporate into microtubules, and that the chemical state of the nucleotide is crucial for the incorporation. Recent observations reveal that both tubulin dimers and oligomers can add to microtubule ends and that the chemical state of the nucleotide is not decisive for tubulin addition. Together with structural studies of tubulin, these results show tubulin assembly polymorphism, which could play a crucial role in microtubule-dependent cellular functions.

Intrinsic bending of microtubule protofilaments

The complex polymerization dynamics of the microtubule (MT) plus end are closely linked to the hydrolysis of the GTP nucleotide bound to the β-tubulin. The destabilization is thought to be associated with the conformational change of the tubulin dimers from the straight conformation in the MT lattice to a curved conformation. It remains under debate whether this transformation is directly related to the nucleotide state, or a consequence of the longitudinal or lateral contacts in the MT lattice. Here, we present large-scale atomistic simulations of short tubulin protofilaments with both nucleotide states, starting from both extreme conformations. Our simulations indicate that both interdimer and intradimer contacts in both GDP and GTP-bound tubulin dimers and protofilaments in solution bend. There are no observable differences between the mesoscopic properties of the contacts in GTP and GDP-bound tubulin or the intradime and interdimer interfaces.

Mean-field study of the role of lateral cracks in microtubule dynamics

A link between dimer-scale processes and microtubule (MT) dynamics at macroscale is studied by comparing simulations obtained using computational dimer-scale model with its mean-field approximation. The novelty of the mean-field model (MFM) is in its explicit representation of inter-protofilament cracks, as well as in the direct incorporation of the dimer-level kinetics. Due to inclusion of both longitudinal and lateral dimer interactions, the MFM is two dimensional, in contrast to previous theoretical models of MTs. It is the first analytical model that predicts and quantifies crucial features of MT dynamics such as (i) existence of a minimal soluble tubulin concentration needed for the polymerization (with concentration represented as a function of model parameters), (ii) existence of steady-state growth and shortening phases (given with their respective velocities), and (iii) existence of an unstable pause state near zero velocity. In addition, the size of the GTP cap of a growing MT is estimated. Theoretical predictions are shown to be in good agreement with the numerical simulations.

Drugs that target dynamic microtubules: a new molecular perspective

Microtubules have long been considered an ideal target for anticancer drugs because of the essential role they play in mitosis, forming the dynamic spindle apparatus. As such, there is a wide variety of compounds currently in clinical use and in development that act as antimitotic agents by altering microtubule dynamics. Although these diverse molecules are known to affect microtubule dynamics upon binding to one of the three established drug domains (taxane, vinca alkaloid, or colchicine site), the exact mechanism by which each drug works is still an area of intense speculation and research. In this study, we review the effects of microtubule-binding chemotherapeutic agents from a new perspective, considering how their mode of binding induces conformational changes and alters biological function relative to the molecular vectors of microtubule assembly or disassembly. These "biological vectors" can thus be used as a spatiotemporal context to describe molecular mechanisms by which microtubule-targeting drugs work.

Design and synthesis of pironetin analogues with simplified structure and study of their interactions with microtubules

The preparation of a series of pironetin analogues with simplified structure is described. Their cytotoxic activity and their interactions with tubulin have been investigated. It has been found that, while less active than the parent molecule, the pironetin analogues still share the mechanism of action of the latter and compete for the same binding site to α-tubulin. Variations in the configurations of their stereocenters do not translate into relevant differences between biological activities.

Hallmarks of molecular action of microtubule stabilizing agents: effects of epothilone B, ixabepilone, peloruside A, and laulimalide on microtubule conformation

Microtubule stabilizing agents (MSAs) comprise a class of drugs that bind to microtubule (MT) polymers and stabilize them against disassembly. Several of these agents are currently in clinical use as anticancer drugs, whereas others are in various stages of development. Nonetheless, there is insufficient knowledge about the molecular modes of their action. Recent studies from our laboratory utilizing hydrogen-deuterium exchange in combination with mass spectrometry (MS) provide new information on the conformational effects of Taxol and discodermolide on microtubules isolated from chicken erythrocytes (CET). We report here a comprehensive analysis of the effects of epothilone B, ixabepilone (IXEMPRA(TM)), laulimalide, and peloruside A on CET conformation. The results of our comparative hydrogen-deuterium exchange MS studies indicate that all MSAs have significant conformational effects on the C-terminal H12 helix of α-tubulin, which is a likely molecular mechanism for the previously observed modulations of MT interactions with microtubule-associated and motor proteins. More importantly, the major mode of MT stabilization by MSAs is the tightening of the longitudinal interactions between two adjacent αβ-tubulin heterodimers at the interdimer interface. In contrast to previous observations reported with bovine brain tubulin, the lateral interactions between the adjacent protofilaments in CET are particularly strongly stabilized by peloruside A and laulimalide, drugs that bind outside the taxane site. This not only highlights the significance of tubulin isotype composition in modulating drug effects on MT conformation and stability but also provides a potential explanation for the synergy observed when combinations of taxane and alternative site binding drugs are used.

Novel trisubstituted benzimidazoles, targeting Mtb FtsZ, as a new class of antitubercular agents

Libraries of novel trisubstituted benzimidazoles were created through rational drug design. A good number of these benzimidazoles exhibited promising MIC values in the range of 0.5-6 μg/mL (2-15 μM) for their antibacterial activity against Mtb H37Rv strain. Moreover, five of the lead compounds also exhibited excellent activity against clinical Mtb strains with different drug-resistance profiles. All lead compounds did not show appreciable cytotoxicity (IC(50) > 200 μM) against Vero cells, which inhibited Mtb FtsZ assembly in a dose dependent manner. The two lead compounds unexpectedly showed enhancement of the GTPase activity of Mtb FtsZ. The result strongly suggests that the increased GTPase activity destabilizes FtsZ assembly, leading to efficient inhibition of FtsZ polymerization and filament formation. The TEM and SEM analyses of Mtb FtsZ and Mtb cells, respectively, treated with a lead compound strongly suggest that lead benzimidazoles have a novel mechanism of action on the inhibition of Mtb FtsZ assembly and Z-ring formation.

Intrabundle microtubule dynamics in the Arabidopsis cortical array

We tested the general hypothesis that bundling stabilizes the dynamic properties of the constituent microtubules (MTs) in vivo. We quantified the assembly dynamics of bundled and unbundled MTs in the interphase cortical array of Arabidopsis hypocotyl cells using high dynamic range spinning disk confocal microscopy. We find no evidence that bundled MTs are stabilized against depolymerization through changes to their dynamic properties. Our observations of MT plus and minus ends indicate that both bundled and unbundled polymers undergo persistent treadmilling in this system. We conclude that the temporal persistence of MT subassemblies in the Arabidopsis cortical array is largely dependent upon recruitment or nucleation of new treadmilling MTs and not on polymer stabilization. Monte Carlo simulations suggest that small differences discovered in the dynamic properties between bundled and unbundled polymers would produce relatively small macroscopic effects on the larger MT array.

Stathmin and interfacial microtubule inhibitors recognize a naturally curved conformation of tubulin dimers

Tubulin is able to switch between a straight microtubule-like structure and a curved structure in complex with the stathmin-like domain of the RB3 protein (T(2)RB3). GTP hydrolysis following microtubule assembly induces protofilament curvature and disassembly. The conformation of the labile tubulin heterodimers is unknown. One important question is whether free GDP-tubulin dimers are straightened by GTP binding or if GTP-tubulin is also curved and switches into a straight conformation upon assembly. We have obtained insight into the bending flexibility of tubulin by analyzing the interplay of tubulin-stathmin association with the binding of several small molecule inhibitors to the colchicine domain at the tubulin intradimer interface, combining structural and biochemical approaches. The crystal structures of T(2)RB3 complexes with the chiral R and S isomers of ethyl-5-amino-2-methyl-1,2-dihydro-3-phenylpyrido[3,4-b]pyrazin-7-yl-carbamate, show that their binding site overlaps with colchicine ring A and that both complexes have the same curvature as unliganded T(2)RB3. The binding of these ligands is incompatible with a straight tubulin structure in microtubules. Analytical ultracentrifugation and binding measurements show that tubulin-stathmin associations (T(2)RB3, T(2)Stath) and binding of ligands (R, S, TN-16, or the colchicine analogue MTC) are thermodynamically independent from one another, irrespective of tubulin being bound to GTP or GDP. The fact that the interfacial ligands bind equally well to tubulin dimers or stathmin complexes supports a bent conformation of the free tubulin dimers. It is tempting to speculate that stathmin evolved to recognize curved structures in unassembled and disassembling tubulin, thus regulating microtubule assembly.

Coarse-Grained Representations of Large Biomolecular Complexes from Low-Resolution Structural Data

High-resolution atomistic structures of many large biomolecular complexes have not yet been solved by experiments, such as X-ray crystallography or NMR. Often however low-resolution information is obtained by alternative techniques, such as cryo-electron microscopy or small-angle X-ray scattering. Coarse-grained (CG) models are an appropriate choice to computationally study these complexes given the limited resolution experimental data. One of the important questions therefore is how to define CG representations from these low-resolution density maps. This work provides a space-based essential dynamics coarse-graining (ED-CG) method to define a CG representation from a density map without detailed knowledge of its underlying atomistic structure and primary sequence information. This method is demonstrated on G-actin (both the atomic structure and its density map). It is then applied to the density maps of the Escherichia coli 70S ribosome and the microtubule. The results indicate that the method can define highly CG models that still preserve functionally important dynamics of large biomolecular complexes.

Mapping flexibility and the assembly switch of cell division protein FtsZ by computational and mutational approaches

The molecular switch for nucleotide-regulated assembly and disassembly of the main prokaryotic cell division protein FtsZ is unknown despite the numerous crystal structures that are available. We have characterized the functional motions in FtsZ with a computational consensus of essential dynamics, structural comparisons, sequence conservation, and networks of co-evolving residues. Employing this information, we have constructed 17 mutants, which alter the FtsZ functional cycle at different stages, to modify FtsZ flexibility. The mutant phenotypes ranged from benign to total inactivation and included increased GTPase, reduced assembly, and stabilized assembly. Six mutations clustering at the long cleft between the C-terminal beta-sheet and core helix H7 deviated FtsZ assembly into curved filaments with inhibited GTPase, which still polymerize cooperatively. These mutations may perturb the predicted closure of the C-terminal domain onto H7 required for switching between curved and straight association modes and for GTPase activation. By mapping the FtsZ assembly switch, this work also gives insight into FtsZ druggability because the curved mutations delineate the putative binding site of the promising antibacterial FtsZ inhibitor PC190723.

Two new families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea

Several recent discoveries reveal unexpected versatility of the bacterial and archaeal cytoskeleton systems that are involved in cell division and other processes based on membrane remodeling. Here we apply methods for distant protein sequence similarity detection, phylogenetic approaches, and genome context analysis to described two previously unnoticed families of the FtsZ-tubulin superfamily. One of these families is limited in its spread to Proteobacteria whereas the other is represented in diverse bacteria and archaea, and might be the key component of a novel, multicomponent membrane remodeling system that also includes a Von Willebrand A domain-containing protein, a distinct GTPase and membrane transport proteins of the OmpA family.

This article was reviewed by Purificación López-García and Gáspár Jékely; for complete reviews, see the Reviewers Reports section.

Microtubule dynamics at the cell cortex probed by TIRF microscopy

Total internal reflection fluorescence (TIRF) microscopy is a technique that allows selective excitation of fluorescence at a liquid/solid interface within a short distance from the boundary. The penetration depth of TIRF microscopy depends on the angle of illumination resulting in a range of depths, which typically vary from approximately similar 70-200 nm up to reverse approximately 500 nm. The advantages of TIRF microscopy include excellent signal-to-noise ratio, high sensitivity, low photobleaching, and low photodamage. TIRF microscopy is widely used for studying cell adhesion, exo- and endocytosis, and the dynamics of plasma membrane-associated molecules. TIRF microscopy can also be applied for selective visualization of any other cellular processes that occur near the basal membrane even if their localization is not restricted to this part of the cell. For example, microtubules are distributed throughout the cytoplasm, but the use of TIRF microscopy makes it possible to visualize specifically the microtubule subpopulation in the vicinity of the basal cortex and thus study cortical microtubule attachment and stabilization, interactions between microtubules and matrix adhesion structures, and the behavior of specific molecules involved in these processes. In this chapter we describe the application of a commercially available setup to analyze microtubule behavior in live mammalian cells using TIRF microscopy.

Cryo-electron tomography of cellular microtubules

Microtubules are intrinsically dynamic structures. In the cellular environment many proteins and protein complexes are associated with microtubules that influence or functionalize microtubule dynamics. Therefore, investigation of the structure and dynamics of microtubules with their associated complexes inside the cellular environment lies at the heart of fully understanding their function. Cryo electron microscopy has been essential in structural microtubule research since the atomic structure of tubulin and the structure of microtubules were unraveled using this technique. Furthermore, the specific structures at the microtubule ends linked to the growing or shrinking states were also detected by cryo electron microscopy. Electron microscopy studies on microtubules were mainly performed in vitro but microtubules can also be investigated inside cells, using cryo electron tomography. Cryo electron tomography is an important tool in structural biology research because it enables visualization of single and unique protein complexes in a cellular environment and at a molecular resolution. Cryo electron tomography is a three-dimensional (3D) imaging technique in which electron microscopy tomographic imaging is performed on cryogenically cooled, vitrified specimens after which the object is computationally reconstructed. Here, I describe the materials and methods for cryo electron tomography of microtubules and in whole cells, describing cell growth, specimen vitrification, localization of microtubules, cryo electron tomography recording, tomographic image reconstruction, and 3D visualization techniques.

Catechol-o-methyltransferase expression and 2-methoxyestradiol affect microtubule dynamics and modify steroid receptor signaling in leiomyoma cells

Context

Development of optimal medicinal treatments of uterine leiomyomas represents a significant challenge. 2-Methoxyestradiol (2ME) is an endogenous estrogen metabolite formed by sequential action of CYP450s and catechol-O-methyltransferase (COMT). Our previous study demonstrated that 2ME is a potent antiproliferative, proapoptotic, antiangiogenic, and collagen synthesis inhibitor in human leiomyomas cells (huLM).

Objectives

Our objectives were to investigate whether COMT expression, by the virtue of 2ME formation, affects the growth of huLM, and to explore the cellular and molecular mechanisms whereby COMT expression or treatment with 2ME affect these cells.

Results

Our data demonstrated that E₂-induced proliferation was less pronounced in cells over-expressing COMT or treated with 2ME (500 nM). This effect on cell proliferation was associated with microtubules stabilization and diminution of estrogen receptor α (ERα) and progesterone receptor (PR) transcriptional activities, due to shifts in their subcellular localization and sequestration in the cytoplasm. In addition, COMT over expression or treatment with 2ME reduced the expression of hypoxia-inducible factor -1α (HIF-1 α) and the basal level as well as TNF-α-induced aromatase (CYP19) expression.

Conclusions

COMT over expression or treatment with 2ME stabilize microtubules, ameliorates E₂-induced proliferation, inhibits ERα and PR signaling, and reduces HIF-1 α and CYP19 expression in human uterine leiomyoma cells. Thus, microtubules are a candidate target for treatment of uterine leiomyomas. In addition, the naturally occurring microtubule-targeting agent 2ME represents a potential new therapeutic for uterine leiomyomas.

Regulation of microtubule dynamics by inhibition of the tubulin deacetylase HDAC6

We studied the role of a class II histone deacetylase, HDAC6, known to function as a potent alpha-tubulin deacetylase, in the regulation of microtubule dynamics. Treatment of cells with the class I and II histone deacetylase inhibitor TSA, as well as the selective HDAC6 inhibitor tubacin, increased microtubule acetylation and significantly reduced velocities of microtubule growth and shrinkage. siRNA-mediated knockdown of HDAC6 also increased microtubule acetylation but, surprisingly, had no effect on microtubule growth velocity. At the same time, HDAC6 knockdown abolished the effect of tubacin on microtubule growth, demonstrating that tubacin influences microtubule dynamics via specific inhibition of HDAC6. Thus, the physical presence of HDAC6 with impaired catalytic activity, rather than tubulin acetylation per se, is the factor responsible for the alteration of microtubule growth velocity in HDAC6 inhibitor-treated cells. In support of this notion, HDAC6 mutants bearing inactivating point mutations in either of the two catalytic domains mimicked the effect of HDAC6 inhibitors on microtubule growth velocity. In addition, HDAC6 was found to be physically associated with the microtubule end-tracking protein EB1 and a dynactin core component, Arp1, both of which accumulate at the tips of growing microtubules. We hypothesize that inhibition of HDAC6 catalytic activity may affect microtubule dynamics by promoting the interaction of HDAC6 with tubulin and/or with other microtubule regulatory proteins.

Structural mass spectrometry of the alpha beta-tubulin dimer supports a revised model of microtubule assembly

The molecular basis of microtubule lattice instability derives from the hydrolysis of GTP to GDP in the lattice-bound state of alphabeta-tubulin. While this has been appreciated for many years, there is ongoing debate over the molecular basis of this instability and the possible role of altered nucleotide occupancy in the induction of a conformational change in tubulin. The debate has organized around seemingly contradictory models. The allosteric model invokes nucleotide-dependent states of curvature in the free tubulin dimer, such that hydrolysis leads to pronounced bending and thus disruption of the lattice. The more recent lattice model describes a predominant role for the lattice in straightening free dimers that are curved regardless of their nucleotide state. In this model, lattice-bound GTP-tubulin provides the necessary force to straighten an incoming dimer. Interestingly, there is evidence for both models. The enduring nature of this debate stems from a lack of high-resolution data on the free dimer. In this study, we have prepared alphabeta-tubulin samples at high dilution and characterized the nature of nucleotide-induced conformational stability using bottom-up hydrogen/deuterium exchange mass spectrometry (H/DX-MS) coupled with isothermal urea denaturation experiments. These experiments were accompanied by molecular dynamics simulations of the free dimer. We demonstrate an intermediate state unique to GDP-tubulin, suggestive of the curved colchicine-stabilized structure at the intradimer interface but show that intradimer flexibility is an important property of the free dimer regardless of nucleotide occupancy. Our results indicate that the assembly properties of the free dimer may be better described on the basis of this flexibility. A blended model of assembly emerges in which free-dimer allosteric effects retain importance, in an assembly process dominated by lattice-induced effects.

Microtubule dynamics as a target in oncology

Drugs that affect microtubule dynamics, including the taxanes and vinca alkaloids, have been a mainstay in the treatment of leukemias and solid tumors for decades. New, more effective microtubule-targeting agents continue to enter into clinical trials and some, including the epothilone ixapebilone, have been approved for use. In contrast, several other drugs of this class with promising preclinical data were later shown to be ineffective or intolerable in animal models or clinical trials. In this review, we discuss the molecular mechanisms as well as preclinical and clinical results for a variety of microtubule-targeting agents in various stages of development. We also offer a frank discussion of which microtubule-targeting agents are amenable to further development based on their availability, efficacy and toxic profile.

Inhibition of microtubule assembly in osteoblasts stimulates bone morphogenetic protein 2 expression and bone formation through transcription factor Gli2

Bone morphogenetic protein 2 (BMP-2) is essential for postnatal bone formation and fracture repair. By screening chemical libraries for BMP-2 mimics using a cell-based assay, we identified inhibitors of microtubule assembly as stimulators of BMP-2 transcription. These microtubule inhibitors increased osteoblast differentiation in vitro, stimulated periosteal bone formation when injected locally over murine calvaria, and enhanced trabecular bone formation when administered systemically in vivo. To explore molecular mechanisms mediating these responses, we examined effects of microtubule inhibitors on the hedgehog (Hh) pathway, since this pathway is known to regulate BMP-2 transcription in osteoblasts and microtubules have been shown to be involved in Hh signaling in Drosophila. Here we show that in osteoblasts, inhibition of microtubule assembly increased cytoplasmic levels and transcriptional activity of Gli2, a transcriptional mediator of Hh signaling that we have previously shown to enhance BMP-2 expression in osteoblasts (M. Zhao et al., Mol. Cell. Biol. 26:6197-6208, 2006). Microtubule inhibition blocked beta-TrCP-mediated proteasomal processing of Gli2 in osteoblasts. In summary, inhibition of microtubule assembly enhances BMP-2 gene transcription and subsequent bone formation, in part, through inhibiting proteasomal processing of Gli2 and increasing intracellular Gli2 concentrations.

Probing the origin of tubulin rigidity with molecular simulations

Tubulin heterodimers are the building blocks of microtubules, a major component of the cytoskeleton, whose mechanical properties are fundamental for the life of the cell. We uncover the microscopic origins of the mechanical response in microtubules by probing features of the energy landscape of the tubulin monomers and tubulin heterodimer. To elucidate the structures of the unfolding pathways and reveal the multiple unfolding routes, we performed simulations of a self-organized polymer (SOP) model of tubulin. The SOP representation, which is a coarse-grained description of chains, allows us to perform force-induced simulations at loading rates and time scales that closely match those used in single-molecule experiments. We show that the forced unfolding of each monomer involves a bifurcation in the pathways to the stretched state. After the unfolding of the C-term domain, the unraveling continues either from the N-term domain or from the middle domain, depending on the monomer and the pathway. In contrast to the unfolding complexity of the monomers, the dimer unfolds according to only one route corresponding to the unraveling of the C-term domain and part of the middle domain of beta-tubulin. We find that this surprising behavior is due to the viscoelastic properties of the interface between the monomers. We map precise features of the complex energy landscape of tubulin by surveying the structures of the various metastable intermediates, which, in the dimer case, are characterized only by changes in the beta-tubulin monomer.

Structural model for strain-dependent microtubule activation of Mg-ADP release from kinesin

Mg-ADP release is considered to be a crucial process for the regulation and motility of kinesin. To gain insight into the structural basis of this process, we solved the atomic structures of kinesin superfamily protein-1A (KIF1A) during and after Mg(2+) release. On the basis of new structural and mutagenesis data, we propose a model mechanism for microtubule activation of Mg-ADP release from KIF1A. In our model, a specific interaction between loop L7 of KIF1A and beta-tubulin reconfigures the KIF1A active site by shifting the relative positions of switches I and II. This leads to the sequential release of a group of water molecules that sits over the Mg(2+) in the active site, followed by Mg(2+) and finally the ADP. We further propose that this set of events is linked to a strain-dependent docking of the neck linker to the motor core, which produces a two-step power stroke.

Secondary mutations correct fitness defects in Toxoplasma gondii with dinitroaniline resistance mutations

Dinitroanilines (oryzalin, trifluralin, ethafluralin) disrupt microtubules in protozoa but not in vertebrate cells, causing selective death of intracellular Toxoplasma gondii parasites without affecting host cells. Parasites containing alpha1-tubulin point mutations are dinitroaniline resistant but show increased rates of aberrant replication relative to wild-type parasites. T. gondii parasites bearing the F52Y mutation were previously demonstrated to spontaneously acquire two intragenic mutations that decrease both resistance levels and replication defects. Parasites bearing the G142S mutation are largely dependent on oryzalin for viable growth in culture. We isolated 46 T. gondii lines that have suppressed microtubule defects associated with the G142S or the F52Y mutations by acquiring secondary mutations. These compensatory mutations were alpha1-tubulin pseudorevertants or extragenic suppressors (the majority alter the beta1-tubulin gene). Many secondary mutations were located in tubulin domains that suggest that they function by destabilizing microtubules. Most strikingly, we identified seven novel mutations that localize to an eight-amino-acid insert that stabilizes the alpha1-tubulin M loop, including one (P364R) that acts as a compensatory mutation in both F52Y and G142S lines. These lines have reduced dinitroaniline resistance but most perform better than parental lines in competition assays, indicating that there is a trade-off between resistance and replication fitness.

Allosteric models for cooperative polymerization of linear polymers

In the cytoskeleton, unfavorable nucleation steps allow cells to regulate where, when, and how many polymers assemble. Nucleated polymerization is traditionally explained by a model in which multistranded polymers assemble cooperatively, whereas linear, single-stranded polymers do not. Recent data on the assembly of FtsZ, the bacterial homolog of tubulin, do not fit either category. FtsZ can polymerize into single-stranded protofilaments that are stable in the absence of lateral interactions, but that assemble cooperatively. We developed a model for cooperative polymerization that does not require polymers to be multistranded. Instead, a conformational change allows subunits in oligomers to associate with high affinity, whereas a lower-affinity conformation is favored in monomers. We derive equations for calculating polymer concentrations, subunit conformations, and the apparent affinity of subunits for polymer ends. Certain combinations of equilibrium constants produce the sharp critical concentrations characteristic of cooperative polymerization. In these cases, the low-affinity conformation predominates in monomers, whereas virtually all polymers are composed of high-affinity subunits. Our model predicts that the three routes to forming HH dimers all involve unstable intermediates, limiting nucleation. The mathematical framework developed here can represent allosteric assembly systems with a variety of biochemical interpretations, some of which can show cooperativity, and others of which cannot.