Structural basis for α-tubulin-specific and modification state-dependent glutamylation.

Microtubules have spatiotemporally complex posttranslational modification patterns. Tubulin tyrosine ligase-like (TTLL) enzymes introduce the most prevalent modifications on α-tubulin and ß-tubulin. How TTLLs specialize for specific substrate recognition and ultimately modification-pattern generation is largely unknown. TTLL6, a glutamylase implicated in ciliopathies, preferentially modifies tubulin α-tails in microtubules. Cryo-electron microscopy, kinetic analysis and single-molecule biochemistry reveal an unprecedented quadrivalent recognition that ensures simultaneous readout of microtubule geometry and posttranslational modification status. By binding to a ß-tubulin subunit, TTLL6 modifies the α-tail of the longitudinally adjacent tubulin dimer. Spanning two tubulin dimers along and across protofilaments (PFs) ensures fidelity of recognition of both the α-tail and the microtubule. Moreover, TTLL6 reads out and is stimulated by glutamylation of the ß-tail of the laterally adjacent tubulin dimer, mediating crosstalk between α-tail and ß-tail. This positive feedback loop can generate localized microtubule glutamylation patterns. Our work uncovers general principles that generate tubulin chemical and topographic complexity.

The Tubulin Code, from Molecules to Health and Disease.

Microtubules are essential dynamic polymers composed of α/ß-tubulin heterodimers. They support intracellular trafficking, cell division, cellular motility, and other essential cellular processes. In many species, both α-tubulin and ß-tubulin are encoded by multiple genes with distinct expression profiles and functionality. Microtubules are further diversified through abundant posttranslational modifications, which are added and removed by a suite of enzymes to form complex, stereotyped cellular arrays. The genetic and chemical diversity of tubulin constitute a tubulin code that regulates intrinsic microtubule properties and is read by cellular effectors, such as molecular motors and microtubule-associated proteins, to provide spatial and temporal specificity to microtubules in cells. In this review, we synthesize the rapidly expanding tubulin code literature and highlight limitations and opportunities for the field. As complex microtubule arrays underlie essential physiological processes, a better understanding of how cells employ the tubulin code has important implications for human disease ranging from cancer to neurological disorders.

Glutamylation is a negative regulator of microtubule growth.

Microtubules are noncovalent polymers built from αß-tubulin dimers. The disordered C-terminal tubulin tails are functionalized with multiple glutamate chains of variable lengths added and removed by tubulin tyrosine ligases (TTLLs) and carboxypeptidases (CCPs). Glutamylation is abundant on stable microtubule arrays such as in axonemes and axons, and its dysregulation leads to human pathologies. Despite this, the effects of glutamylation on intrinsic microtubule dynamics are unclear. Here we generate tubulin with short and long glutamate chains and show that glutamylation slows the rate of microtubule growth and increases catastrophes as a function of glutamylation levels. This implies that the higher stability of glutamylated microtubules in cells is due to effectors. Interestingly, EB1 is minimally affected by glutamylation and thus can report on the growth rates of both unmodified and glutamylated microtubules. Finally, we show that glutamate removal by CCP1 and 5 is synergistic and occurs preferentially on soluble tubulin, unlike TTLL enzymes that prefer microtubules. This substrate preference establishes an asymmetry whereby once the microtubule depolymerizes, the released tubulin is reset to a less-modified state, while polymerized tubulin accumulates the glutamylation mark. Our work shows that a modification on the disordered tubulin tails can directly affect microtubule dynamics and furthers our understanding of the mechanistic underpinnings of the tubulin code.

Combinatorial and antagonistic effects of tubulin glutamylation and glycylation on katanin microtubule severing.

Microtubules have spatiotemporally complex posttranslational modification patterns. How cells interpret this tubulin modification code is largely unknown. We show that C. elegans katanin, a microtubule severing AAA ATPase mutated in microcephaly and critical for cell division, axonal elongation, and cilia biogenesis, responds precisely, differentially, and combinatorially to three chemically distinct tubulin modifications-glycylation, glutamylation, and tyrosination-but is insensitive to acetylation. Glutamylation and glycylation are antagonistic rheostats with glycylation protecting microtubules from severing. Katanin exhibits graded and divergent responses to glutamylation on the α- and ß-tubulin tails, and these act combinatorially. The katanin hexamer central pore constrains the polyglutamate chain patterns on ß-tails recognized productively. Elements distal to the katanin AAA core sense α-tubulin tyrosination, and detyrosination downregulates severing. The multivalent microtubule recognition that enables katanin to read multiple tubulin modification inputs explains in vivo observations and illustrates how effectors can integrate tubulin code signals to produce diverse functional outcomes.

Microtubule-severing enzymes.

Stephanie Sarbanes et al. discuss microtubule-severing enzymes, highlighting their shared structure and mechanism and the diversity of processes in which they participate.

Phosphinic acid-based inhibitors of tubulin polyglycylation.

Tubulin polyglycylation is a posttranslational modification that occurs primarily on the axonemes of flagella and cilia and has been shown to be essential for proper sperm motility. Inhibitors of both the initiase and elongase ligases (TTLL8 and TTLL10) are shown to inhibit tubulin glycylation in the low micromolar range.

ER proteins decipher the tubulin code to regulate organelle distribution.

Organelles move along differentially modified microtubules to establish and maintain their proper distributions and functions1,2. However, how cells interpret these post-translational microtubule modification codes to selectively regulate organelle positioning remains largely unknown. The endoplasmic reticulum (ER) is an interconnected network of diverse morphologies that extends promiscuously throughout the cytoplasm3, forming abundant contacts with other organelles4. Dysregulation of endoplasmic reticulum morphology is tightly linked to neurologic disorders and cancer5,6. Here we demonstrate that three membrane-bound endoplasmic reticulum proteins preferentially interact with different microtubule populations, with CLIMP63 binding centrosome microtubules, kinectin (KTN1) binding perinuclear polyglutamylated microtubules, and p180 binding glutamylated microtubules. Knockout of these proteins or manipulation of microtubule populations and glutamylation status results in marked changes in endoplasmic reticulum positioning, leading to similar redistributions of other organelles. During nutrient starvation, cells modulate CLIMP63 protein levels and p180-microtubule binding to bidirectionally move endoplasmic reticulum and lysosomes for proper autophagic responses.

α-tubulin tail modifications regulate microtubule stability through selective effector recruitment, not changes in intrinsic polymer dynamics.

Microtubules are non-covalent polymers of αß-tubulin dimers. Posttranslational processing of the intrinsically disordered C-terminal α-tubulin tail produces detyrosinated and Δ2-tubulin. Although these are widely employed as proxies for stable cellular microtubules, their effect (and of the α-tail) on microtubule dynamics remains uncharacterized. Using recombinant, engineered human tubulins, we now find that neither detyrosinated nor Δ2-tubulin affect microtubule dynamics, while the α-tubulin tail is an inhibitor of microtubule growth. Consistent with the latter, molecular dynamics simulations show the α-tubulin tail transiently occluding the longitudinal microtubule polymerization interface. The marked differential in vivo stabilities of the modified microtubule subpopulations, therefore, must result exclusively from selective effector recruitment. We find that tyrosination quantitatively tunes CLIP-170 density at the growing plus end and that CLIP170 and EB1 synergize to selectively upregulate the dynamicity of tyrosinated microtubules. Modification-dependent recruitment of regulators thereby results in microtubule subpopulations with distinct dynamics, a tenet of the tubulin code hypothesis.

Author Correction: Structural basis for polyglutamate chain initiation and elongation by TTLL family enzymes.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Structural basis for polyglutamate chain initiation and elongation by TTLL family enzymes.

Glutamylation, introduced by tubulin tyrosine ligase-like (TTLL) enzymes, is the most abundant modification of brain tubulin. Essential effector proteins read the tubulin glutamylation pattern, and its misregulation causes neurodegeneration. TTLL glutamylases post-translationally add glutamates to internal glutamates in tubulin carboxy-terminal tails (branch initiation, through an isopeptide bond), and additional glutamates can extend these (elongation). TTLLs are thought to specialize in initiation or elongation, but the mechanistic basis for regioselectivity is unknown. We present cocrystal structures of murine TTLL6 bound to tetrahedral intermediate analogs that delineate key active-site residues that make this enzyme an elongase. We show that TTLL4 is exclusively an initiase and, through combined structural and phylogenetic analyses, engineer TTLL6 into a branch-initiating enzyme. TTLL glycylases add glycines post-translationally to internal glutamates, and we find that the same active-site residues discriminate between initiase and elongase glycylases. These active-site specializations of TTLL glutamylases and glycylases ultimately yield the chemical complexity of cellular microtubules.

The Tubulin Code in Microtubule Dynamics and Information Encoding.

Microtubules are non-covalent mesoscale polymers central to the eukaryotic cytoskeleton. Microtubule structure, dynamics, and mechanics are modulated by a cell's choice of tubulin isoforms and post-translational modifications, a "tubulin code," which is thought to support the diverse morphology and dynamics of microtubule arrays across various cell types, cell cycle, and developmental stages. We give a brief historical overview of research into tubulin diversity and highlight recent progress toward uncovering the mechanistic underpinnings of the tubulin code. As a large number of essential pathways converge upon the microtubule cytoskeleton, understanding how cells utilize tubulin diversity is crucial to understanding cellular physiology and disease.

Mechanisms of microtubule dynamics and force generation examined with computational modeling and electron cryotomography.

Microtubules are dynamic tubulin polymers responsible for many cellular processes, including the capture and segregation of chromosomes during mitosis. In contrast to textbook models of tubulin self-assembly, we have recently demonstrated that microtubules elongate by addition of bent guanosine triphosphate tubulin to the tips of curving protofilaments. Here we explore this mechanism of microtubule growth using Brownian dynamics modeling and electron cryotomography. The previously described flaring shapes of growing microtubule tips are remarkably consistent under various assembly conditions, including different tubulin concentrations, the presence or absence of a polymerization catalyst or tubulin-binding drugs. Simulations indicate that development of substantial forces during microtubule growth and shortening requires a high activation energy barrier in lateral tubulin-tubulin interactions. Modeling offers a mechanism to explain kinetochore coupling to growing microtubule tips under assisting force, and it predicts a load-dependent acceleration of microtubule assembly, providing a role for the flared morphology of growing microtubule ends.

Author Correction: An allosteric network in spastin couples multiple activities required for microtubule severing.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Katanin Grips the ß-Tubulin Tail through an Electropositive Double Spiral to Sever Microtubules.

The AAA ATPase katanin severs microtubules. It is critical in cell division, centriole biogenesis, and neuronal morphogenesis. Its mutation causes microcephaly. The microtubule templates katanin hexamerization and activates its ATPase. The structural basis for these activities and how they lead to severing is unknown. Here, we show that ß-tubulin tails are necessary and sufficient for severing. Cryoelectron microscopy (cryo-EM) structures reveal the essential tubulin tail glutamates gripped by a double spiral of electropositive loops lining the katanin central pore. Each spiral couples allosterically to the ATPase and binds alternating, successive substrate residues, with consecutive residues coordinated by adjacent protomers. This tightly couples tail binding, hexamerization, and ATPase activation. Hexamer structures in different states suggest an ATPase-driven, ratchet-like translocation of the tubulin tail through the pore. A disordered region outside the AAA core anchors katanin to the microtubule while the AAA motor exerts the forces that extract tubulin dimers and sever the microtubule.

In Vitro Reconstitution Assays of Microtubule Amplification and Lattice Repair by the Microtubule-Severing Enzymes Katanin and Spastin.

Microtubules are non-covalent dynamic polymers essential for the life of all eukaryotic cells. Their dynamic behavior is regulated by a large array of cellular effectors. In vitro microtubule assays have been instrumental in dissecting the mechanism of microtubule-associated proteins. In this chapter, we focus on microtubule-severing enzymes katanin and spastin. They are AAA ATPases that generate internal breaks in microtubules by extracting tubulin dimers out of the microtubule lattice. We present protocols for TIRF microscopy-based assays that were instrumental in proving that these enzymes not only sever microtubules but also remodel the microtubule lattice by promoting the exchange of lattice GDP-tubulin with GTP-tubulin from the soluble pool. This activity can modulate microtubule dynamics and support microtubule-dependent microtubule amplification in the absence of a nucleating factor.

In Vitro Microtubule Dynamics Assays Using Dark-Field Microscopy.

Microtubules are dynamic non-covalent mesoscopic polymers. Their dynamic behavior is essential for cell biological processes ranging from intracellular transport to cell division and neurogenesis. Fluorescence microscopy has been the method of choice for monitoring microtubule dynamics in the last two decades. However, fluorescent microtubules are prone to photodamage that alters their dynamics, and the fluorescent label itself can affect microtubule properties. Dark-field imaging is a label-free technique that can generate high signal-to-noise, low-background images of microtubules at high acquisition rates without the photobleaching inherent to fluorescence microscopy. Here, we describe how to image in vitro microtubule dynamics using dark-field microscopy. The ability to image microtubules label-free allows the investigation of the dynamic properties of non-abundant tubulin species where fluorescent labeling is not feasible, free from the confounding effects arising from the addition of fluorescent labels.

Structural determinants of microtubule minus end preference in CAMSAP CKK domains.

CAMSAP/Patronins regulate microtubule minus-end dynamics. Their end specificity is mediated by their CKK domains, which we proposed recognise specific tubulin conformations found at minus ends. To critically test this idea, we compared the human CAMSAP1 CKK domain (HsCKK) with a CKK domain from Naegleria gruberi (NgCKK), which lacks minus-end specificity. Here we report near-atomic cryo-electron microscopy structures of HsCKK- and NgCKK-microtubule complexes, which show that these CKK domains share the same protein fold, bind at the intradimer interprotofilament tubulin junction, but exhibit different footprints on microtubules. NMR experiments show that both HsCKK and NgCKK are remarkably rigid. However, whereas NgCKK binding does not alter the microtubule architecture, HsCKK remodels its microtubule interaction site and changes the underlying polymer structure because the tubulin lattice conformation is not optimal for its binding. Thus, in contrast to many MAPs, the HsCKK domain can differentiate subtly specific tubulin conformations to enable microtubule minus-end recognition.