Cyclical bending of two outer-doublet microtubules in frayed axonemes ofChlamydomonas

Structural determination and modeling of ciliary microtubules

The axoneme, a microtubule-based array at the center of every cilium, has been the subject of structural investigations for decades, but only recent advances in cryo-EM and cryo-ET have allowed a molecular-level interpretation of the entire complex to be achieved. The unique properties of the nine doublet microtubules and central pair of singlet microtubules that form the axoneme, including the highly decorated tubulin lattice and the docking of massive axonemal complexes, provide opportunities and challenges for sample preparation, 3D reconstruction and atomic modeling. Here, the approaches used for cryo-EM and cryo-ET of axonemes are reviewed, while highlighting the unique opportunities provided by the latest generation of AI-guided tools that are transforming structural biology.

A Synthetic Minimal Beating Axoneme

Cilia and flagella are beating rod-like organelles that enable the directional movement of microorganisms in fluids and fluid transport along the surface of biological organisms or inside organs. The molecular motor axonemal dynein drives their beating by interacting with microtubules. Constructing synthetic beating systems with axonemal dynein capable of mimicking ciliary beating still represents a major challenge. Here, the bottom-up engineering of a sustained beating synthoneme consisting of a pair of microtubules connected by a series of periodic arrays of approximately eight axonemal dyneins is reported. A model leads to the understanding of the motion through the cooperative, cyclic association-dissociation of the molecular motor from the microtubules. The synthoneme represents a bottom-up self-organized bio-molecular machine at the nanoscale with cilia-like properties.

Structure of a microtubule-bound axonemal dynein

Axonemal dyneins are tethered to doublet microtubules inside cilia to drive ciliary beating, a process critical for cellular motility and extracellular fluid flow. Axonemal dyneins are evolutionarily and biochemically distinct from cytoplasmic dyneins that transport cargo, and the mechanisms regulating their localization and function are poorly understood. Here, we report a single-particle cryo-EM reconstruction of a three-headed axonemal dynein natively bound to doublet microtubules isolated from cilia. The slanted conformation of the axonemal dynein causes interaction of its motor domains with the neighboring dynein complex. Our structure shows how a heterotrimeric docking complex specifically localizes the linear array of axonemal dyneins to the doublet microtubule by directly interacting with the heavy chains. Our structural analysis establishes the arrangement of conserved heavy, intermediate and light chain subunits, and provides a framework to understand the roles of individual subunits and the interactions between dyneins during ciliary waveform generation.

The geometric clutch at 20: stripping gears or gaining traction?

It has been 20 years since the geometric clutch (GC) hypothesis was first proposed. The core principle of the GC mechanism is fairly simple. When the axoneme of a eukaryotic flagellum is bent, mechanical stress generates forces transverse to the outer doublets (t-forces). These t-forces can push doublets closer together or pry them apart. The GC hypothesis asserts that changes in the inter-doublet spacing caused by t-forces are responsible for the activation and deactivation of the dynein motors, that creates the beat cycle. A series of computer models utilizing the clutch mechanism has shown that it can simulate ciliary and flagellar beating. The objective of the present review is to assess where things stand with the GC hypothesis in the clarifying light of new information. There is considerable new evidence to support the hypothesis. However, it is also clear that it is necessary to modify some of the original conceptions of the hypothesis so that it can be consistent with the results of recent experimental and ultrastructural studies. In particular, dynein deactivation by t-forces must be able to occur with dyneins that remain attached to the B-subtubule of the adjacent doublet.

Computer simulation of flagellar movement X: doublet pair splitting and bend propagation modeled using stochastic dynein kinetics

Experimental observations on cyclic splitting and bending by a flagellar doublet pair are modeled using forces obtained from a model for dynein mechanochemistry, based on ideas introduced by Andrew Huxley and Terrill Hill and extended previously for modeling flagellar movements. The new feature is elastic attachment of dynein to the A doublet, which allows movement perpendicular to the A doublet and provides adhesive force that can strain attached dyneins. This additional strain influences the kinetics of dynein attachment and detachment. Computations using this dynein model demonstrate that very simple and realistic ideas about dynein mechanochemistry are sufficient for explaining the separation and reattachment seen experimentally with flagellar doublet pairs. Additional simulations were performed after adding a "super-adhesion" elasticity. This elastic component is intended to mimic interdoublet connections, normally present in an intact axoneme, that would prevent visible splitting but allow sufficient separation to cause dynein detachment and cessation of shear force generation. This is the situation envisioned by Lindemann's "geometric clutch" hypothesis for control of dynein function in flagella and cilia. The simulations show abrupt disengagement of the "clutch" at one end of a bend, and abrupt reengagement of the "clutch" at the other end of a bend, ensuring that active sliding is only operating where it will cause bend propagation from base to tip.

Flagellar and ciliary beating: the proven and the possible

The working mechanism of the eukaryotic flagellar axoneme remains one of nature's most enduring puzzles. The basic mechanical operation of the axoneme is now a story that is fairly complete; however, the mechanism for coordinating the action of the dynein motor proteins to produce beating is still controversial. Although a full grasp of the dynein switching mechanism remains elusive, recent experimental reports provide new insights that might finally disclose the secrets of the beating mechanism: the special role of the inner dynein arms, especially dynein I1 and the dynein regulatory complex, the importance of the dynein microtubule-binding affinity at the stalk, and the role of bending in the selection of the active dynein group have all been implicated by major new evidence. This Commentary considers this new evidence in the context of various hypotheses of how axonemal dynein coordination might work.

Simulation of cyclic dynein-driven sliding, splitting, and reassociation in an outer doublet pair

A regular cycle of dynein-driven sliding, doublet separation, doublet reassociation, and resumption of sliding was previously observed by Aoyama and Kamiya in outer doublet pairs obtained after partial dissociation of Chlamydomonas flagella. In the work presented here, computer programming based on previous simulations of oscillatory bending of microtubules was extended to simulate the cycle of events observed with doublet pairs. These simulations confirm the straightforward explanation of this oscillation by inactivation of dynein when doublets separate and resumption of dynein activity after reassociation. Reassociation is augmented by a dynein-dependent "adhesive force" between the doublets. The simulations used a simple mathematical model to generate velocity-dependent shear force, and an independent elastic model for adhesive force. Realistic results were obtained with a maximum adhesive force that was 36% of the maximum shear force. Separation between a pair of doublets is the result of a buckling instability that also initiates a period of uniform sliding that enlarges the separation. A similar instability may trigger sliding initiation events in flagellar bending cycles.

The Geometric Clutch as a Working Hypothesis for Future Research on Cilia and Flagella

The Geometric Clutch hypothesis contends that the forces transverse to the flagellar axis (t-forces) act on the axonemal scaffold to regulate flagellar beating. T-forces develop as the product of the curvature and the accumulated tension or compression on the doublet microtubules. In this respect, t-force is a mediator of self-organizing behavior. It arises from the collective action of the assemblage of dynein motors on the structural components of the axoneme and, in turn, imparts order to the sequence of activation and deactivation of the dynein. At the switch point of the flagellar beat, the magnitude of the t-force per micron of flagellum is approximately equal to the sum total of dynein force that can be generated per micron of flagellum. This suggests that the t-force could directly overcome the force-producing dynein bridges and terminate their action. However, many questions remain to be answered concerning the behavior of the axonemal scaffold under stress. Little is known of the force-bearing capacity of the radial spokes and the central pair (cp) projections. The properties of these structures will determine how t-force is distributed within the axoneme. The mechanical and elastic properties of the dynein arms and nexin links need to be better understood to determine how they respond to the application of t-force. In the framework of the Geometric Clutch hypothesis these are the issues that are most important to explore if we are to understand how the flagellum works.

Cyclical interactions between two outer doublet microtubules in split flagellar axonemes

The beating of cilia and flagella is based on the localized sliding between adjacent outer doublet microtubules; however, the mechanism that produces oscillatory bending is unclear. To elucidate this mechanism, we examined the behavior of frayed axonemes of Chlamydomonas by using high-speed video recording. A pair of doublet microtubules frequently displayed association and dissociation cycles in the presence of ATP. In many instances, the dissociation of two microtubules was not accompanied by noticeable bending, suggesting that the dynein-microtubule interaction is not necessarily regulated by the microtubule curvature. On rare occasions, association and dissociation occurred simultaneously in the same interacting pair, resulting in a tip-directed movement of a stretch of gap between the pair. Based on these observations, we propose a model for cyclical bend propagation in the axoneme.

Basal sliding and the mechanics of oscillation in a mammalian sperm flagellum

The mechanism of oscillation in cilia and flagella has been a long-standing mystery. This article raises the possibility of a mechanical explanation based on new findings relating to where in the flagellum microtubule sliding can occur--and where it cannot occur. All theoretical analyses of flagellar bending have until now made the assumption that sliding displacements at the base of the flagellum cannot occur. One consequence of this has been the need to accept that sliding must be transmitted through propagating bends, an idea that has been tolerated even though it becomes paradoxical if bends are the result of resistance to sliding. Our observations, of spermatozoa from the chinchilla, have led us to a contradictory view. We have shown directly, by light microscopy and by two methods of electron microscopy, that basal sliding does occur. Also, evidence from video microscopy indicates that a propagating bend cannot transmit sliding through it. We have analyzed a movement pattern in which the beat frequency increases fourfold in a phasic manner. Our analysis of this suggests that new bends terminate when no further sliding is possible. At this point the bend direction immediately reverses. That is, the flagellar beat frequency increases when there is a limitation to sliding. One can see directly the alternation in basal sliding direction under these circumstances. This suggests a mechanism for the initiation of a new bend in the opposite direction to the bend just completed: we propose that the initiating trigger is the reversal of elastic deformations at the base, which reverses the direction of interdoublet sliding.

Structural-functional relationships of the dynein, spokes, and central-pair projections predicted from an analysis of the forces acting within a flagellum

In the axoneme of eukaryotic flagella the dynein motor proteins form crossbridges between the outer doublet microtubules. These motor proteins generate force that accumulates as linear tension, or compression, on the doublets. When tension or compression is present on a curved microtubule, a force per unit length develops in the plane of bending and is transverse to the long axis of the microtubule. This transverse force (t-force) is evaluated here using available experimental evidence from sea urchin sperm and bull sperm. At or near the switch point for beat reversal, the t-force is in the range of 0.25-1.0 nN/ micro m, with 0.5 nN/ micro m the most likely value. This is the case in both beating and arrested bull sperm and in beating sea urchin sperm. The total force that can be generated (or resisted) by all the dyneins on one micron of outer doublet is also approximately 0.5 nN. The equivalence of the maximum dynein force/ micro m and t-force/ micro m at the switch point may have important consequences. Firstly, the t-force acting on the doublets near the switch point of the flagellar beat is sufficiently strong that it could terminate the action of the dyneins directly by strongly favoring the detached state and precipitating a cascade of detachment from the adjacent doublet. Secondly, after dynein release occurs, the radial spokes and central-pair apparatus are the structures that must carry the t-force. The spokes attached to the central-pair projections will bear most of the load. The central-pair projections are well-positioned for this role, and they are suitably configured to regulate the amount of axoneme distortion that occurs during switching. However, to fulfill this role without preventing flagellar bend formation, moveable attachments that behave like processive motor proteins must mediate the attachment between the spoke heads and the central-pair structure.

Functional diversity of axonemal dyneins as studied in Chlamydomonas mutants

Cilia and flagella of most organisms are equipped with two kinds of motor protein complex, the inner and outer dynein arms. The two arms were previously thought to be similar to each other, but recent studies using Chlamydomonas mutants indicate that they differ significantly in subunit structure and arrangement within the axoneme. For example, whereas the outer dynein arm exists as a single protein complex containing three heavy chains, the inner dynein arm comprises seven different subspecies each containing one or two discrete heavy chains. Furthermore, the two kinds of arms appear to differ in function also. Most strikingly, our studies suggest that inner-arm dynein, but not outer-arm dynein, is under the control of the central pair microtubules and radial spokes. The axoneme thus appears to be equipped with two rather distinct systems for beating: one involving inner-arm dyneins, the central pair and radial spokes, and the other involving outer-arm dynein alone.

A study of helical and planar waves on sea urchin sperm flagella, with a theory of how they are generated

When the spermatozoon of Echinus esculentus swims in sea water containing methyl cellulose (viscosity 1.5-4 Pa s), its flagellum may generate either a helical or a planar waveform, each type being stable. The helical wave, which is dextral, is complicated by the concurrent passage of miniature waves along it. These miniature waves have a pulsatile origin in the neck region of the spermatozoon. Our videotape analysis indicates that there are two pulses of mechanical activity for each true cycle of the helical wave. (The true helical frequency was obtained from the apparent wave frequency and the roll frequency of the sperm head, the latter being detectable in some sperm when lit stroboscopically.) The planar wave has a meander shape. During the propagation of planar waves, the sliding displacements are adjustable in either direction; moribund flagella can undergo unrestricted sliding. The planar waves are, in fact, exactly planar only at interfaces. Otherwise, there tend to be torsions in the interbend segments between planar bends. Mechanical stimulation of the flagellum can cause a sudden transition from the helical to the planar waveform. To account for the two modes of beating, we advance the hypothesis that circumferential linkages yield beyond a threshold strain. Whether this yield point is exceeded, we suggest, depends upon the balance between the active shear force and the external viscosity (among other factors). We propose that a subthreshold force originates in one array and then triggers the other dynein arrays circumferentially, but unidirectionally, around the base of the flagellum; whereas a suprathreshold force provokes bi-directional circumferential triggering. These may be the two patterns of activation that result in helical and planar waveforms, respectively. The transition from helical to planar bending may result from an increment in the force produced by the dynein motors. The pulsatile origin of the helical wave resembles behaviour described previously for spermatozoa of Ciona intestinalis and of the quail Coturnix coturnix.

Transient disruptions of axonemal structure and microtubule sliding during bend propagation by Ciona sperm flagella

Demembranated sperm flagella of Ciona were reactivated at increased salt concentrations (0.45 to 0.5 M K acetate). In addition to a decrease in amplitude of propagated bends, some flagella switch between "stable" and "transient" bending cycles. In the transient bending cycles, there is increased intermicrotubule sliding, in the direction that forms a new principal bend at the base of the flagellum, during the first half of a bending cycle. The magnitude of this increased sliding may be as much as 1 radian, or 0.06 micron between adjacent doublet microtubules. Most transient bending patterns also show a characteristic disruption of axonemal structure, involving separation between strands of microtubule doublets over a distance of up to 5 microns, occurring within a principal bend, typically about 16 microns from the base of the flagellum. The disruptions usually disappear after the principal bend propagates beyond the region of the disruption. Formation of these disruptions requires additional sliding, in the direction that would form a principal bend at the base of the flagellum, of up to about 0.3 micron. Formation of these disruptions may be explained by weakening of structural interactions by increased salt concentration and transverse forces, proportional to curvature and transmitted force, that will tend to separate doublets in a bend. These observations indicate that an actively beating flagellum possesses active sliding capability that is activated but not expressed during normal bend initiation and propagation. The initiation and propagation of flagellar bends may not be explicable solely in terms of local activation and inactivation of dynein-driven sliding.

A model for flagellar motility

Experimental investigation has provided a wealth of structural, biochemical, and physiological information regarding the motile mechanism of eukaryotic flagella/cilia. This chapter surveys the available literature, selectively focusing on three major objectives. First, it attempts to identify those conserved structural components essential to providing motile function in eukaryotic axonemes. Second, it examines the relationship between these structural elements to determine the interactions that are vital to the mechanism of flagellar/ciliary beating. Third, the vital principles of these interactions are incorporated into a tractable theoretical model, referred to as the Geometric Clutch, and this hypothetical scheme is examined to assess its compatibility with experimental observations.

Ability of paralyzed flagella mutants of Chlamydomonas to move

Chlamydomonas mutants missing the central pair or radial spokes are paralyzed despite the fact that they have the full wild-type complement of functional dynein ATPases. We show here that these mutants can move under conditions of low ATP concentration, a combination of ATP and ADP, and a combination of ATP and ribose-modified ATP analogs. These conditions suggest an inhibitory role of ATP and that this inhibition can be relieved by ADP or analogs. The function of the central-pair/radial spoke complex may be to release this ATP inhibition in a controlled manner.

Novel mode of hyper-oscillation in the paralyzed axoneme of a Chlamydomonas mutant lacking the central-pair microtubules

The flagellar axoneme of the mutant pf18 lacking the central pair does not beat, but undergoes a nanometer-scale, high-frequency oscillation (hyper-oscillation) in the presence of ATP [Yagi et al., 1994: Cell Motil. Cytoskeleton 29:177-185]. The present study demonstrates that the amplitude of the hyper-oscillation increases significantly in the simultaneous presence of ATP and ADP. In addition, the hyper-oscillation under these conditions sometimes takes on an exceptionally simple asymmetric pattern, in which the maximal shearing velocity exceeds 50 microns/sec, much higher than the maximal velocity of ordinary dynein-microtubule sliding. The asymmetric oscillation thus appears to be at least partly driven by an internal elastic force. Its amplitude suggests that the axoneme has an elastic component that can be stretched by as long as 0.1 micron. Analyses of the asymmetric pattern further suggests that the axonemal dyneins have a tendency to attach to and detach from the doublets cooperatively and that the mechanochemical cycle of dynein has an inherent refractory period of about 2 msec, during which dynein cannot interact with microtubules.

A model of flagellar and ciliary functioning which uses the forces transverse to the axoneme as the regulator of dynein activation

Ciliary and flagellar motion is driven by the dynein-tubulin interaction between adjacent doublets of the axoneme, and the resulting sliding displacements are converted into axonemal bends that are propagated. When the axoneme is bent in the normal beating plane, force develops across the axoneme in the plane of the bend. This transverse force (t-force) has maximal effect on the interdoublet spacing of outer doublets 2-4 on one side of the axoneme and doublets 7-9 on the opposite side. Episodes of sliding originates as the t-force brings these doublets into closer proximity (allowing dynein bridges to form) and are terminated when these doublets are separated from each other by the t-force. A second factor, the adhesive force of the dynein-tubulin attachments (bridges), also acts to pull neighboring doublets closer together. This force resists termination of a sliding episode once initiated, and acts locally to give the population of dynein bridges a type of excitability. In other words, as bridges form, the probability of nearby bridges attaching is increased by a positive feedback exerted through the interdoublet spacing. A conceptual working hypothesis explaining the behavior of cilia and flagella is proposed based on the above concepts. Additionally, the feasibility of this proposed mechanism is demonstrated using a computer simulation. The simulation uses a Monte Carlo-type algorithm for dynein attachment and adhesive force, together with a geometric evaluation of the t-force on the key microtubule pairs. This model successfully develops spontaneous oscillations from any starting configuration (including a straight position). It is compatible with the physical dimensions, mechanical properties and bridge forces measured in real cilia and flagella. In operation, it exhibits many of the observed actions of cilia and flagella, most notably wave propagation and the ability to produce both cilia-like and flagella-like waveforms.

Excitable dynein model with multiple active sites for large-amplitude oscillations and bend propagation in flagella

The formal excitable dynein model proposed by Murase et al. (1989, J. theor. Biol. 139, 413-430) is modified to produce large-amplitude oscillations and excitability. The present model assumes that (i) each dynein arm has multiple active sites, which are distributed along most of the 24-nm distance between adjacent B-subtubule attachment sites; and (ii) any given dynein molecule tends to produce force continuously during interdoublet sliding in one direction and to produce little force during sliding in the opposite direction. Since no sliding motion occurs without superthreshold perturbations in the form of the sliding displacement, this new model also possesses an excitable nature. Once passive elastic components (e.g. nexin links and radial spokes) are incorporated into this model, oscillations with large amplitudes result. To test the ability of the model for bend propagation without a curvature-control mechanism, forced oscillations are applied to the basal end of the flagellum by the sliding displacement. It is found that bend propagation can occur even in the absence of a curvature-control mechanism.