The architecture of outer dynein arms in situ

Cryo-electron tomography: gaining insight into cellular processes by structural approaches

Visualization of cellular processes at a resolution of the individual protein should involve integrative and complementary approaches that can eventually draw realistic functional and cellular landscapes. Electron tomography of vitrified but otherwise unaltered cells emerges as a central method for three-dimensional reconstruction of cellular architecture at a resolution of 2-6 nm. While a combination of correlative light-based microscopy with cryo-electron tomography (cryo-ET) provides medium-resolution insight into pivotal cellular processes, fitting high-resolution structural approaches, for example, X-ray crystallography, into reconstructed macromolecular assemblies provides unprecedented information on native protein assemblies. Thus, cryo-ET bridges the resolution gap between cellular and structural biology. In this article, we focus on the study of eukaryotic cells and macromolecular complexes in a close-to-life-state. We discuss recent developments and structural findings enabling major strides to be made in understanding complex physiological functions.

Sperm flagella: comparative and phylogenetic perspectives of protein components

Sperm motility is necessary for the transport of male DNA to eggs in species with both external and internal fertilization. Flagella comprise several proteins for generating and regulating motility. Central cytoskeletal structures called axonemes have been well conserved through evolution. In mammalian sperm flagella, two accessory structures (outer dense fiber and the fibrous sheath) surround the axoneme. The axonemal bend movement is based on the active sliding of axonemal doublet microtubules by the molecular motor dynein, which is divided into outer and inner arm dyneins according to positioning on the doublet microtubule. Outer and inner arm dyneins play different roles in the production and regulation of flagellar motility. Several regulatory mechanisms are known for both dyneins, which are important in motility activation and chemotaxis at fertilization. Although dynein itself has certain properties that contribute to the formation and propagation of flagellar bending, other axonemal structures-specifically, the radial spoke/central pair apparatus-have essential roles in the regulation of flagellar bending. Recent genetic and proteomic studies have explored several new components of axonemes and shed light on the generation and regulation of sperm motility during fertilization.

Cholesterol attenuates and prevents bilayer damage and breakdown in lipoperoxidized model membranes. A spin labeling EPR study

The stabilizing effect of cholesterol on oxidized membranes has been studied in planar phospholipid bilayers and multilamellar 1-palmitoyl-2-linoleoyl-phosphatidylcholine vesicles also containing either 1-palmitoyl-2-glutaroyl-phosphatidylcholine or 1-palmitoyl-2-(13-hydroxy-9,11-octadecanedienoyl)-phosphatidylcholine oxidized phosphatidylcholine in variable ratio. Lipid peroxidation-dependent membrane alterations in the absence and in the presence of cholesterol were analyzed using Electron Paramagnetic Resonance spectroscopy of the model membranes spin labelled with either cholestane spin label (3-DC) or phosphatidylcholine spin label (5-DSPC). Cholesterol, added to lipid mixtures up to 40% final molar ratio, decreased the inner bilayer disorder as compared to cholesterol-free membranes and strongly reduced bilayer alterations brought about by the two oxidized phosphatidylcholine species. Furthermore, Sepharose 4B gel-chromatography and cryo electron microscopy of aqueous suspensions of the lipid mixtures clearly showed that cholesterol is able to counteract the micelle forming tendency of pure 1-palmitoyl-2-glutaroyl-phosphatidylcholine and to sustain multilamellar vesicles formation. It is concluded that membrane cholesterol may exert a beneficial and protective role against bilayer damage caused by oxidized phospholipids formation following reactive oxygen species attack to biomembranes.

Single-particle electron cryotomography (cryoET)

Electron cryotomography (cryoET) is capable of yielding 3D reconstructions of cells and large-macromolecular machines. It does not depend on fixing, staining, or embedding, so the contrast is related to the mass density of the specimen. The 3D reconstruction itself does not require that the specimen consist of identical, conformationally homogeneous units in random orientations, as is the ideal case for single-particle reconstruction from 2D images. However, if the specimen contains multiple copies of a macromolecular assembly, these copies can be extracted as 3D subvolumes from the tomographic reconstruction, aligned to each other, and averaged to achieve higher signal-to-noise (S/N) ratios and higher resolution. If conformational variability is present, it is more straightforward to separate the conformational heterogeneity from the orientation of the particles using the 3D information from the subvolumes than it is for single-particle reconstructions. This chapter covers the techniques of detecting, classifying, aligning, and averaging subvolumes (subtomograms) extracted from cryoET reconstructions. It considers methods for dealing with the unique problems encountered in tomographic analysis, such as the absence of data in the "missing wedge," and the overall extremely low S/N ratio inherent in cryoET. It also reviews applications of the inverse problem, that of orienting a template back into a tomogram, to determine the position of a molecule in the context of a whole cell.

Towards quantitative 3D imaging of the osteocyte lacuno-canalicular network

Osteocytes are the most abundant cells in bone and the only cells embedded in the bone mineral matrix. They form an extended, three-dimensional (3D) network, whose processes interconnecting the cell bodies reside in thin canals, the canaliculi. Together with the osteocyte lacunae, the canaliculi form the lacuno-canalicular network (LCN). As the negative imprint of the cellular network within bone tissue, the LCN morphology is considered to play a central role for bone mechanosensation and mechanotransduction. However, the LCN has neither been visualized nor quantified in an adequate way up to now. On this account, this article summarizes the current state of knowledge of the LCN morphology and then reviews different imaging methods regarding the quantitative 3D assessment of bone tissue in general and of the LCN in particular. These imaging methods will provide new insights in the field of bone mechanosensation and mechanotransduction and thus, into processes of strain sensation and transduction, which are tightly associated with osteocyte viability and bone quality.

Silencing of a putative inner arm dynein heavy chain results in flagellar immotility in Trypanosoma brucei

The Trypanosoma brucei flagellum controls motility and is crucial for cell polarity and division. Unique features of trypanosome motility suggest that flagellar beat regulation in this organism is unusual and worthy of study. The flagellar axoneme, required for motility, has a structure that is highly conserved among eukaryotes. Of the several dyneins in the axonemal inner arm complex, dynein f is thought to control flagellar waveform shape. A T. brucei gene predicted to encode the dynein f alpha heavy chain, TbDNAH10, was silenced using RNA interference in procyclic T. brucei cells. This resulted in immotile flagella, showing no movement except for occasional slight twitches at the tips. Cell growth slowed dramatically and cells were found in large clusters. Microscopic analysis of silenced cultures showed many cells with detached flagella, sometimes entangled between multiple cells. DAPI staining showed an increased frequency of mis-positioned kinetoplasts and multinucleate cells, suggesting that these cells experience disruption at an early cell cycle stage, probably secondary to the motility defect. TEM images showed apparently normal axonemes and no discernable defects in inner arm structure. This study demonstrates the use of RNAi as an effective method to study very large genes such as dynein heavy chains (HCs), and the immotility phenotype of these dynein knockdowns suggests that an intact inner arm is necessary for flagellar beating in T. brucei. Since analogous mutants in Chlamydomonas reinhardtii retain motility, this phenotype likely reflects differences in requirements for motility and/or dynein assembly between the two organisms and these comparative studies will help elucidate the mechanisms of flagellar beat regulation.

Strikingly fast microtubule sliding in bundles formed by Chlamydomonas axonemal dynein

Chlamydomonas axonemal extracts containing outer-arm dynein bundle microtubules when added in the absence of ATP. The bundles dissociate after addition of ATP (Haimo et al., Proc Natl Acad Sci USA 76:5759-5768, 1979). In the present study, we investigated the ATP-induced bundle dissociation process using caged ATP. Application of approximately 0.5 mM ATP induced microtubule sliding at approximately 30 microm.s(-1), which was 1.5 times faster than the microtubule sliding observed in protease-treated axonemes and five times faster than microtubule gliding on glass surfaces coated with outer-arm dynein. Bundles formed by mutant dynein molecules that lack one of the three heavy chains (HCs) displayed similar high-speed intermicrotubule sliding. These results suggest that Chlamydomonas outer-arm dynein molecules, when aligned, can translocate microtubules at high speed and that the high-speed sliding under load-free conditions does not require the complete set of the three HCs. It is likely that each of the three HCs has the ability to produce high-speed sliding, which should be an important property for their cooperation.

Bending of the "9+2" axoneme analyzed by the finite element method

Many data demonstrate that the regulation of the bending polarity of the "9+2" axoneme is supported by the curvature itself, making the internal constraints central in this process, adjusting either the physical characteristics of the machinery or the activity of the enzymes involved in different pathways. Among them, the very integrated Geometric Clutch model founds this regulation on the convenient adjustments of the probability of interaction between the dynein arms and the beta-tubulin monomers of the outer doublet pairs on which they walk. Taking into consideration (i) the deviated bending of the outer doublets pairs (Cibert, C., Heck, J.-V., 2004. Cell Motil. Cytoskeleton 59, 153-168), (ii) the internal tensions of the radial spokes and the tangential links (nexin links, dynein arms), (iii) a theoretical 5 microm long proximal segment of the axoneme and (iv) the short proximal segment of the axoneme, we have reevaluated the adjustments of these intervals using a finite element approach. The movements we have calculated within the axonemal cylinder are consistent with the basic hypothesis that found the Geometric Clutch model, except that the axonemal side where the dynein arms are active increases the intervals between the two neighbor outer doublet pairs. This result allows us to propose a mechanism of bending reversion of the axoneme, involving the concerted ignition of the molecular engines along the two opposite sides of the axoneme delineated by the bending plane.

Nucleotide-induced global conformational changes of flagellar dynein arms revealed by in situ analysis

Outer and inner dynein arms generate force for the flagellar/ciliary bending motion. Although nucleotide-induced structural change of dynein heavy chains (the ATP-driven motor) was proven in vitro, our lack of knowledge in situ has precluded an understanding of the bending mechanism. Here we reveal nucleotide-induced global structural changes of the outer and inner dynein arms of Chlamydomonas reinhardtii flagella in situ using electron cryotomography. The ATPase domains of the dynein heavy chains move toward the distal end, and the N-terminal tail bends sharply during product release. This motion could drive the adjacent microtubule to cause a sliding motion. In contrast to in vitro results, in the presence of nucleotides, outer dynein arms coexist as clusters of apo or nucleotide-bound forms in situ. This implies a cooperative switching, which may be related to the mechanism of bending.

Is the curvature of the flagellum involved in the apparent cooperativity of the dynein arms along the "9+2" axoneme?

In a recent study [Cibert, 2008. Journal of Theoretical Biology 253, 74-89], by assuming that walls of microtubules are involved in cyclic compression/dilation equilibriums as a consequence of cyclic curvature of the axoneme, it was proposed that local adjustments of spatial frequencies of both dynein arms and beta-tubulin monomers facing series create propagation of joint probability waves of interaction (JPI) between these two necessary partners. Modeling the occurrence of these probable interactions along the entire length of an axoneme between each outer doublet pair (without programming any cooperative dialog between molecular complexes) and the cyclic attachment of two facing partners, we show that such constituted active couples are clustered. Along a cluster the dynein arms exhibit a small phase shift with respect to the order according to which they began their cycle after being linked to a beta-tubulin monomer. The number of couples included in these clusters depends on the probability of interaction between the dynein arms and the beta-tubulin, on the location of the outer doublet pairs around the axonemal cylinder, and on the local bending of the axoneme; around the axonemal cylinder, the faster and the larger the sliding, the shorter the clusters. This mechanism could be involved in the apparent cooperativity of molecular motors and the beta-tubulin monomers, since it is partially controlled by local curvature, and the cluster length is inversely proportional to the sliding activity of the outer doublet pairs they link.

Novel type of bicellar disks from a mixture of DMPC and DMPE-DTPA with complexed lanthanides

We report on the formation of bicelles from a mixture of dimyristoylphosphatidylcholine (DMPC) and the chelator-lipid dimyristoylphosphatidylethanolamine-diethylenetriaminepentaacetate (DMPE-DTPA) with complexed lanthanides, either thulium (Tm(3+)) or lanthanum (La(3+)). The two phospholipids used have the same acyl-chain length but differ in headgroup size and chemical structure. The total lipid concentration was 15 mM, and the molar ratio of DMPC to DMPE-DTPA was 4:1. The system was studied with small angle neutron scattering (SANS) in a magnetic field, cryo-transmission electron microscopy (cryo-TEM), and (31)P NMR spectroscopy. We found that, after appropriate preparation steps, that is, extrusion through a polycarbonate membrane followed by a cooling step, monodisperse small unilamellar disks (flat cylinders called bicelles) are formed. They have a radius of 20 nm and a bilayer thickness of about 4 nm and are stable in the investigated temperature range of 2.5-30 degrees C. Fitting of SANS data with a form factor for partly aligned flat cylinders shows that the bicelles are slightly orientable in a magnetic field of 8 T if DMPE-DTPA is complexed with Tm(3+).

Quick shear-flow alignment of biological filaments for X-ray fiber diffraction facilitated by methylcellulose

X-ray fiber diffraction is one of the most useful methods for examining the structural details of live biological filaments under physiological conditions. To investigate biologically active or labile materials, it is crucial to finish fiber alignment within seconds before diffraction analysis. However, the conventional methods, e.g., magnetic field alignment and low-speed centrifugations, are time-consuming and not very useful for such purposes. Here, we introduce a new alignment method using a rheometer with two parallel disks, which was applied to observe fiber diffractions of axonemes, tobacco mosaic tobamovirus, and microtubules. We found that fibers were aligned within 5 s by giving high shear flow (1000-5000 s(-1)) to the medium and that methylcellulose contained in the medium (approximately 1%) was essential to the accomplishment of uniform orientation with a small angular deviation (<5 degrees). The new alignment method enabled us to execute structure analyses of axonemes by small-angle x-ray diffraction. Since this method was also useful for the quick alignment of purified microtubules, as well as tobacco mosaic tobamovirus, we expect that we can apply it to the structural analysis of many other biological filaments.

The dynein regulatory complex is the nexin link and a major regulatory node in cilia and flagella

Elegant cryoelectron tomography reveals that the nexin link between microtubule doublets in 9 + 2 axonemal structures, critical for their ability to bend, is the dynein regulatory complex.

Cilia and flagella are highly conserved microtubule (MT)-based organelles with motile and sensory functions, and ciliary defects have been linked to several human diseases. The 9 + 2 structure of motile axonemes contains nine MT doublets interconnected by nexin links, which surround a central pair of singlet MTs. Motility is generated by the orchestrated activity of thousands of dynein motors, which drive interdoublet sliding. A key regulator of motor activity is the dynein regulatory complex (DRC), but detailed structural information is lacking. Using cryoelectron tomography of wild-type and mutant axonemes from Chlamydomonas reinhardtii, we visualized the DRC in situ at molecular resolution. We present the three-dimensional structure of the DRC, including a model for its subunit organization and intermolecular connections that establish the DRC as a major regulatory node. We further demonstrate that the DRC is the nexin link, which is thought to be critical for the generation of axonemal bending.

Chlamydomonas cryopreparation methods for the 3-D analysis of cellular organelles

Chlamydomonas reinhardtii is a popular model organism in modern cell biology. Historically, methods for preparing this cell for transmission electron microscopy have used conventional chemical fixation that can result in artifacts that affect the 3-D organization of the cell. We have developed improved methods of specimen preparation that involve high-pressure freezing followed by freeze-substitution that are particularly well suited for 3-D studies (O'Toole et al., 2003, 2007). In this chapter, we describe the details of our cryopreparation methods for the optimal preservation of whole cells for immunocytochemistry and electron tomography. Examples are presented that show the utility of this approach for studying the 3-D architecture of membrane systems and cytoskeletal arrays in intact cells.

Electron-tomographic analysis of intraflagellar transport particle trains in situ

Ultrastructural study of Chlamydomonas cilia shows that anterograde IFT particles form trains that are long and narrow, while retrograde IFT form short, compact particle trains.

Intraflagellar transport (IFT) is the bidirectional movement of multipolypeptide particles between the ciliary membrane and the axonemal microtubules, and is required for the assembly, maintenance, and sensory function of cilia and flagella. In this paper, we present the first high-resolution ultrastructural analysis of trains of flagellar IFT particles, using transmission electron microscopy and electron-tomographic analysis of sections from flat-embedded Chlamydomonas reinhardtii cells. Using wild-type and mutant cells with defects in IFT, we identified two different types of IFT trains: long, narrow trains responsible for anterograde transport; and short, compact trains underlying retrograde IFT. Both types of trains have characteristic repeats and patterns that vary as one sections longitudinally through the trains of particles. The individual IFT particles are highly complex, bridged to each other and to the outer doublet microtubules, and are closely apposed to the inner surface of the flagellar membrane.

Asymmetry of inner dynein arms and inter-doublet links in Chlamydomonas flagella

Although the widely shared “9 + 2” structure of axonemes is thought to be highly symmetrical, axonemes show asymmetrical bending during planar and conical motion. In this study, using electron cryotomography and single particle averaging, we demonstrate an asymmetrical molecular arrangement of proteins binding to the nine microtubule doublets in Chlamydomonasreinhardtii flagella. The eight inner arm dynein heavy chains regulate and determine flagellar waveform. Among these, one heavy chain (dynein c) is missing on one microtubule doublet (this doublet also lacks the outer dynein arm), and another dynein heavy chain (dynein b or g) is missing on the adjacent doublet. Some dynein heavy chains either show an abnormal conformation or were replaced by other proteins, possibly minor dyneins. In addition to nexin, there are two additional linkages between specific pairs of doublets. Interestingly, all these exceptional arrangements take place on doublets on opposite sides of the axoneme, suggesting that the transverse functional asymmetry of the axoneme causes an in-plane bending motion.

An outer arm dynein light chain acts in a conformational switch for flagellar motility

A system distinct from the central pair-radial spoke complex was proposed to control outer arm dynein function in response to alterations in the mechanical state of the flagellum. In this study, we examine the role of a Chlamydomonas reinhardtii outer arm dynein light chain that associates with the motor domain of the gamma heavy chain (HC). We demonstrate that expression of mutant forms of LC1 yield dominant-negative effects on swimming velocity, as the flagella continually beat out of phase and stall near or at the power/recovery stroke switchpoint. Furthermore, we observed that LC1 interacts directly with tubulin in a nucleotide-independent manner and tethers this motor unit to the A-tubule of the outer doublet microtubules within the axoneme. Therefore, this dynein HC is attached to the same microtubule by two sites: via both the N-terminal region and the motor domain. We propose that this gamma HC-LC1-microtubule ternary complex functions as a conformational switch to control outer arm activity.

Cryo-electron tomography in biology and medicine

During the last six decades electron microscopy (EM) has been essential to ultra-structural studies of the cell to understand the fundamentals of cellular morphology and processes underlying diseases. More recently, electron tomography (ET) has emerged as a novel approach able to provide three-dimensional (3D) information on cells and tissues at molecular level. Electron tomography is comparable to medical tomographic techniques like CAT, PET and MRI in the sense that it provides a 3D view of an object, yet it does so at a cellular scale and with nanometer resolution. Electron tomography has the unique ability to visualize molecular assemblies, cytoskeletal elements and organelles within cells. The three-dimensional perspective it provides has revised our understanding of cellular organization and its relation with morphological changes in normal development and disease. Cryo-electron tomography of vitrified samples at cryogenic temperatures combines excellent structural preservation with direct high-resolution imaging. The use of cryo-preparation and imaging techniques eliminates artifacts induced by plastic embedding and staining of the samples is circumvented. This review describes the technique of cryo-electron tomography, its basic principles, cryo-specimen preparation, tomographic data acquisition and image processing. A number of illustrative examples ranging from whole cells, cytoskeletal filaments, viruses and organelles are presented along with a comprehensive list of research articles employing cryo-electron tomography as the key ultrastuctural technique.

AAA+ Ring and linker swing mechanism in the dynein motor

Dynein ATPases power diverse microtubule-based motilities. Each dynein motor domain comprises a ring-like head containing six AAA+ modules and N- and C-terminal regions, together with a stalk that binds microtubules. How these subdomains are arranged and generate force remains poorly understood. Here, using electron microscopy and image processing of tagged and truncated Dictyostelium cytoplasmic dynein constructs, we show that the heart of the motor is a hexameric ring of AAA+ modules, with the stalk emerging opposite the primary ATPase site (AAA1). The C-terminal region is not an integral part of the ring but spans between AAA6 and near the stalk base. The N-terminal region includes a lever-like linker whose N terminus swings by ∼17 nm during the ATPase cycle between AAA2 and the stalk base. Together with evidence of stalk tilting, which may communicate changes in microtubule binding affinity, these findings suggest a model for dynein's structure and mechanism.

Dynein pulls microtubules without rotating its stalk

Dynein is a microtubule motor that powers motility of cilia and flagella. There is evidence that the relative sliding of the doublet microtubules is due to a conformational change in the motor domain that moves a microtubule bound to the end of an extension known as the stalk. A predominant model for the movement involves a rotation of the head domain, with its stalk, toward the microtubule plus end. However, stalks bound to microtubules have been difficult to observe. Here, we present the clearest views so far of stalks in action, by observing sea urchin, outer arm dynein molecules bound to microtubules, with a new method, "cryo-positive stain" electron microscopy. The dynein molecules in the complex were shown to be active in in vitro motility assays. Analysis of the electron micrographs shows that the stalk angles relative to microtubules do not change significantly between the ADP.vanadate and no-nucleotide states, but the heads, together with their stalks, shift with respect to their A-tubule attachments. Our results disagree with models in which the stalk acts as a lever arm to amplify structural changes. The observed movement of the head and stalk relative to the tail indicates a new plausible mechanism, in which dynein uses its stalk as a grappling hook, catching a tubulin subunit 8 nm ahead and pulling on it by retracting a part of the tail (linker).

Molecular architecture of inner dynein arms in situ in Chlamydomonas reinhardtii flagella

The inner dynein arm regulates axonemal bending motion in eukaryotes. We used cryo-electron tomography to reconstruct the three-dimensional structure of inner dynein arms from Chlamydomonas reinhardtii. All the eight different heavy chains were identified in one 96-nm periodic repeat, as expected from previous biochemical studies. Based on mutants, we identified the positions of the AAA rings and the N-terminal tails of all the eight heavy chains. The dynein f dimer is located close to the surface of the A-microtubule, whereas the other six heavy chain rings are roughly colinear at a larger distance to form three dyads. Each dyad consists of two heavy chains and has a corresponding radial spoke or a similar feature. In each of the six heavy chains (dynein a, b, c, d, e, and g), the N-terminal tail extends from the distal side of the ring. To interact with the B-microtubule through stalks, the inner-arm dyneins must have either different handedness or, more probably, the opposite orientation of the AAA rings compared with the outer-arm dyneins.

Axoneme beta-tubulin sequence determines attachment of outer dynein arms

Axonemes of motile eukaryotic cilia and flagella have a conserved structure of nine doublet microtubules surrounding a central pair of microtubules. Outer and inner dynein arms on the doublets mediate axoneme motility [1]. Outer dynein arms (ODAs) attach to the doublets at specific interfaces [2-5]. However, the molecular contacts of ODA-associated proteins with tubulins of the doublet microtubules are not known. We report here that attachment of ODAs requires glycine 56 in the beta-tubulin internal variable region (IVR). We show that in Drosophila spermatogenesis, a single amino acid change at this position results in sperm axonemes markedly deficient in ODAs. Moreover, we found that axonemal beta-tubulins throughout the phylogeny have invariant glycine 56 and a strongly conserved IVR, whereas nonaxonemal beta-tubulins vary widely in IVR sequences. Our data reveal a deeply conserved physical requirement for assembly of the macromolecular architecture of the motile axoneme. Amino acid 56 projects into the microtubule lumen [6]. Imaging studies of axonemes indicate that several proteins may interact with the doublet-microtubule lumen [3, 4, 7, 8]. This region of beta-tubulin may determine the conformation necessary for correct attachment of ODAs, or there may be sequence-specific interaction between beta-tubulin and a protein involved in ODA attachment or stabilization.

Partially functional outer-arm dynein in a novel Chlamydomonas mutant expressing a truncated gamma heavy chain

The outer dynein arm of Chlamydomonas flagella contains three heavy chains (alpha, beta, and gamma), each of which exhibits motor activity. How they assemble and cooperate is of considerable interest. Here we report the isolation of a novel mutant, oda2-t, whose gamma heavy chain is truncated at about 30% of the sequence. While the previously isolated gamma chain mutant oda2 lacks the entire outer arm, oda2-t retains outer arms that contain alpha and beta heavy chains, suggesting that the N-terminal sequence (corresponding to the tail region) is necessary and sufficient for stable outer-arm assembly. Thin-section electron microscopy and image analysis localize the gamma heavy chain to a basal region of the outer-arm image in the axonemal cross section. The motility of oda2-t is lower than that of the wild type and oda11 (lacking the alpha heavy chain) but higher than that of oda2 and oda4-s7 (lacking the motor domain of the beta heavy chain). Thus, the outer-arm dynein lacking the gamma heavy-chain motor domain is partially functional. The availability of mutants lacking individual heavy chains should greatly facilitate studies on the structure and function of the outer-arm dynein.

Molecular motors: not quite like clockwork

Models commonly used to explain the mechanism of myosin motors typically include a power stroke that is attributed to a conformational change in the motor domain and amplified by a long lever arm that connects the motor domain to the cargo. Similar models have proved less enlightening in the case of microtubule motors, for which it may be more helpful to consider models involving thermally driven mechanisms.

New insights into the cell biology of insect axonemes

Insects do not possess ciliated epithelia, and cilia/flagella are present in the sperm tail and--as modified cilia--in mechano- and chemosensory neurons. The core cytoskeletal component of these organelles, the axoneme, is a microtubule-based structure that has been conserved throughout evolution. However, in insects the sperm axoneme exhibits distinctive structural features; moreover, several insect groups are characterized by an unusual sperm axoneme variability. Besides the abundance of morphological data on insect sperm flagella, most of the available molecular information on the insect axoneme comes from genetic studies on Drosophila spermatogenesis, and only recently other insect species have been proposed as useful models. Here, we review the current knowledge on the cell biology of insect axoneme, including contributions from both Drosophila and other model insects.

Three-dimensional structure of cytoplasmic dynein bound to microtubules

Cytoplasmic dynein is a large, microtubule-dependent molecular motor (1.2 MDa). Although the structure of dynein by itself has been characterized, its conformation in complex with microtubules is still unknown. Here, we used cryoelectron microscopy (cryo-EM) to visualize the interaction between dynein and microtubules. Most dynein molecules in the nucleotide-free state are bound to the microtubule in a defined conformation and orientation. A 3D image reconstruction revealed that dynein's head domain, formed by a ring-like arrangement of AAA+ domains, is located approximately 280 A away from the center of the microtubule. The order of the AAA+ domains in the ring was determined by using recombinant markers. Furthermore, a 3D helical image reconstruction of microtubules with a dynein's microtubule binding domain [dynein stalk (DS)] revealed that the stalk extends perpendicular to the microtubule. By combining the 3D maps of the dynein-microtubule and DS-microtubule complexes, we present a model for how dynein in the nucleotide-free state binds to microtubules and discuss models for dynein's power stroke.

Recent developments of bio-molecular motors as on-chip devices using single molecule techniques

The integration of microfluidic devices with single molecule motor detection techniques allows chip based devices to reach sensitivity levels previously unattainable.

Molecular determination by electron microscopy of the dynein-microtubule complex structure

Dynein is a minus-end-directed microtubule (MT) motor that is responsible for the wide range of MT-based motility in eukaryotic cells. Detailed mechanism of the dynein chemomechanical conversion is still unknown, partly because the structure of dynein is not studied at high resolution. To address this problem and reconstruct the dynein-MT complex at higher resolution, we have developed new procedures based on single particle analysis. To accurately determine the orientation of the dynein-MT complex, we introduced a "dynein track model" to restrict the possible dynein positions on the images. We tested our procedures by reconstructing structures from simulated dynein-MT complex images. Starting from the simulated noisy images generated using three different models of the dynein-MT complex, we have successfully recovered the original three-dimensional (3-D) structure. We also showed that our procedure is robust against fluctuation of the dynein molecules and can determine the structure even when the dynein position fluctuates to a certain extent. Convergence of the final 3-D structure can be tested with a "two-dimensional (2-D) agreement value," which we introduced to see whether the final structure is a result of overfit from fluctuating dynein or not. When the procedures did not work well due to the fluctuation, we could recognize the failure by this 2-D agreement value. Finally, the actual structure of the dynein-MT complex was determined from actual cryoelectron micrographs of Dictyostelium cytoplasmic dynein-MT complex. This method has revealed the detailed 3-D structures of the dynein-MT complex and will shed light on the motor mechanism of the dynein molecule.

Mechanical properties of inner-arm dynein-f (dynein I1) studied with in vitro motility assays

Inner-arm dynein-f of Chlamydomonas flagella is a heterodimeric dynein. We performed conventional in vitro motility assays showing that dynein-f translocates microtubules at the comparatively low velocity of approximately 1.2 microm/s. From the dependence of velocity upon the surface density of dynein-f, we estimate its duty ratio to be 0.6-0.7. The relation between microtubule landing rate and surface density of dynein-f are well fitted by the first-power dependence, as expected for a processive motor. At low dynein densities, progressing microtubules rotate erratically about a fixed point on the surface, at which a single dynein-f molecule is presumably located. We conclude that dynein-f has high processivity. In an axoneme, however, slow and processive dynein-f could impede microtubule sliding driven by other fast dyneins (e.g., dynein-c). To obtain insight into the in vivo roles of dynein-f, we measured the sliding velocity of microtubules driven by a mixture of dyneins -c and -f at various mixing ratios. The velocity is modulated as a function of the ratio of dynein-f in the mixture. This modulation suggests that dynein-f acts as a load in the axoneme, but force pushing dynein-f molecules forward seems to accelerate their dissociation from microtubules.