Outer Dynein Arms Research Articles

Atomic models of microtubule doublets and dyneins in cilia revealed by cryo-electron microscopy

Microtubule doublets (MTD) in cilia consist of the A-tubule (13 protofilaments) and the B-tubule (likely 10 protofilaments). While 3D molecular arrangement of ciliary proteins is our interest, our knowledge about how dyneins, radial spokes and other proteins bind to MTD was limited, due to the limitation of resolution. We have been investigating the conformation and localization of inner and outer dynein isoforms (Bui et al. (2012) JCB 198, 913) and their conformational change induced by ATP (Movassagh et al. (2010) NSMB 17, 761), radial spokes (Pigino et al. (2011) JCB 195, 673) by cryo-electron tomography (resolution 30A). We newly employed single particle cryo-EM technique and improved resolution to 20A. This enabled us to locate tubulin isoforms and describe interaction and binding of dyneins and other proteins precisely. The arrangement of tubulin dimers in MTD demonstrates difference from the reconstituted microtubule, indicating specific building mechanism of MTDs. Microtubule binding domains (MTBD) of outer arm dyneins bind to the three adjacent protofilaments, between alpha and beta-tubulins within one dimer. The orientation of the stalk changes ~5 degrees during the power stroke caused by rearrangement of the linker domain of dynein with respect to the AAA-ring as we reported (Ueno et al. (2014) Cytoskeleton 71, 412). MTBD of inner arm dyneins bind to one protofilament of the B-tubule, with the exception of dimeric dynein f. The interface of N-terminal tails of inner dyneins and the A-tubule spans over two protofilaments. We will extend our discussion of how this architecture is maintained during the bending motion.

Structure of outer arm dynein molecule in respiratory cilia suggests an alternative mechanism of force generation

Background Cilia are microtubule (MT)-based organelles that extend from the surface of eukaryotic cells. The ciliary movement is generated by microtubule (MT) sliding with axonemal dynein motors, and plays important roles in cell migration and generation of external fluid flow. Since cilia have diverse roles in many tissues and organs in mammal, defects in ciliary activity causes a number of diseases called ciliopathy.

Gene discovery for motile cilia disorders: mutation spectrum in primary ciliary dyskinesia and discovery of mutations in CCDC151

We present a stratification of the genetic basis of primary ciliary dyskinesia (PCD), based on screening >230 individuals for gene mutations using various approaches including whole exome sequencing. PCD is a genetically heterogeneous recessive ciliopathy, characterized by chronic lung disease and laterality and fertility defects arising from cilia and sperm dysmotility. Most PCD is caused by loss of the ciliary outer dynein arm motors (ODA) essential for motility, arising from mutations in ODA subunits or ODA docking and targeting proteins. Gene panel resequencing of candidate ciliopathy genes in affected children from a consanguineous Bedouin-Arabic family has recently revealed a homozygous protein truncating variant in CCDC151 (c.925G>T; p.Glu308*). Parallel exome sequencing combined with autozygosity mapping in a consanguineous UK-Pakistani-origin family highlighted a large autozygous region on chr 19p13 harbouring a homozygous CCDC151 protein-truncating variant (c.1256C>T; pSer419*). Sanger sequencing of CCDC151 in 150 more PCD cases identified another individual carrying c.925G>T. Transmission electron microscopy of respiratory cilia from individuals carrying CCDC151 mutations showed loss of ODA. Consistent with laterality defects in these individuals, we find Ccdc151 expressed in vertebrate left-right organizers. Both homozygous zebrafish and mouse Ccdc151-deficient mutants display situs defects associated with complex heart defects. Immunofluorescence analysis in patients shows that CCDC151 mutations abolish assembly of CCDC151 into respiratory cilia, and furthermore cause a failure in assembly of the ODA component DNAH5 and ODA docking proteins CCDC114 and ARMC4. We conclude that CCDC151 mutations appear to cause PCD by disruption of the axonemal ODA docking complex machinery.

X-Ray Fiber Diffraction Recordings from Oriented Demembranated Chlamydomonas Flagellar Axonemes

The high homology of its axonemal components with humans and a large repertoire of axonemal mutants make Chlamydomonas a useful model system for experiments on the structure and function of eukaryotic cilia and flagella. Using this organism, we explored the spatial arrangement of axonemal components under physiological conditions by small-angle x-ray fiber diffraction. Axonemes were oriented in physiological solution by continuous shear flow and exposed to intense and stable x rays generated in the synchrotron radiation facility SPring-8, BL45XU. We compared diffraction patterns from axonemes isolated from wild-type and mutant strains lacking the whole outer arm (oda1), radial spoke (pf14), central apparatus (pf18), or the α-chain of the outer arm dynein (oda11). Diffraction of the axonemes showed a series of well-defined meridional/layer-line and equatorial reflections. Diffraction patterns from mutant axonemes exhibited a systematic loss/attenuation of meridional/layer-line reflections, making it possible to determine the origin of various reflections. The 1/24 and 1/12 nm−1 meridional reflections of oda1 and oda11 were much weaker than those of the wild-type, suggesting that the outer dynein arms are the main contributor to these reflections. The weaker 1/32 and 1/13.7 nm−1 meridional reflections from pf14 compared with the wild-type suggest that these reflections come mainly from the radial spokes. The limited contribution of the central pair apparatus to the diffraction patterns was confirmed by the similarity between the patterns of the wild-type and pf18. The equatorial reflections were complex, but a comparison with electron micrograph-based models allowed the density of each axonemal component to be estimated. Addition of ATP to rigor-state axonemes also resulted in subtle changes in equatorial intensity profiles, which could report nucleotide-dependent structural changes of the dynein arms. The first detailed description of axonemal reflections presented here serves as a landmark for further x-ray diffraction studies to monitor the action of constituent proteins in functional axonemes.

Kartagener's syndrome: review of a case series.

BackgroundKartagener Syndrome (KS) is a rare autosomal recessive genetic disorder, resulting in a group of clinical manifestations, including bronchiectasis, chronic pansinusitis and situs inversus.MethodsWe hereby reviewed eight cases of this rare entity selected from patients attending our outpatients Respiratory Unit since 2006. Samples of respiratory epithelium were obtained with the method of nasal brushing and sent to a specialized center in order to be studied with electron microscopy. At least 50 cross sections of different cilia from different cells were observed in each specimen to study the axonemal structure. Electron micrographs were taken at a magnification of X 50,000 to determine the orientation of the cilia and at a magnification of X 110,000 to study the axonemal pattern. The incidence of abnormal cilia was expressed as a percentage.ResultsWe observed different ultrastructural defects in our KS patients, including absence of outer dynein arms, absence of outer and inner dynein arms, and absence of the central pair with transposition of a peripheral doublet into the central position. Patient’s follow up lasted till 2014, however two patients with more severe clinical behavior died before.ConclusionsThis is a review of a case series, yet our data has shown that nasal brushing with ultrastructural pathological differentiation may be useful to identify patients with high risk and to develop more complex clinical presentations.

Kartagener’s syndrome: review of a case series

Background: Kartagener Syndrome (KS) is a rare autosomal recessive genetic disorder, resulting in a group of clinical manifestations, including bronchiectasis, chronic pansinusitis and situs inversus.
 Methods: We hereby reviewed eight cases of this rare entity selected from patients attending our outpatients Respiratory Unit since 2006. Samples of respiratory epithelium were obtained with the method of nasal brushing and sent to a specialized center in order to be studied with electron microscopy. At least 50 cross sections of different cilia from different cells were observed in each specimen to study the axonemal structure. Electron micrographs were taken at a magnification of X 50,000 to determine the orientation of the cilia and at a magnification of X 110,000 to study the axonemal pattern. The incidence of abnormal cilia was expressed as a percentage.
 Results: We observed different ultrastructural defects in our KS patients, including absence of outer dynein arms, absence of outer and inner dynein arms, and absence of the central pair with transposition of a peripheral doublet into the central position. Patient’s follow up lasted till 2014, however two patients with more severe clinical behavior died before.
 Conclusions: This is a review of a case series, yet our data has shown that nasal brushing with ultrastructural pathological differentiation may be useful to identify patients with high risk and to develop more complex clinical presentations.

Branchial cilia and sperm flagella recruit distinct axonemal components.

Eukaryotic cilia and flagella have highly conserved 9 + 2 structures. They are functionally diverged to play cell-type-specific roles even in a multicellular organism. Although their structural components are therefore believed to be common, few studies have investigated the molecular diversity of the protein components of the cilia and flagella in a single organism. Here we carried out a proteomic analysis and compared protein components between branchial cilia and sperm flagella in a marine invertebrate chordate, Ciona intestinalis. Distinct feature of protein recruitment in branchial cilia and sperm flagella has been clarified; (1) Isoforms of α- and β-tubulins as well as those of actins are distinctly used in branchial cilia or sperm flagella. (2) Structural components, such as dynein docking complex, tektins and an outer dense fiber protein, are used differently by the cilia and flagella. (3) Sperm flagella are specialized for the cAMP- and Ca2+-dependent regulation of outer arm dynein and for energy metabolism by glycolytic enzymes. Our present study clearly demonstrates that flagellar or ciliary proteins are properly recruited according to their function and stability, despite their apparent structural resemblance and conservation.

Calcium sensors of ciliary outer arm dynein: functions and phylogenetic considerations for eukaryotic evolution.

The motility of eukaryotic cilia and flagella is modulated in response to several extracellular stimuli. Ca2+ is the most critical intracellular factor for these changes in motility, directly acting on the axonemes and altering flagellar asymmetry. Calaxin is an opisthokont-specific neuronal calcium sensor protein first described in the sperm of the ascidian Ciona intestinalis. It binds to a heavy chain of two-headed outer arm dynein in a Ca2+-dependent manner and regulates ‘asymmetric’ wave propagation at high concentrations of Ca2+. A Ca2+-binding subunit of outer arm dynein in Chlamydomonas reinhardtii, the light chain 4 (LC4), which is a Ca2+-sensor phylogenetically different from calaxin, shows Ca2+-dependent binding to a heavy chain of three-headed outer arm dynein. However, LC4 appears to participate in ‘symmetric’ wave propagation at high concentrations of Ca2+. LC4-type dynein light chain is present in bikonts, except for some subclasses of the Excavata. Thus, flagellar asymmetry-symmetry conversion in response to Ca2+ concentration represents a ‘mirror image’ relationship between Ciona and Chlamydomonas. Phylogenetic analyses indicate the duplication, divergence, and loss of heavy chain and Ca2+-sensors of outer arm dynein among excavate species. These features imply a divergence point with respect to Ca2+-dependent regulation of outer arm dynein in cilia and flagella during the evolution of eukaryotic supergroups.

Motile and Sensory Cilia Function in Zebrafish

Advances in developmental genetics and human disease gene cloning have highlighted the essential roles played by cilia in developmental cell fate decisions, left–right asymmetry, and the pathology of human congenital disorders. Cilia-driven fluid flow in the embryonic node highlights the role of motile cilia in the generation of mechanical signals in development. Sensory cilia in photoreceptors and olfactory neurons highlight the role of cilia in phototransduction and G-protein coupled receptor signaling. Using a zebrafish knockdown screen of cilia candidate genes as an in vivo screening platform, we identified c21orf59, ccdc65, and c15orf26 as critical for cilia motility and generation of proper left-right asymmetry. c21orf59 and c15orf26 knockdown in zebrafish blocked outer dynein arm assembly, while ccdc65 knockdown altered cilia beat pattern. To study sensory cilia function we generated a new cilia assay based on calcium biosensor (GCaMP5) expression in zebrafish ciliated olfactory neurons (OSNs). Ciliated OSNs are activated by bile acid olfactory receptors on outward facing terminal sensory cilia. We found that ciliated OSNs responded with a robust fluorescence signal to specific odorants and that the cilia mutant fish oval, (ift88-/-) and ift172 knockdown larvae showed severely shortened OSN cilia and markedly reduced responses to bile acids while other odorant responses were unaffected. In summary, the zebrafish provides a robust platform for cilia gene discovery, in vivo functional assays of cilia mutant allele strength, and mechanisms of sensory cilia assembly and function. Supported by NIH grant DK053093

The Oligomeric Outer Dynein Arm Assembly Factor CCDC103 Is Tightly Integrated within the Ciliary Axoneme and Exhibits Periodic Binding to Microtubules

CCDC103 is an ∼29-kDa protein consisting of a central RPAP3_C domain flanked by N- and C-terminal coiled coils. Defects in CCDC103 lead to primary ciliary dyskinesia caused by the loss of outer dynein arms. This protein is present along the entire length of the ciliary axoneme and does not require other dynein or docking complex components for its integration. Unlike other known dynein assembly factors within the axoneme, CCDC103 is not solubilized by 0.6 M NaCl and requires more chaotropic conditions, such as 0.5 M KI. Alternatively, it can be extracted using 0.3% sarkosyl. CCDC103 forms stable dimers and other oligomers in solution through interactions involving the central domain. The smallest particle observed by dynamic light scattering has a hydrodynamic diameter of ∼25 nm. Furthermore, CCDC103 binds microtubules directly, forming ∼9-nm diameter particles that exhibit a 12-nm spacing on the microtubule lattice, suggesting that there may be two CCDC103 units per outer arm dynein repeat. Although the outer dynein arm docking complex is necessary to form arrays of dyneins along microtubules, it is not sufficient to set up a single array in a precise location on each axonemal doublet. We propose that CCDC103 helps generate a high-affinity site on the doublets for outer arm assembly, either through direct interactions or indirectly, perhaps by modifying the underlying microtubule lattice.

Torque Generation by Axonemal Outer-Arm Dynein

Outer-arm dynein is the main engine providing the motive force in cilia. Using three-dimensional tracking microscopy, we found that contrary to previous reports Tetrahymena ciliary three-headed outer-arm dynein (αβγ) as well as proteolytically generated two-headed (βγ) and one-headed (α) subparticles showed clockwise rotation of each sliding microtubule around its longitudinal axis in microtubule corkscrewing assays. By measuring the rotational pitch as a function of ATP concentration, we also found that the microtubule corkscrewing pitch is independent of ATP concentration, except at low ATP concentrations where the pitch generated by both three-headed αβγ and one-headed α exhibited significantly longer pitch. In contrast, the pitch driven by two-headed βγ did not display this sensitivity. In the assays on lawns containing mixtures of α and βγ at various ratios, the corkscrewing pitch increased dramatically in a nonlinear fashion as the ratio of α in the mixture increased. Even small proportions of α-subparticle could significantly increase the corkscrewing pitch of the mixture. Our data show that torque generation does not require the three-headed outer-arm dynein (αβγ) but is an intrinsic property of the subparticles of axonemal dyneins and also suggest that each subparticle may have distinct mechanical properties.

Alcohol-induced ciliary dysfunction targets the outer dynein arm.

Alcohol abuse results in an increased incidence of pulmonary infection, in part attributable to impaired mucociliary clearance. Analysis of motility in mammalian airway cilia has revealed that alcohol impacts the ciliary dynein motors by a mechanism involving altered axonemal protein phosphorylation. Given the highly conserved nature of cilia, it is likely that the mechanisms for alcohol-induced ciliary dysfunction (AICD) are conserved. Thus we utilized the experimental advantages offered by the model organism, Chlamydomonas, to determine the precise effects of alcohol on ciliary dynein activity and identify axonemal phosphoproteins that are altered by alcohol exposure. Analysis of live cells or reactivated cell models showed that alcohol significantly inhibits ciliary motility in Chlamydomonas via a mechanism that is part of the axonemal structure. Taking advantage of informative mutant cells, we found that alcohol impacts the activity of the outer dynein arm. Consistent with this finding, alcohol exposure results in a significant reduction in ciliary beat frequency, a parameter of ciliary movement that requires normal outer dynein arm function. Using mutants that lack specific heavy-chain motor domains, we have determined that alcohol impacts the β- and γ-heavy chains of the outer dynein arm. Furthermore, using a phospho-threonine-specific antibody, we determined that the phosphorylation state of DCC1 of the outer dynein arm-docking complex is altered in the presence of alcohol, and its phosphorylation correlates with AICD. These results demonstrate that alcohol targets specific outer dynein arm components and suggest that DCC1 is part of an alcohol-sensitive mechanism that controls outer dynein arm activity.

Chlamydomonas axonemal dynein assembly locus ODA8 encodes a conserved flagellar protein needed for cytoplasmic maturation of outer dynein arm complexes.

The Chlamydomonas reinhardtii oda8 mutation blocks assembly of flagellar outer dynein arms (ODAs), and interacts genetically with ODA5 and ODA10, which encode axonemal proteins thought to aid dynein binding onto axonemal docking sites. We positionally cloned ODA8 and identified the gene product as the algal homolog of vertebrate LRRC56. Its flagellar localization depends on ODA5 and ODA10, consistent with genetic interaction studies, but phylogenomics suggests that LRRC56 homologs play a role in intraflagellar transport (IFT)-dependent assembly of outer row dynein arms, not axonemal docking. ODA8 distribution between cytoplasm and flagella is similar to that of IFT proteins and about half of flagellar ODA8 is in the soluble matrix fraction. Dynein extracted in vitro from wild type axonemes will rebind efficiently to oda8 mutant axonemes, without re-binding of ODA8, further supporting a role in dynein assembly or transport, not axonemal binding. Assays comparing preassembled ODA complexes from the cytoplasm of wild type and mutant strains show that dynein in oda8 mutant cytoplasm has not properly preassembled and cannot bind normally onto oda axonemes. We conclude that ODA8 plays an important role in formation and transport of mature dynein complexes during flagellar assembly. © 2014 The Authors. Cytoskeleton Published by Wiley Periodicals, Inc.

A Structural Basis for How Motile Cilia Beat.

The motile cilium is a mechanical wonder, a cellular nanomachine that produces a high-speed beat based on a cycle of bends that move along an axoneme made of 9+2 microtubules. The molecular motors, dyneins, power the ciliary beat. The dyneins are compacted into inner and outer dynein arms, whose activity is highly regulated to produce microtubule sliding and axonemal bending. The switch point hypothesis was developed long ago to account for how sliding in the presence of axonemal radial spoke-central pair interactions causes the ciliary beat. Since then, a new genetic, biochemical, and structural complexity has been discovered, in part, with Chlamydomonas mutants, with high-speed, high-resolution analysis of movement and with cryoelectron tomography. We stand poised on the brink of new discoveries relating to the molecular control of motility that extend and refine our understanding of the basic events underlying the switching of arm activity and of bend formation and propagation.

Detailed structural and biochemical characterization of the nexin-dynein regulatory complex.

The nexin-dynein regulatory complex (N-DRC) forms a cross-bridge between the outer doublet microtubules of the axoneme and regulates dynein motor activity in cilia/flagella. Although the molecular composition and the three-dimensional structure of N-DRC have been studied using mutant strains lacking N-DRC subunits, more accurate approaches are necessary to characterize the structure and function of N-DRC. In this study, we precisely localized DRC1, DRC2, and DRC4 using cryo-electron tomography and structural labeling. All three N-DRC subunits had elongated conformations and spanned the length of N-DRC. Furthermore, we purified N-DRC and characterized its microtubule-binding properties. Purified N-DRC bound to the microtubule and partially inhibited microtubule sliding driven by the outer dynein arms (ODAs). Of interest, microtubule sliding was observed even in the presence of fourfold molar excess of N-DRC relative to ODA. These results provide insights into the role of N-DRC in generating the beating motions of cilia/flagella.

S88 Electron Tomography Detects Ultrastructural Abnormalities In Patients With Pcd Due To A Dnah11 Defect

Primary Ciliary Dyskinesia (PCD) is a genetically heterogeneous condition. characterised by impaired mucociliary clearance and chronic sino-pulmonary disease. Over 30 causative gene mutations resulting in dysfunctional ciliary motility and structure have been identified. Ciliary ultrastructure examined by Transmission Electron Microscopy (TEM) is currently the diagnostic gold standard. Patients with mutations in the gene DNAH11 have a hyperfrequent ciliary beat and clinical symptoms of PCD. Diagnosis of a DNAH11 defect by TEM is difficult due to apparently normal ciliary ultrastructure. The electron tomography technique, an extension of TEM, produces 3D models of cilia with superior resolution. The aim of this study was to determine if electron tomography can detect ultrastructural abnormalities in patients with DNAH11 defects. Immunofluorescence by specific antibodies for DNAH11 showed localisation to the proximal portion of cilia. Proximal cilia cross sections from araldite embedded nasal brush biopsies were examined. Dual axis tomograms were collected on a Philips CM200 electron microscope. The data were analysed using IMOD software and averaged using PEET. Electron tomography and averaging of cilia cross sections indicated a deficiency in the outer dynein arm, consistent across all patients with a DNAH11 defect (n = 5) compared to healthy controls (n = 3) and patients with PCD due to a defect of the central pair or nexin link (n = 3) (Figure 1). A reduction in outer dynein arm volume of 30% was identified compared to healthy and PCD controls. In conclusion, a mutation in DNAH11 results in a subtle abnormality in ultrastructure. The defects are specific to the ‘forearm’ of the outer dynein arm and only detectable at the base of the cilium where DNAH11 is located. Electron tomography is highly effective in visualising this defect.

Functional diversity of axonemal dyneins as assessed by in vitro and in vivo motility assays of Chlamydomonas mutants.

This review outlines the current knowledge of the functional diversity of axonemal dyneins, as revealed by studies with the model organism Chlamydomonas. Axonemal dyneins, which comprise outer and inner dynein arms, power cilia and flagella beating by producing sliding movements between adjacent outer-doublet microtubules. Outer- and inner-arm dyneins have traditionally been considered similar in structure and function. However, recent evidence suggests that they differ rather strikingly in subunit composition, axonemal arrangement, and molecular motor properties. We posit that these arms make up two largely independent motile systems; whereas outer-arm dynein can generate axonemal beating by itself under certain conditions, inner-arm dynein can generate beating only in cooperation with the central pair/radial spokes. This conclusion is supported by genome analyses of various organisms. Outer-arm dynein appears to be particularly important for nodal cilia of mammalian embryos that function for determination of left-right body asymmetry.

Engaging the “Clutch” to Move Forward

Engaging the “Clutch” to Move Forward

Motor domain-based motility system and motile properties of alpha heavy chain in Tetrahymena outer arm dynein

Axonemal dynein plays an essential role in ciliary motility, and impaired ciliary motility causes human diseases such as primary ciliary dyskinesia (PCD). The motor domain of axonemal dynein powers ciliary motility and its function is regulated by several accessary proteins bound to the tail region. Therefore, to understand the essential properties of dynein motility, examining the motile properties of the motor domain without the tail is necessary. In this study, the functional motor domain of the alpha heavy chain in Tetrahymena outer arm dynein was purified, and its motile properties were examined using an in vitro motility system. The purified protein caused microtubules to glide at a velocity of 5.0μm/s with their minus-end trailing, and motility was inhibited in an ATP concentration-dependent manner, which is in contrast with kinesin1. This method could be applicable to other axonemal dyneins and will enable further molecular studies on diverse axonemal dyneins and ciliary motility.

HEATR2 plays a conserved role in assembly of the ciliary motile apparatus.

Cilia are highly conserved microtubule-based structures that perform a variety of sensory and motility functions during development and adult homeostasis. In humans, defects specifically affecting motile cilia lead to chronic airway infections, infertility and laterality defects in the genetically heterogeneous disorder Primary Ciliary Dyskinesia (PCD). Using the comparatively simple Drosophila system, in which mechanosensory neurons possess modified motile cilia, we employed a recently elucidated cilia transcriptional RFX-FOX code to identify novel PCD candidate genes. Here, we report characterization of CG31320/HEATR2, which plays a conserved critical role in forming the axonemal dynein arms required for ciliary motility in both flies and humans. Inner and outer arm dyneins are absent from axonemes of CG31320 mutant flies and from PCD individuals with a novel splice-acceptor HEATR2 mutation. Functional conservation of closely arranged RFX-FOX binding sites upstream of HEATR2 orthologues may drive higher cytoplasmic expression of HEATR2 during early motile ciliogenesis. Immunoprecipitation reveals HEATR2 interacts with DNAI2, but not HSP70 or HSP90, distinguishing it from the client/chaperone functions described for other cytoplasmic proteins required for dynein arm assembly such as DNAAF1-4. These data implicate CG31320/HEATR2 in a growing intracellular pre-assembly and transport network that is necessary to deliver functional dynein machinery to the ciliary compartment for integration into the motile axoneme.