A Structural Basis for How Motile Cilia Beat

Cryo-EM of dynein microtubule-binding domains shows how an axonemal dynein distorts the microtubule

Dyneins are motor proteins responsible for transport in the cytoplasm and the beating of axonemes in cilia and flagella. They bind and release microtubules via a compact microtubule-binding domain (MTBD) at the end of a coiled-coil stalk. We address how cytoplasmic and axonemal dynein MTBDs bind microtubules at near atomic resolution. We decorated microtubules with MTBDs of cytoplasmic dynein-1 and axonemal dynein DNAH7 and determined their cryo-EM structures using helical Relion. The majority of the MTBD is rigid upon binding, with the transition to the high-affinity state controlled by the movement of a single helix at the MTBD interface. DNAH7 contains an 18-residue insertion, found in many axonemal dyneins, that contacts the adjacent protofilament. Unexpectedly, we observe that DNAH7, but not dynein-1, induces large distortions in the microtubule cross-sectional curvature. This raises the possibility that dynein coordination in axonemes is mediated via conformational changes in the microtubule.

Fifty years of microtubule sliding in cilia

Motility of cilia (also known as flagella in some eukaryotes) is based on axonemal doublet microtubule sliding that is driven by the dynein molecular motors. Dyneins are organized into intricately patterned inner and outer rows of arms, whose collective activity is to produce inter-microtubule movement. However, to generate a ciliary bend, not all dyneins can be active simultaneously. The switch point model accounts, in part, for how dynein motors are regulated during ciliary movement. On the basis of this model, supported by key direct experimental observations as well as more recent theoretical and structural studies, we are now poised to understand the mechanics of how ciliary dynein coordination controls axonemal bend formation and propagation.

Microtubule-bundling protein Spef1 enables mammalian ciliary central apparatus formation

Cilia are cellular protrusions containing nine microtubule (MT) doublets and function to propel cell movement or extracellular liquid flow through beating or sense environmental stimuli through signal transductions. Cilia require the central pair (CP) apparatus, consisting of two CP MTs covered with projections of CP proteins, for planar strokes. How the CP MTs of such '9 + 2' cilia are constructed, however, remains unknown. Here we identify Spef1, an evolutionarily conserved microtubule-bundling protein, as a core CP MT regulator in mammalian cilia. Spef1 was selectively expressed in mammalian cells with 9 + 2 cilia and specifically localized along the CP. Its depletion in multiciliated mouse ependymal cells by RNAi completely abolished the CP MTs and markedly attenuated ciliary localizations of CP proteins such as Hydin and Spag6, resulting in rotational beat of the ependymal cilia. Spef1, which binds to MTs through its N-terminal calponin-homologous domain, formed homodimers through its C-terminal coiled coil region to bundle and stabilize MTs. Disruption of either the MT-binding or the dimerization activity abolished the ability of exogenous Spef1 to restore the structure and functions of the CP apparatus. We propose that Spef1 bundles and stabilizes central MTs to enable the assembly and functions of the CP apparatus.

Paramecium Biology

Imagine that in 1678 you are Christiaan Huygens or Antonie van Leeuwenhoek seeing paramecia swim gracefully across the field of view of your new microscope. These unicellular, free-living, and swimming cells might have remained a curiosity if not for the ability of H.S. Jennings (Behavior of the lower organisms. Indiana University Press, Bloomington, 1906) and T.M. Sonneborn (Proc Natl Acad Sci USA 23:378-385, 1937) to recognize them for their behavior and genetics, both Mendelian and non-Mendelian. Following many years of painstaking work by Sonneborn and other researchers, Paramecium now serves as a modern model organism that has made specific contributions to cell and molecular biology and development. We will review the continuing usefulness and contributions of Paramecium species in this chapter.Even without a microscope, Paramecium species is visible to the naked eye because of their size (50-300 μ long). Paramecia are holotrichous ciliates, that is, unicellular organisms in the phylum Ciliophora that are covered with cilia. It was the beating of these cilia that propelled them across the slides of the first microscopes and continue to fascinate us today. Over time, Paramecium became a favorite model organism for a large variety of studies. Denis Lyn has called Paramecium the "white rat" of the Ciliophora for their manipulability and amenity to research. We will touch upon the use of Paramecium species to examine swimming behavior, ciliary structure and function, ion channel function, basal body duplication and patterning, non-Mendelian cortical inheritance, programmed DNA rearrangements, regulated secretion and exocytosis, and cell trafficking. In particular, we will focus on the use of P. tetraurelia and P. caudatum.

Rsph9 is critical for ciliary radial spoke assembly and central pair microtubule stability

BACKGROUND INFORMATION

In the "9+2"-type motile cilia, radial spokes (RSs) protruded from the nine peripheral microtubule doublets surround and interact with the central pair (CP) apparatus to regulate ciliary beat. RSPH9 is the human homologue of the essential protozoan RS head protein Rsp9. Its mutations in human primary ciliary dyskinesia patients, however, cause CP loss in a small portion of airway cilia without affecting the ciliary localization of other head proteins.

RESULTS

We characterized mouse Rsph9 and investigated its function in ependymal motile cilia. Rsph9 was specifically expressed in mouse tissues containing motile cilia and upregulated during multiciliation. Its ciliary localization complied with its putative role as an RS subunit. Depletion of Rsph9 by RNAi in mouse ependymal cilia resulted in a near complete CP loss and altered the ciliary beat pattern from planar to rotational. Multiple RS proteins, including those in the head, were also markedly downregulated in the Rsph9-depleted cilia.

CONCLUSION

Rsph9 is essential for both the RS head assembly and the CP maintenance in mammalian ependymal cilia.

SIGNIFICANCE

Our results help to understand the assembly and functions of mammalian RS and pathology of RS-related ciliopathy.

Four-dimensional analysis by high-speed holographic imaging reveals a chiral memory of sperm flagella

Here high-speed Digital Holographic Microscopy (DHM) records sperm flagellar waveforms and swimming paths in 4 dimensions (X, Z, and t). We find flagellar excursions into the Z-plane nearly as large as the envelope of the flagellar waveform projected onto the XY-plane. These Z-plane excursions travel as waves down the flagellum each beat cycle. DHM also tracks the heads of free-swimming sperm and the dynamics and chirality of rolling of sperm around their long axis. We find that mouse sperm roll CW at the maximum positive Z-plane excursion of the head, then roll CCW at the subsequent maximum negative Z-plane excursion. This alternating chirality of rolling indicates sperm have a chiral memory. Procrustes alignments of path trajectories for sequences of roll-counterroll cycles show that path chirality is always CW for the cells analyzed in this study. Human and bull sperm lack distinguishable left and right surfaces, but DHM still indicates coordination of Z-plane excursions and rolling events. We propose that sperm have a chiral memory that resides in a hypothetical elastic linkage within the flagellar machinery, which stores some of the torque required for a CW or CCW roll to reuse in the following counter-roll. Separate mechanisms control path chirality.

Microfluidic pumping using artificial magnetic cilia

One of the vital functions of naturally occurring cilia is fluid transport. Biological cilia use spatially asymmetric strokes to generate a net fluid flow that can be utilized for feeding, swimming, and other functions. Biomimetic synthetic cilia with similar asymmetric beating can be useful for fluid manipulations in lab-on-chip devices. In this paper, we demonstrate the microfluidic pumping by magnetically actuated synthetic cilia arranged in multi-row arrays. We use a microchannel loop to visualize flow created by the ciliary array and to examine pumping for a range of cilia and microchannel parameters. We show that magnetic cilia can achieve flow rates of up to 11 μl/min with the pressure drop of ~1 Pa. Such magnetic ciliary array can be useful in microfluidic applications requiring rapid and controlled fluid transport.

Chlamydomonas DYX1C1/PF23 is essential for axonemal assembly and proper morphology of inner dynein arms

Cytoplasmic assembly of ciliary dyneins, a process known as preassembly, requires numerous non-dynein proteins, but the identities and functions of these proteins are not fully elucidated. Here, we show that the classical Chlamydomonas motility mutant pf23 is defective in the Chlamydomonas homolog of DYX1C1. The pf23 mutant has a 494 bp deletion in the DYX1C1 gene and expresses a shorter DYX1C1 protein in the cytoplasm. Structural analyses, using cryo-ET, reveal that pf23 axonemes lack most of the inner dynein arms. Spectral counting confirms that DYX1C1 is essential for the assembly of the majority of ciliary inner dynein arms (IDA) as well as a fraction of the outer dynein arms (ODA). A C-terminal truncation of DYX1C1 shows a reduction in a subset of these ciliary IDAs. Sucrose gradients of cytoplasmic extracts show that preassembled ciliary dyneins are reduced compared to wild-type, which suggests an important role in dynein complex stability. The role of PF23/DYX1C1 remains unknown, but we suggest that DYX1C1 could provide a scaffold for macromolecular assembly.

Most animal cells have antenna-like organelles called “cilia”. These organelles have various important functions both in motility and sensing the environment. Motile cilia are essential for moving cells as well as moving fluids across a surface. The waveform of motile cilia requires large macromolecular motors; these are the ciliary dyneins. These dynein complexes are assembled in the cytoplasm in a pathway called preassembly, and then transported into cilia. Defects in this process cause a heterogeneous human disease called primary ciliary dyskinesia that results, for example, in the disruption of the motility of respiratory tract cilia, sperm and nodal cilia during development. The mechanisms of the preassembly pathway are not fully understood. In this study, we use a mutation in the well-conserved DYX1C1/PF23 gene of the green alga, Chlamydomonas reinhardtii. Loss of a conserved domain (DYX) reveals a failure to assemble most ciliary dyneins. Preassembly of inner arm dyneins is particularly affected. We find that if dynein arms are not assembled, dynein subunits in the cytoplasm are unstable. We suggest that DYX1C1 may play a role as a scaffold for other preassembly factors and the dynein subunits.

Ciliary Motility: Regulation of Axonemal Dynein Motors

Ciliary motility is crucial for the development and health of many organisms. Motility depends on the coordinated activity of multiple dynein motors arranged in a precise pattern on the outer doublet microtubules. Although significant progress has been made in elucidating the composition and organization of the dyneins, a comprehensive understanding of dynein regulation is lacking. Here, we focus on two conserved signaling complexes located at the base of the radial spokes. These include the I1/f inner dynein arm associated with radial spoke 1 and the calmodulin- and spoke-associated complex and the nexin-dynein regulatory complex associated with radial spoke 2. Current research is focused on understanding how these two axonemal hubs coordinate and regulate the dynein motors and ciliary motility.

Mutations in PIH1D3 Cause X-Linked Primary Ciliary Dyskinesia with Outer and Inner Dynein Arm Defects

Defects in motile cilia and sperm flagella cause primary ciliary dyskinesia (PCD), characterized by chronic airway disease, infertility, and left-right body axis disturbance. Here we report maternally inherited and de novo mutations in PIH1D3 in four men affected with PCD. PIH1D3 is located on the X chromosome and is involved in the preassembly of both outer (ODA) and inner (IDA) dynein arms of cilia and sperm flagella. Loss-of-function mutations in PIH1D3 lead to absent ODAs and reduced to absent IDAs, causing ciliary and flagellar immotility. Further, PIH1D3 interacts and co-precipitates with cytoplasmic ODA/IDA assembly factors DNAAF2 and DNAAF4. This result has clinical and genetic counseling implications for genetically unsolved male case subjects with a classic PCD phenotype that lack additional phenotypes such as intellectual disability or retinitis pigmentosa.

Axoneme Structure from Motile Cilia

The axoneme is the main extracellular part of cilia and flagella in eukaryotes. It consists of a microtubule cytoskeleton, which normally comprises nine doublets. In motile cilia, dynein ATPase motor proteins generate sliding motions between adjacent microtubules, which are integrated into a well-orchestrated beating or rotational motion. In primary cilia, there are a number of sensory proteins functioning on membranes surrounding the axoneme. In both cases, as the study of proteomics has elucidated, hundreds of proteins exist in this compartmentalized biomolecular system. In this article, we review the recent progress of structural studies of the axoneme and its components using electron microscopy and X-ray crystallography, mainly focusing on motile cilia. Structural biology presents snapshots (but not live imaging) of dynamic structural change and gives insights into the force generation mechanism of dynein, ciliary bending mechanism, ciliogenesis, and evolution of the axoneme.

Asymmetrically localized proteins stabilize basal bodies against ciliary beating forces

Basal bodies (BBs) organize and anchor motile cilia. This study uncovers components that asymmetrically localize to the rotationally symmetric BBs, where they fortify specific BB domains. Asymmetrically localized BB components are necessary to resist asymmetric ciliary forces.

Basal bodies are radially symmetric, microtubule-rich structures that nucleate and anchor motile cilia. Ciliary beating produces asymmetric mechanical forces that are resisted by basal bodies. To resist these forces, distinct regions within the basal body ultrastructure and the microtubules themselves must be stable. However, the molecular components that stabilize basal bodies remain poorly defined. Here, we determine that Fop1 functionally interacts with the established basal body stability components Bld10 and Poc1. We find that Fop1 and microtubule glutamylation incorporate into basal bodies at distinct stages of assembly, culminating in their asymmetric enrichment at specific triplet microtubule regions that are predicted to experience the greatest mechanical force from ciliary beating. Both Fop1 and microtubule glutamylation are required to stabilize basal bodies against ciliary beating forces. Our studies reveal that microtubule glutamylation and Bld10, Poc1, and Fop1 stabilize basal bodies against the forces produced by ciliary beating via distinct yet interdependent mechanisms.

The nexin link and B-tubule glutamylation maintain the alignment of outer doublets in the ciliary axoneme

We developed quantitative assays to test the hypothesis that the N-DRC is required for integrity of the ciliary axoneme. We examined reactivated motility of demembranated drc cells, commonly termed "reactivated cell models." ATP-induced reactivation of wild-type cells resulted in the forward swimming of ∼90% of cell models. ATP-induced reactivation failed in a subset of drc cell models, despite forward motility in live drc cells. Dark-field light microscopic observations of drc cell models revealed various degrees of axonemal splaying. In contrast, >98% of axonemes from wild-type reactivated cell models remained intact. The sup-pf4 and drc3 mutants, unlike other drc mutants, retain most of the N-DRC linker that interconnects outer doublet microtubules. Reactivated sup-pf4 and drc3 cell models displayed nearly wild-type levels of forward motility. Thus, the N-DRC linker is required for axonemal integrity. We also examined reactivated motility and axoneme integrity in mutants defective in tubulin polyglutamylation. ATP-induced reactivation resulted in forward swimming of >75% of tpg cell models. Analysis of double mutants defective in tubulin polyglutamylation and different regions of the N-DRC indicate B-tubule polyglutamylation and the distal lobe of the linker region are both important for axonemal integrity and normal N-DRC function. © 2016 Wiley Periodicals, Inc.

Absence of Radial Spokes in Mouse Node Cilia Is Required for Rotational Movement but Confers Ultrastructural Instability as a Trade-Off

Determination of left-right asymmetry in mouse embryos is established by a leftward fluid flow that is generated by clockwise rotation of node cilia. How node cilia achieve stable unidirectional rotation has remained unknown, however. Here we show that brief exposure to the microtubule-stabilizing drug paclitaxel (Taxol) induces randomly directed rotation and changes the ultrastructure of node cilia. In vivo observations and a computer simulation revealed that a regular 9+0 arrangement of doublet microtubules is essential for stable unidirectional rotation of node cilia. The 9+2 motile cilia of the airway, which manifest planar beating, are resistant to Taxol treatment. However, the airway cilia of mice lacking the radial spoke head protein Rsph4a undergo rotational movement instead of planar beating, are prone to microtubule rearrangement, and are sensitive to Taxol. Our results suggest that the absence of radial spokes allows node cilia to rotate unidirectionally but, as a trade-off, renders them ultrastructurally fragile.

Analysis of Axonemal Assembly During Ciliary Regeneration in Chlamydomonas

Chlamydomonas reinhardtii is an outstanding model genetic organism for study of assembly of cilia. Here, methods are described for synchronization of ciliary regeneration in Chlamydomonas to analyze the sequence in which ciliary proteins assemble. In addition, the methods described allow analysis of the mechanisms involved in regulation of ciliary length, the proteins required for ciliary assembly, and the temporal expression of genes encoding ciliary proteins. Ultimately, these methods can contribute to discovery of conserved genes that when defective lead to abnormal ciliary assembly and human disease.

Novel Insights into the Development and Function of Cilia Using the Advantages of the Paramecium Cell and Its Many Cilia

Paramecium species, especially P. tetraurelia and caudatum, are model organisms for modern research into the form and function of cilia. In this review, we focus on the ciliary ion channels and other transmembrane proteins that control the beat frequency and wave form of the cilium by controlling the signaling within the cilium. We put these discussions in the context of the advantages that Paramecium brings to the understanding of ciliary motility: mutants for genetic dissections of swimming behavior, electrophysiology, structural analysis, abundant cilia for biochemistry and modern proteomics, genomics and molecular biology. We review the connection between behavior and physiology, which allows the cells to broadcast the function of their ciliary channels in real time. We build a case for the important insights and advantages that this model organism continues to bring to the study of cilia.

Cilia and Diseases

In recent decades, cilia have moved from relative obscurity to a position of importance for understanding multiple complex human diseases. Now termed the ciliopathies, these diseases inflict devastating effects on millions of people worldwide. In this review, written primarily for teachers and students who may not yet be aware of the recent exciting developments in this field, we provide a general overview of our current understanding of cilia and human disease. We start with an introduction to cilia structure and assembly and indicate where they are found in the human body. We then discuss the clinical features of selected ciliopathies, with an emphasis on primary ciliary dyskinesia, polycystic kidney disease, and retinal degeneration. The history of ciliopathy research involves a fascinating interplay between basic and clinical sciences, highlighted in a timeline. Finally, we summarize the relative strengths of individual model organisms for ciliopathy research; many of these are suitable for classroom use.