The Methylome of Motile Cilia.

Cilia are highly complex motile, sensory, and secretory organelles that contain perhaps 1,000 or more distinct protein components, many of which are subject to various post-translational modifications such as phosphorylation, N-terminal acetylation, and proteolytic processing. Another common modification is the addition of one or more methyl groups to the side chains of arginine and lysine residues. These tunable additions delocalize the side-chain charge, decrease hydrogen bond capacity, and increase both bulk and hydrophobicity. Methylation is usually mediated by S-adenosylmethionine (SAM)-dependent methyltransferases and reversed by demethylases. Previous studies have identified several ciliary proteins that are subject to methylation including axonemal dynein heavy chains that are modified by a cytosolic methyltransferase. Here we have performed an extensive proteomic analysis of multiple independently derived cilia samples to assess the potential for SAM metabolism and the extent of methylation in these organelles. We find that cilia contain all the enzymes needed for generation of the SAM methyl donor and recycling of the S-adenosylhomocysteine and tetrahydrofolate byproducts. In addition, we find that at least one hundred and fifty-five distinct ciliary proteins are methylated, in some cases at multiple sites. These data provide a comprehensive resource for studying the consequences of methyl marks on ciliary biology.

Cilia Provide a Platform for the Generation, Regulated Secretion, and Reception of Peptidergic Signals.

Cilia are microtubule-based cellular projections that act as motile, sensory, and secretory organelles. These structures receive information from the environment and transmit downstream signals to the cell body. Cilia also release vesicular ectosomes that bud from the ciliary membrane and carry an array of bioactive enzymes and peptide products. Peptidergic signals represent an ancient mode of intercellular communication, and in metazoans are involved in the maintenance of cellular homeostasis and various other physiological processes and responses. Numerous peptide receptors, subtilisin-like proteases, the peptide-amidating enzyme, and bioactive amidated peptide products have been localized to these organelles. In this review, we detail how cilia serve as specialized signaling organelles and act as a platform for the regulated processing and secretion of peptidergic signals. We especially focus on the processing and trafficking pathways by which a peptide precursor from the green alga Chlamydomonas reinhardtii is converted into an amidated bioactive product-a chemotactic modulator-and released from cilia in ectosomes. Biochemical dissection of this complex ciliary secretory pathway provides a paradigm for understanding cilia-based peptidergic signaling in mammals and other eukaryotes.

Methylation of ciliary dynein motors involves the essential cytosolic assembly factor DNAAF3/PF22.

Axonemal dynein motors drive ciliary motility and can consist of up to twenty distinct components with a combined mass of ~2 MDa. In mammals, failure of dyneins to assemble within the axonemal superstructure leads to primary ciliary dyskinesia. Syndromic phenotypes include infertility, rhinitis, severe bronchial conditions, and situs inversus. Nineteen specific cytosolic factors (Dynein Axonemal Assembly Factors; DNAAFs) are necessary for axonemal dynein assembly, although the detailed mechanisms involved remain very unclear. Here, we identify the essential assembly factor DNAAF3 as a structural ortholog of S-adenosylmethionine-dependent methyltransferases. We demonstrate that dynein heavy chains, especially those forming the ciliary outer arms, are methylated on key residues within various nucleotide-binding sites and on microtubule-binding domain helices directly involved in the transition to low binding affinity. These variable modifications, which are generally missing in a Chlamydomonas null mutant for the DNAAF3 ortholog PF22 (DAB1), likely impact on motor mechanochemistry fine-tuning the activities of individual dynein complexes.

Controlling 1D Nanostructures and Handedness by Polar Residue Chirality of Amphiphilic Peptides.

Peptide assemblies are promising nanomaterials, with their properties and technological applications being highly hinged on their supramolecular architectures. Here, how changing the chirality of the terminal charged residues of an amphiphilic hexapeptide sequence Ac-I4 K2 -NH2 gives rise to distinct nanostructures and supramolecular handedness is reported. Microscopic imaging and neutron scattering measurements show thin nanofibrils, thick nanofibrils, and wide nanotubes self-assembled from four stereoisomers. Spectroscopic and solid-state nuclear magnetic resonance (NMR) analyses reveal that these isomeric peptides adopt similar anti-parallel ß-sheet secondary structures. Further theoretical calculations demonstrate that the chiral alterations of the two C-terminal lysine residues cause the formation of diverse single ß-strand conformations, and the final self-assembled nanostructures and handedness are determined by the twisting direction and degree of single ß-strands. This work not only lays a useful foundation for the fabrication of diverse peptide nanostructures by manipulating the chirality of specific residues but also provides a framework for predicting the supramolecular structures and handedness of peptide assemblies from single molecule conformations.

N-Terminal Processing and Modification of Ciliary Dyneins.

Axonemal dyneins are highly complex microtubule motors that power ciliary motility. These multi-subunit enzymes are assembled at dedicated sites within the cytoplasm. At least nineteen cytosolic factors are specifically needed to generate dynein holoenzymes and/or for their trafficking to the growing cilium. Many proteins are subject to N-terminal processing and acetylation, which can generate degrons subject to the AcN-end rule, alter N-terminal electrostatics, generate new binding interfaces, and affect subunit stoichiometry through targeted degradation. Here, we have used mass spectrometry of cilia samples and electrophoretically purified dynein heavy chains from Chlamydomonas to define their N-terminal processing; we also detail the N-terminal acetylase complexes present in this organism. We identify four classes of dynein heavy chain based on their processing pathways by two distinct acetylases, one of which is dependent on methionine aminopeptidase activity. In addition, we find that one component of both the outer dynein arm intermediate/light chain subcomplex and the docking complex is processed to yield an unmodified Pro residue, which may provide a setpoint to direct the cytosolic stoichiometry of other dynein complex subunits that contain N-terminal degrons. Thus, we identify and describe an additional level of processing and complexity in the pathways leading to axonemal dynein formation in cytoplasm.

Inherently disordered regions of axonemal dynein assembly factors.

The dynein-driven beating of cilia is required to move individual cells and to generate fluid flow across surfaces and within cavities. These motor enzymes are highly complex and can contain upwards of 20 different protein components with a total mass approaching 2 MDa. The dynein heavy chains are enormous proteins consisting of ~4500 residues and ribosomes take approximately 15 min to synthesize one. Studies in a broad array of organisms ranging from the green alga Chlamydomonas to humans has identified 19 cytosolic factors (DNAAFs) that are needed to specifically build axonemal dyneins; defects in many of these proteins lead to primary ciliary dyskinesia in mammals which can result in infertility, severe bronchial problems, and situs inversus. How all these factors cooperate in a spatially and temporally regulated manner to promote dynein assembly in cytoplasm remains very uncertain. These DNAAFs contain a variety of well-folded domains many of which provide protein interaction surfaces. However, many also exhibit large regions that are predicted to be inherently disordered. Here I discuss the nature of these unstructured segments, their predicted propensity for driving protein phase separation, and their potential for adopting more defined conformations during the dynein assembly process.

Outer-arm dynein light chain LC1 is required for normal motor assembly kinetics, ciliary stability, and motility.

Light chain 1 (LC1) is a highly conserved leucine-rich repeat protein associated with the microtubule-binding domain of the Chlamydomonas outer-dynein arm γ heavy chain. LC1 mutations in humans and trypanosomes lead to motility defects, while its loss in oomycetes results in aciliate zoospores. Here we describe a Chlamydomonas LC1 null mutant (dlu1-1). This strain has reduced swimming velocity and beat frequency, can undergo waveform conversion, but often exhibits loss of hydrodynamic coupling between the cilia. Following deciliation, Chlamydomonas cells rapidly rebuild cytoplasmic stocks of axonemal dyneins. Loss of LC1 disrupts the kinetics of this cytoplasmic preassembly so that most outer-arm dynein heavy chains remain monomeric even after several hours. This suggests that association of LC1 with its heavy chain-binding site is a key step or checkpoint in the outer-arm dynein assembly process. Similarly to strains lacking the entire outer arm and inner arm I1/f, we found that loss of LC1 and I1/f in dlu1-1 ida1 double mutants resulted in cells unable to build cilia under normal conditions. Furthermore, dlu1-1 cells do not exhibit the usual ciliary extension in response to lithium treatment. Together, these observations suggest that LC1 plays an important role in the maintenance of axonemal stability.

Isolation of ciliary ectosomes and analysis of amidated peptide-mediated chemotaxis in Chlamydomonas.

Ciliary ectosomes are vesicles that bud from the ciliary membrane. Isolation and analysis of these structures can shed light on their bioactive cargoes and identify proteins and biomolecules involved in intercellular communication and various physiological processes. Most published methods to isolate ciliary ectosomes are based on their size (100nm to 1µm) to separate cilia-derived vesicles from isolated cilia and/or intact cells. However, it is often difficult to determine the origin of extracellular vesicles and to distinguish ciliary ectosomes from ectosomes budded from the plasma membrane or from exosomes that derive from multivesicular bodies. Here, we describe procedures to isolate and purify ciliary ectosomes from the unicellular green alga, Chlamydomonas reinhardtii, through differential and iodixanol density gradient ultracentrifugation; in this organism, the ciliary membrane is the only membrane directly exposed to the environment and thus ectosomes are of known origin. Ciliary ectosomes contain enzymes and α-amidated peptide products required to mediate peptidergic-signaling cascades; one identified amidated peptide acts as a chemotactic modulator for C. reinhardtii gametes. Classical methods used to assess chemotaxis do not provide quantitative measurements of the chemotactic gradient or the real-time effects on the migration of fast moving cells. Consequently, we developed a chemotaxis assay protocol using microfluidic channel slides that provides quantitative and qualitative measurements of the chemotactic gradient and cell migration. Here, we describe how to establish a stable gradient of a bioactive substance in microfluidic channel slides and perform quantitative assays to assess chemotaxis of both individual cells and populations of C. reinhardtii.

Peptide Self-Assemblies from Unusual α-Sheet Conformations Based on Alternation of d/l Amino Acids.

Peptide self-assembly is a hierarchical process during which secondary structures formed in the initial stages play a critical role in determining the subsequent assembling processes and final structural ordering. Unusual secondary structures hold promise as a source to develop novel supramolecular architectures with unique properties. In this work, we report the design of a new peptide self-assembly strategy based on unusual α-sheet secondary structures. In light of the strong propensity of leucine toward forming helical conformations and its high hydrophobicity, we design two short amphiphilic peptides Ac-LDLLDLK-NH2 and Ac-DLLDLLDK-NH2 with alternating l- and d-form amino acids. Microscopic imaging, neutron scattering, and spectroscopic measurements indicate that the two heterochiral peptides form highly ordered wide nanotubes and helical ribbons with monolayer thickness, in sharp contrast to twisted nanofibrils formed by the homochiral peptide Ac-LLLLK-NH2. Molecular dynamics simulations from monomers to trimers reveal that the two heteropeptides fold into α-sheets instead of ß-sheets, which readily pack into tubular architectures in oligomer simulations. Simulated circular dichroism spectra based on α-sheet oligomers validate the proposed α-sheet secondary structures. These results form an important basis for the rational design of higher-order peptide assemblies with novel properties based on unusual α-sheet secondary structures.

River metabolic fingerprints and regimes reveal ecosystem responses to enhanced wastewater treatment.

Although many studies have examined how improvements in wastewater treatment impact river nutrient concentrations and loads, there has been much less focus on measuring river metabolism to evaluate the wider aquatic ecosystem benefits of reducing nutrient inputs to rivers. The objectives of this study were to evaluate the effects of enhanced wastewater treatment (nitrification) on river metabolism in the Grand River, Canada's largest river draining into Lake Erie. Metabolic fingerprints and regimes (calculated from high-frequency dissolved oxygen [DO] measurements) were used to visualize whole-river ecosystem functional responses to these wastewater treatment upgrades. There was a 60% reduction in ecosystem respiration during summer, in response to reductions in effluent total ammonia inputs, causing a shift from net heterotrophy to net autotrophy, and contraction of river metabolic fingerprints. This resulted in major improvements in summer DO concentrations, with reductions in the percentage of days during summer that DO minima fell below water-quality guidelines for protection of aquatic early life stages, from 88% to ≤16%. The results also point to potential cascading impacts on coupled phosphorus and nitrogen cycles, which may generate further improvements in river water quality. During the summer, high rates of river metabolism and nutrient retention may result in measured water-column nutrient concentrations potentially underestimating nutrient pressures. This study also demonstrates the value of combining river metabolism with nutrient monitoring for a more holistic understanding of the role of nutrients in river ecosystem health and function.

Flow blockage disrupts cilia-driven fluid transport in the epileptic brain.

A carpet of ependymal motile cilia lines the brain ventricular system, forming a network of flow channels and barriers that pattern cerebrospinal fluid (CSF) flow at the surface. This CSF transport system is evolutionary conserved, but its physiological function remains unknown. Here we investigated its potential role in epilepsy with studies focused on CDKL5 deficiency disorder (CDD), a neurodevelopmental disorder with early-onset epilepsy refractory to seizure medications and the most common cause of infant epilepsy. CDKL5 is a highly conserved X-linked gene suggesting its function in regulating cilia length and motion in the green alga Chlamydomonas might have implication in the etiology of CDD. Examination of the structure and function of airway motile cilia revealed both the CDD patients and the Cdkl5 knockout mice exhibit cilia lengthening and abnormal cilia motion. Similar defects were observed for brain ventricular cilia in the Cdkl5 knockout mice. Mapping ependymal cilia generated flow in the ventral third ventricle (v3V), a brain region with important physiological functions showed altered patterning of flow. Tracing of cilia-mediated inflow into v3V with fluorescent dye revealed the appearance of a flow barrier at the inlet of v3V in Cdkl5 knockout mice. Analysis of mice with a mutation in another epilepsy-associated kinase, Yes1, showed the same disturbance of cilia motion and flow patterning. The flow barrier was also observed in the Foxj1± and FOXJ1CreERT:Cdkl5y/fl mice, confirming the contribution of ventricular cilia to the flow disturbances. Importantly, mice exhibiting altered cilia-driven flow also showed increased susceptibility to anesthesia-induced seizure-like activity. The cilia-driven flow disturbance arises from altered cilia beating orientation with the disrupted polarity of the cilia anchoring rootlet meshwork. Together these findings indicate motile cilia disturbances have an essential role in CDD-associated seizures and beyond, suggesting cilia regulating kinases may be a therapeutic target for medication-resistant epilepsy.

Exploring Nanoscale Structure in Perovskite Precursor Solutions Using Neutron and Light Scattering.

Tailoring the solution chemistry of metal halide perovskites requires a detailed understanding of precursor aggregation and coordination. In this work, we use various scattering techniques, including dynamic light scattering (DLS), small angle neutron scattering (SANS), and spin-echo SANS (SESANS) to probe the nanostructures from 1 nm to 10 µm within two different lead-halide perovskite solution inks (MAPbI3 and a triple-cation mixed-halide perovskite). We find that DLS can misrepresent the size distribution of the colloidal dispersion and use SANS/SESANS to confirm that these perovskite solutions are mostly comprised of 1-2 nm-sized particles. We further conclude that if there are larger colloids present, their concentration must be <0.005% of the total dispersion volume. With SANS, we apply a simple fitting model for two component microemulsions (Teubner-Strey), demonstrating this as a potential method to investigate the structure, chemical composition, and colloidal stability of perovskite solutions, and we here show that MAPbI3 solutions age more drastically than triple cation solutions.

Regulated processing and secretion of a peptide precursor in cilia.

Cilia are sensory and secretory organelles that both receive information from the environment and transmit signals. Cilia-derived vesicles (ectosomes), formed by outward budding of the ciliary membrane, carry enzymes and other bioactive products; this process represents an ancient mode of regulated secretion. Peptidergic intercellular communication controls a wide range of physiological and behavioral responses and occurs throughout eukaryotes. The Chlamydomonas reinhardtii genome encodes what appear to be numerous prepropeptides and enzymes homologous to those used to convert metazoan prepropeptides into bioactive peptide products. Since C. reinhardtii, a green alga, lack the dense core vesicles in which metazoan peptides are processed and stored, we explored the hypothesis that propeptide processing and secretion occur through the regulated release of ciliary ectosomes. A synthetic peptide (GATI-amide) that could be generated from a 91-kDa peptide precursor (proGATI) serves as a chemotactic modulator, attracting minus gametes while repelling plus gametes. Here we dissect the processing pathway that leads to formation of an amidated peptidergic sexual signal specifically on the ciliary ectosomes of plus gametes. Unlike metazoan propeptides, modeling studies identified stable domains in proGATI. Mass spectrometric analysis of a potential prohormone convertase and the amidated proGATI-derived products found in cilia and mating ectosomes link endoproteolytic cleavage to ectosome entry. Extensive posttranslational modification of proGATI confers stability to its amidated product. Analysis of this pathway affords insight into the evolution of peptidergic signaling; this will facilitate studies of the secretory functions of metazoan cilia.

Developmental changes in ciliary composition during gametogenesis in Chlamydomonas.

Chlamydomonas reinhardtii transitions from mitotically dividing vegetative cells to sexually competent gametes of two distinct mating types following nutrient deprivation. Gametes of opposite mating type interact via their cilia, initiating an intraciliary signaling cascade and ultimately fuse forming diploid zygotes. The process of gametogenesis is genetically encode, and a previous study revealed numerous significant changes in mRNA abundance during this life-cycle transition. Here we describe a proteomic analysis of cilia derived from vegetative and gametic cells of both mating types in an effort to assess the global changes that occur within the organelle during this process. We identify numerous membrane- and/or matrix-associated proteins in gametic cilia that were not detected in cilia from vegetative cells. This includes the pro-protein from which the GATI-amide gametic chemotactic modulator derives, as well as receptors, a dynamin-related protein, ammonium transporters, two proteins potentially involved in the intraciliary signaling cascade-driven increase in cAMP, and multiple proteins with a variety of interaction domains. These changes in ciliary composition likely directly affect the functional properties of this organelle as the cell transitions between life-cycle stages.

A guide to designing graphene-philic surfactants.

HYPOTHESIS: As compared to common aliphatic surfactants, increasing the number of pendant or incorporated aromatic groups in a surfactant is expected to offer significant enhancement in the affinity for graphene surfaces. The basis for enhanced graphene-philicity of aromatic surfactants is that they can develop appreciable π - π interactions with graphene. Furthermore, charged (anionic) surfactants are expected to confer electrostatic stabilization on surfactant-graphene composites. Hence, it is expected that anionic aromatic surfactants combine these two properties for effective stabilization of graphene dispersions in water. EXPERIMENTAL: The properties of two custom made graphene-compatible surfactants carrying two and three aromatic moieties in the hydrophobic tails, namely DC3Ph2 (sodium 1,4-dioxo-1,4-bis(3-phenylpropoxy)butane-2-sulfonate) and TC3Ph3 (sodium 1,5-dioxo-1,5-bis(3-phenylpropoxy)-3-((3-phenylpropoxy)carbonyl) pentane-2-sulfonate) were compared with other common ionic commercial surfactants. Air-water (a/w) surface tension measurements were used to assess the surfactant adsorption and interfacial packing in the absence and presence of graphene. The surfactant coverage index for graphene (Ф) was calculated using surfactant headgroup areas derived from a/w surface tension data, chain volumes, and molecular fragment volumes from literature. FINDINGS: Increasing the number of aromatic groups and tails per surfactant was shown to increase the ability of surfactants to pack and fill space, as expressed by Ф. Comparison between the values of Ф for surfactants of different chain structure and architecture showed that the affinity for graphene increased with Ф. Hence, there is an implicit link between surfactant-graphene compatibility and the identity, chemical composition and architecture of the surfactant chains.

Cilia-derived vesicles: An ancient route for intercellular communication.

Extracellular vesicles (EVs) provide a mechanism for intercellular communication that transports complex signals in membrane delimited structures between cells, tissues and organisms. Cells secrete EVs of various subtypes defined by the pathway leading to release and by the pathological condition of the cell. Cilia are evolutionarily conserved organelles that can act as sensory structures surveilling the extracellular environment. Here we discuss the secretory functions of cilia and their biological implications. Studies in multiple species - from the nematode Caenorhabditis elegans and the chlorophyte alga Chlamydomonas reinhardtii to mammals - have revealed that cilia shed bioactive EVs (ciliary EVs or ectosomes) by outward budding of the ciliary membrane. The content of ciliary EVs is distinct from that of other vesicles released by cells. Peptides regulate numerous aspects of metazoan physiology and development through evolutionarily conserved mechanisms. Intriguingly, cilia-derived vesicles have recently been found to mediate peptidergic signaling. C. reinhardtii releases the peptide α-amidating enzyme (PAM), bioactive amidated products and components of the peptidergic signaling machinery in ciliary EVs in a developmentally regulated manner. Considering the origin of cilia in early eukaryotes, it is likely that release of peptidergic signals in ciliary EVs represents an alternative and ancient mode of regulated secretion that cells can utilize in the absence of dedicated secretory granules.

Consensus nomenclature for dyneins and associated assembly factors.

Dyneins are highly complex, multicomponent, microtubule-based molecular motors. These enzymes are responsible for numerous motile behaviors in cytoplasm, mediate retrograde intraflagellar transport (IFT), and power ciliary and flagellar motility. Variants in multiple genes encoding dyneins, outer dynein arm (ODA) docking complex subunits, and cytoplasmic factors involved in axonemal dynein preassembly (DNAAFs) are associated with human ciliopathies and are of clinical interest. Therefore, clear communication within this field is particularly important. Standardizing gene nomenclature, and basing it on orthology where possible, facilitates discussion and genetic comparison across species. Here, we discuss how the human gene nomenclature for dyneins, ODA docking complex subunits, and DNAAFs has been updated to be more functionally informative and consistent with that of the unicellular green alga Chlamydomonas reinhardtii, a key model organism for studying dyneins and ciliary function. We also detail additional nomenclature updates for vertebrate-specific genes that encode dynein chains and other proteins involved in dynein complex assembly.

Comparing pH-responsive nanogel swelling in dispersion and inside a polyacrylamide gel using photoluminescence spectroscopy and small-angle neutron scattering.

Nanosized probes that report their changes in dimensions within networks in response to environmental stimuli are potentially important for applications such as drug delivery, load-supporting hydrogels and soft robotics. Recently, we developed a fluorescent pH-responsive nanogel (NG) that used Förster-resonance energy transfer (FRET) to report changes in the probe separation and NG swelling within hydrogels using photoluminescence (PL) spectroscopy. However, FRET cannot measure nanoparticle dimensions and is subject to artefacts. Here, we report the use of small-angle neutron scattering (SANS) to study both the NGs in dispersion and in polyacrylamide (PAAm) gels as a function of pH. We compare the PL and SANS data for both systems and as a function of pH. The SANS data for the dispersed NGs indicate that they have a core-shell structure with a swollen mesh size of ∼1.0 nm. We hypothesized that the NGs inside the PAAm gel would show the same general changes in scattering as the pH is increased, as observed for the dispersed NGs, and this is confirmed by the data. In summary, the data confirm that PL is a suitable (accessible) method for reporting internal environmental changes within gels using NG probes.

Graded Morphologies and the Performance of PffBT4T-2OD:PC71BM Devices Using Additive Choice.

The impact of several solvent processing additives (1-chloronaphthalene, methylnaphthalene, hexadecane, 1-phenyloctane, and p-anisaldehyde), 3% v/v in o-dichlorobenzene, on the performance and morphology of poly[(5,6-difluoro-2,1,3-benzothiadiazol-4,7-diyl)-alt-(3,3‴-di(2-octyldodecyl)-2,2',5',22033,5″,2‴-quaterthiophen-5,5‴-diyl)] (PffBT4T-2OD):[6,6]-phenyl-C71-butyric acid methyl ester (PC71BM)-based polymer solar cells was investigated. Some additives were shown to enhance the power conversion efficiency (PCE) by ~6%, while others decreased the PCE by ~17-25% and a subset of the additives tested completely eliminated any power conversion efficiency and the operation as a photovoltaic device. Grazing-Incidence Wide Angle X-ray Scattering (GIWAXS) revealed a clear stepwise variation in the crystallinity of the systems when changing the additive between the two extreme situations of maximum PCE (1-chloronaphthalene) and null PCE (hexadecane). Small-Angle Neutron Scattering (SANS) revealed that the morphology of devices with PCE ~0% was composed of large domains with correlation lengths of ~30 nm, i.e., much larger than the typical exciton diffusion length (~12 nm) in organic semiconductors. The graded variations in crystallinity and in nano-domain size observed between the two extreme situations (1-chloronaphthalene and hexadecane) were responsible for the observed graded variations in device performance.