Analysis of Flagellar Phosphoproteins from Chlamydomonas reinhardtii

Cilia and flagella are cell organelles that are highly conserved throughout evolution. For many years, the green biflagellate alga Chlamydomonas reinhardtii has served as a model for examination of the structure and function of its flagella, which are similar to certain mammalian cilia. Proteome analysis revealed the presence of several kinases and protein phosphatases in these organelles. Reversible protein phosphorylation can control ciliary beating, motility, signaling, length, and assembly. Despite the importance of this posttranslational modification, the identities of many ciliary phosphoproteins and knowledge about their in vivo phosphorylation sites are still missing. Here we used immobilized metal affinity chromatography to enrich phosphopeptides from purified flagella and analyzed them by mass spectrometry. One hundred forty-one phosphorylated peptides were identified, belonging to 32 flagellar proteins. Thereby, 126 in vivo phosphorylation sites were determined. The flagellar phosphoproteome includes different structural and motor proteins, kinases, proteins with protein interaction domains, and many proteins whose functions are still unknown. In several cases, a dynamic phosphorylation pattern and clustering of phosphorylation sites were found, indicating a complex physiological status and specific control by reversible protein phosphorylation in the flagellum.Cilia and flagella, which are essentially identical, are among the most ancient cellular organelles, providing motility for primitive eukaryotic cells living in aqueous environments. The assembly and motility of flagella have been studied extensively with the unicellular biflagellate green alga Chlamydomonas reinhardtii. This alga uses flagella for motility and for cell-cell recognition during mating. In basal land plants, such as bryophytes and pteridophytes, the only flagellated cells are motile sperm cells, which require water to swim to the egg. With the evolution of pollen tubes in higher gymnosperms and angiosperms, these plant species lost the ability to assemble flagella (24, 42). Flagella of animals have acquired new functions in multicellular organizations during evolution (6). In mammals, cilia and flagella can be motile or immotile. Motile cilia can be found, for example, in airways (respiratory cilia), in the brain (ependymal cilia), or in the male reproductive system (sperm flagella). Defects in cilia in humans can cause severe diseases, such as polycystic kidney disease, retinal degeneration, hydrocephalus, or changes in the left-right symmetry of organs, collectively known as ciliopathies (20, 32).Although C. reinhardtii and mammals are separated by more than 10⁹ years of evolution, C. reinhardtii flagella are amazingly similar in structure and function to the 9+2-type axonemes of most motile mammalian flagella and cilia (42). They are composed of nine microtubular doublets surrounding two central microtubular singlets. The axoneme of motile flagella includes substructures such as dynein arms and radial spokes that generate and control axoneme bending (31). The flagellum also contains matrix proteins that are not tightly associated with the flagellar membrane or the axoneme. They serve diverse functions and can be involved in intraflagellar transport (IFT) (37).Proteome analyses of cilia, including, for example, a human cilium, a mouse photoreceptor sensory cilium, and the flagella of the green alga Chlamydomonas reinhardtii, have unraveled hundreds of so far unknown proteins of this organelle (18, 29, 33) and have paved the way to further study the functions of these proteins. Several kinases and phosphatases were found in these proteomes, suggesting that reversible protein phosphorylation plays an important role in signaling in this organelle. This is underlined by earlier studies showing that phosphorylation and dephosphorylation control flagellar motility (35), signaling (30), length, and assembly (37, 53) in C. reinhardtii. Some phosphoproteins known or assumed to be involved in these processes, such as outer dynein arm heavy chain alpha (13), inner dynein arm intermediate chain protein IC138 (7), and central pair kinesin KLP1 (61), were characterized, but the exact in vivo phosphorylation sites were not determined. From earlier studies, it is known that >80 protein spots, representing axonemal components, are labeled by ³²P by two-dimensional electrophoretic techniques (34), but many of them have not been identified so far. In the past years, the relevance of some of the flagellar kinases has been shown. For example, silencing of casein kinase 1 (CK1) disturbs flagellum formation, among several other effects (41). One of its targets is IC138 (54). Glycogen synthase kinase 3 was suggested to regulate the assembly and length of flagella (53). Also, in mammalian cilia, reversible protein phosphorylation plays an important role in ciliary beating. Second messengers such as cyclic AMP (cAMP) and cGMP, which activate special kinases, are known to be relevant there (39).An understanding of how reversible protein phosphorylation influences the function of cilia and their role in diseases will require increased information not only about the nature of the phosphoproteins but also on their in vivo phosphorylation sites. In order to gain insight into the phosphoproteome of a eukaryotic cilium, we used the green alga C. reinhardtii, whose entire genome has been sequenced, as a model (23). This organism has many advantages for biochemical and molecular genetic studies of the flagellum. Importantly, as mentioned before, its flagellar proteome is known (33), and in addition, the proteome of the centriole that anchors the flagella is also known (11, 12).For the identification of the targets of the kinases and phosphatases in the flagella, phosphoproteomics can be applied. However, phosphoproteome analysis has been and still is a challenging task (19, 36, 47). This is due to a few facts, as follows. (i) Phosphoproteins can have more than one phosphorylation site, and the phosphorylation status of these sites can fluctuate depending on the physiological conditions of the cell. (ii) Only a small portion of a given protein in the cell can be phosphorylated. (iii) Furthermore, phosphoproteins, especially those of signaling pathways, are often proteins found in low abundance. Therefore, it is necessary to enrich the phosphopeptides. Among different methods, immobilized metal affinity chromatography (IMAC) is frequently used for phosphopeptide enrichment. In C. reinhardtii, phosphopeptides from proteins of the cellular, thylakoid, and eyespot phosphoproteomes were identified by this way (49, 50, 51, 52). Thereby, it became obvious that biochemical enrichment of subcellular fractions as it was done with the eyespot apparatus results in an increase of phosphopeptide identification (52). In this study, we used IMAC and tandem mass spectrometry (MS/MS) along with the acquisition of data-dependent neutral loss (MS/MS/MS spectra) to identify phosphopeptides from isolated flagella of C. reinhardtii. In this way, we identified 32 flagellar phosphoproteins, including different functional categories, along with 126 in vivo phosphorylation sites. In many cases, a dynamic phosphorylation pattern within one peptide was observed.     

Protein Structure from X-Ray Diffraction

Protein crystallography is the study of the three-dimensional structures of proteins at near atomic resolution. It has provided at remendous insight into the workings of numerous biological processes over the last few decades. The field has undergone a massive worldwide expansion over the last ten years, not only in academic laboratories, but also in the pharmaceutical industry. The main driving force for this expansion has been the promise of using three-dimensional atomic structures of proteins and other macromolecules to design lead drugs and to improve the action of existing drugs. This revised version was published online in July 2006 with corrections to the Cover Date.     

Flagellar Axonemes with 10 Microtubular Doublets in Spermatozoa from Gall-midges (Diptera,Cecidomyiidae)

Abstract The spermatozoa of some gall-midges (Cecidomyiidae, Lestremiinae), belonging to the tribe Micromyini, were seen to have an axoneme that consists of 10, instead of nine, microtubular doublets surrounding a central cylinder. In some related species within the same tribe the axoneme was found to contain a similar cylinder but to have nine doublets, as in typical flagella, or to have nine doublets and no central structure. These three types of axonemes can be given the shorthand designations “10+cyl”,“9+cyl”, and “9+0”. The tribe Lestremiini is characterized by a giant axoneme having 150 doublets in two rows reversely oriented. Other characteristics of examined spermatozoa are the electron density of the B-tubules of the axoneme, a feature shared by all members of the subfamily Lestremiinae, and the presence of a prominent cytoplasmic droplet containing numerous, regularly spaced microtubules, which is shared by all Micromyidi. These axonemal models are discussed from a phylogenetic point of view.     

Flagellar morphology in stumpy-flagella mutants of Chlamydomonas reinhardtii

Sixteen new mutants of the biflagellate green alga Chlamydomonas reinhardtii with either stumpy-flagella or no flagella at all were examined by electron microscopy. Four of the mutants were found to carry short bulbous flagella containing amorphous electron-dense material which may represent unassembled flagellar protein. Basal bodies of normal ultrastructure were present in all mutants. Dikaryon dominance tests indicated that the stumpy mutations were recessive to wild-type in all cases tested. Stumpy mutations also conferred a measure of detergent resistance to Chlamydomonas, apparently by affecting the detergent-solubility of the flagellar membrane.     

Selective Inhibition of Flagellar Activity in Chlamydomonas by Nickel

Flagellar activity in the biflagellate chlorophyte Chlamydomonas reinhardtii is selectively inhibited by Ni²⁺ or by treatment with Ca²⁺-chelating agents. Inhibitions of swimming speed, geotaxis, phototaxis, and pattern swimming result from qualitative and quantitative losses in the activity of individual flagella and in the coordination of activity beween the 2 flagella of each cell. Addition of Ca²⁺ (a) prevents inhibition and (b) restores normal flagellar activity in inhibited cells. Mg²⁺ is partially effective in reversal of inhibition. Other ions do not cause similar inhibition or reversal of nickel inhibition. The characteristics of inhibition and reversal suggest that the prmary target for nickel is a component of the flagellar apparatus, and that this component uses Ca²⁺ to perform its normal function in the regulation of flagellar activity. A 2nd target for nickel is a Carequiring process specific to phototaxis (and not involved in the photophobic response).     

X-Ray Diffraction Pattern from a Bilayer with Protein Outside

The X-ray diffraction pattern from a lipid bilayer has been reported previously; a series of fairly regularly spaced bands was both predicted and observed. In this note it is predicted that adding protein molecules at one or both surfaces of the bilayer will give rise to a cross-interference effect. For smaller amounts of protein, a more or less obvious ripple will be introduced into the bilayer pattern. The amount of protein, its thickness, and the distance from the bilayer to the protein layer all can be readily estimated from an observed ripple. Deciding whether the protein is all on one side or else distributed on both sides of the bilayer may be more difficult; by carefully recording and measuring the intensity near the center of the pattern one may be able to distinguish between the two possibilities. For larger amounts of protein, there will be more profound changes in the diffraction pattern. The theory developed here is applied in the following paper to a lipid dispersion incubated with cytochrome c and will be applied in a subsequent paper to a bacterial envelope. In an appendix it is shown that the patterns reported previously for several natural membranes do not confirm prediction for a normal, continuous lipid bilayer with all the protein outside. Thus it is doubtful that a structure of this kind is valid for these membranes.     

Flagellar Morphology in Stumpy-Flagella Mutants of Chlamydomonas reinhardtii1

Sixteen new mutants of the biflagellate green alga Chlamydomonas reinhardtii with either stumpy-flagella or no flagella at all were examined by electron microscopy. Four of the mutants were found to carry short bulbous flagella containing amorphous electron-dense material which may represent unassembled flagellar protein. Basal bodies of normal ultrastructure were present in all mutants. Dikaryon dominance tests indicated that the stumpy mutations were recessive to wild-type in all cases tested. Stumpy mutations also conferred a measure of detergent resistance to Chlamydomonas, apparently by affecting the detergent-solubility of the flagellar membrane.     

Flagellar Development During the Cell Cycle in Chlamydomonas reinhardtii

Flagellar development during the asexual synchronous cell cycle of Chlamydomonas reinhardtii (11.32 aM) was studied by light microscopy. Cell walls of sporangia of different developmental status were dissolved using gamete lysin (g-lysin) enabling direct observation of flagellar development. Flagellar growth in progeny cells exhibits a linear kinetic with a growth rate of 28 nm/min at 30°C leading to a flagellar length of 7–7.5 μm in 4–4.5 h. After this time the flagellar growth rate drops to 2.8 nm/min (as in interphase). Both flagella of a single cell and all flagella within a sporangium grow out at the same time and with the same rate. Cycloheximide (10 μg/ml) completely blocks flagellar development. If cycloheximide is removed flagellar growth resumes at the normal rate with no lag-phase. Flagellar development during the cell cycle in C. reinhardtii differs considerably from the well-studied model system of flagellar regeneration following amputation in the same species.     

A Role for the Membrane in Regulating Chlamydomonas Flagellar Length

Flagellar assembly requires coordination between the assembly of axonemal proteins and the assembly of the flagellar membrane and membrane proteins. Fully grown steady-state Chlamydomonas flagella release flagellar vesicles from their tips and failure to resupply membrane should affect flagellar length. To study vesicle release, plasma and flagellar membrane surface proteins were vectorially pulse-labeled and flagella and vesicles were analyzed for biotinylated proteins. Based on the quantity of biotinylated proteins in purified vesicles, steady-state flagella appeared to shed a minimum of 16% of their surface membrane per hour, equivalent to a complete flagellar membrane being released every 6 hrs or less. Brefeldin-A destroyed Chlamydomonas Golgi, inhibited the secretory pathway, inhibited flagellar regeneration, and induced full-length flagella to disassemble within 6 hrs, consistent with flagellar disassembly being induced by a failure to resupply membrane. In contrast to membrane lipids, a pool of biotinylatable membrane proteins was identified that was sufficient to resupply flagella as they released vesicles for 6 hrs in the absence of protein synthesis and to support one and nearly two regenerations of flagella following amputation. These studies reveal the importance of the secretory pathway to assemble and maintain full-length flagella.     

Effects of Organic Solvents on the Coupling Between ATP Hydrolysis and Sliding of Microtubules in Axonemes from Chlamydomonas Flagella

ABSTRACT. The effects of organic solvents on the ATPase activity and the sliding disintegration of axonemes from Chlamydomonas were investigated. The axonemal ATPase was markedly activated by methanol accompanying with marked inhibition of the sliding disintegration of axonemes. On the contrary, glycerol inhibited the ATPase activity without serious inhibition of the sliding disintegration. As far as the axonemes are not irreversibly denatured by extremely high concentration of solvents, the effects of solvents both on the ATPase and the ability of sliding are reversible. Therefore, the inhibition of sliding accompanied by the activation of ATPase is probably due to an inability to couple the hydrolysis of ATP to sliding between dynein and microtubule in the presence of methanol. The axonemal ATPase was less sensitive to vanadate inhibition after exposure to methanol. This indicates that methanol makes the dyneinADP.Pi complex unstable and increases product release. On the other hand, glycerol and ethylene glycol seem to stabilize the force generation responsible for the sliding through stabilizing the dynein.ADP.Pi complex.     

Flagellar tip activation stimulated by membrane adhesions in Chlamydomonas gametes

Membrane adhesions between the flagella of mating-type "plus" and "minus" gametes of Chlamydomonas reinhardi are shown to stimulate a rapid change in the ultrastructure of the flagellar tips, designated as flagellar tip activation (FTA). A dense substance, termed fibrous tip material (FTM), accumulates between the flagellar membrane and the nine single A microtubules of the tip. The A microtubules then elongate, growing into the distal region of the tip, increasing tip length by 30%. This study describes FTA kinetics during normal and mutant matings, presents experiments designed to probe its role in the mating reaction, and offers the following conclusions: (a) FTA is elicited by agents that cross-link flagellar membrane components (including natural sexual agglutinins, antiflagellar antisera, and concanavalin A) but not by flagellar adherence to polylysine-coated films. (b) FTA is reversed by flagellar disadhesion. (c) Gametes can undergo repeated cycles of FTA during successive rounds of adhesion/disadhesion. (d) FTA, flagellar tipping, and sexual signaling are simultaneously blocked by colchicine and by vinblastine, suggesting that tubulinlike molecules, perhaps exposed at the membrane surface, are involved in all three responses. (e) FTA is not blocked by short exposure to chymotrypsin, by cytochalasins B and D, nor by concanavalin A, even though all block cell fusion; the response is therefore autonomous and experimentally dissociable from later stages in the mating reaction. (f) Under no experimental conditions is mating-structure activation observed to occur unless FTA also occurs. This study concludes that FTA is a necessary event in the sexual signaling sequence, and presents a testable working model for its mechanism.     

Electrophysiological Recordings from the Giant Fiber Pathway of D. melanogaster

When startled adult D. melanogaster react by jumping into the air and flying away. In many invertebrate species, including D. melanogaster, the "escape" (or "startle") response during the adult stage is mediated by the multi-component neuronal circuit called the Giant Fiber System (GFS). The comparative large size of the neurons, their distinctive morphology and simple connectivity make the GFS an attractive model system for studying neuronal circuitry. The GFS pathway is composed of two bilaterally symmetrical Giant Fiber (GF) interneurons whose axons descend from the brain along the midline into the thoracic ganglion via the cervical connective. In the mesothoracic neuromere (T2) of the ventral ganglia the GFs form electro-chemical synapses with 1) the large medial dendrite of the ipsilateral motorneuron (TTMn) which drives the tergotrochanteral muscle (TTM), the main extensor for the mesothoracic femur/leg, and 2) the contralateral peripherally synapsing interneuron (PSI) which in turn forms chemical (cholinergic) synapses with the motorneurons (DLMns) of the dorsal longitudinal muscles (DLMs), the wing depressors. The neuronal pathway(s) to the dorsovental muscles (DVMs), the wing elevators, has not yet been worked out (the DLMs and DVMs are known jointly as indirect flight muscles - they are not attached directly to the wings, but rather move the wings indirectly by distorting the nearby thoracic cuticle) (King and Wyman, 1980; Allen et al., 2006). The di-synaptic activation of the DLMs (via PSI) causes a small but important delay in the timing of the contraction of these muscles relative to the monosynaptic activation of TTM (~0.5 ms) allowing the TTMs to first extend the femur and propel the fly off the ground. The TTMs simultaneously stretch-activate the DLMs which in turn mutually stretch-activate the DVMs for the duration of the flight. The GF pathway can be activated either indirectly by applying a sensory (e.g."air-puff" or "lights-off") stimulus, or directly by a supra-threshold electrical stimulus to the brain (described here). In both cases, an action potential reaches the TTMs and DLMs solely via the GFs, PSIs, and TTM/DLM motoneurons, although the TTMns and DLMns do have other, as yet unidentified, sensory inputs. Measuring "latency response" (the time between the stimulation and muscle depolarization) and the "following to high frequency stimulation" (the number of successful responses to a certain number of high frequency stimuli) provides a way to reproducibly and quantitatively assess the functional status of the GFS components, including both central synapses (GF-TTMn, GF-PSI, PSI-DLMn) and the chemical (glutamatergic) neuromuscular junctions (TTMn-TTM and DLMn-DLM). It has been used to identify genes involved in central synapse formation and to assess CNS function.     

Motor Regulation Results in Distal Forces that Bend Partially Disintegrated Chlamydomonas Axonemes into Circular Arcs

The bending of cilia and flagella is driven by forces generated by dynein motor proteins. These forces slide adjacent microtubule doublets within the axoneme, the motile cytoskeletal structure. To create regular, oscillatory beating patterns, the activities of the axonemal dyneins must be coordinated both spatially and temporally. It is thought that coordination is mediated by stresses or strains, which build up within the moving axoneme, and somehow regulate dynein activity. During experimentation with axonemes subjected to mild proteolysis, we observed pairs of doublets associating with each other and forming bends with almost constant curvature. By modeling the statics of a pair of filaments, we show that the activity of the motors concentrates at the distal tips of the doublets. Furthermore, we show that this distribution of motor activity accords with models in which curvature, or curvature-induced normal forces, regulates the activity of the motors. These observations, together with our theoretical analysis, provide evidence that dynein activity can be regulated by curvature or normal forces, which may, therefore, play a role in coordinating the beating of cilia and flagella.