Intraflagellar transport (IFT) during assembly and disassembly of Chlamydomonas - 《JCB》细胞生物学杂志干细胞之家

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Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66049; F% Q0 A/ O; A" k7 O+ T+ {
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Intraflagellar transport (IFT) of particles along flagellar microtubules is required for the assembly and maintenance of eukaryotic flagella and cilia. In Chlamydomonas, anterograde and retrograde particles viewed by light microscopy average 0.12-μm and 0.06-μm diameter, respectively. Examination of IFT particle structure in growing flagella by electron microscopy revealed similar size aggregates composed of small particles linked to each other and to the membrane and microtubules. To determine the relationship between the number of particles and flagellar length, the rate and frequency of IFT particle movement was measured in nongrowing, growing, and shortening flagella. In all flagella, anterograde and retrograde IFT averaged 1.9 μm/s and 2.7 μm/s, respectively, but retrograde IFT was significantly slower in flagella shorter than 4 μm. The number of flagellar IFT particles was not fixed, but depended on flagellar length. Pauses in IFT particle entry into flagella suggest the presence of a periodic "gate" that permits up to 4 particles/s to enter a flagellum.
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Cilia and eukaryotic flagella are microtubule-containing organelles that project from the surfaces of many eukaryotic cells. Motile cilia are widely recognized for their roles in protozoan and sperm motility, for mucus transport over oviduct and respiratory cell surfaces (Dentler, 1987), and for embryonic tissue morphogenesis (Nonaka et al., 1998; Pazour and Rosenbaum, 2002; Nauli et al., 2003; Pazour and Witman, 2003; Snell et al., 2004). Nonmotile sensory cilia detect fluid flow over endothelial cells (Praetorius et al., 2003; Iomini et al., 2004). Typical flagella are composed of a microtubular axoneme, and both the assembly and turnover of microtubule protein occur at the distal tip (Gorovsky et al., 1970; Johnson and Rosenbaum, 1992; Stephens, 2000; Song and Dentler, 2001). Microtubule disassembly is less well understood and may occur at either the distal or proximal ends (Stephens, 2000; Parker and Quarmby, 2003). Flagellar length is determined by the microtubules, but within an axoneme examples of precisely regulated lengths of individual A, B, and central microtubules occur (Dentler, 1981, 1987, 1990). The regulation individual microtubule lengths may be a property of the caps that link the A and central microtubules to the membrane (Dentler, 1980, 1981; LeCluyse and Dentler, 1984), and the length of the entire cilium may be regulated by protein kinases (Pan et al., 2004) or by a family of LF proteins that reside in the cell body (Barsel et al., 1988; Asleson and Lefebvre, 1998; Berman et al., 2003; Tam et al., 2003; Nguyen et al., 2005).

Flagellar assembly and maintenance requires intraflagellar transport (IFT) (Kozminski et al., 1993, 1995). In most cilia, heterotrimeric kinesin-2 is responsible for the anterograde movement of IFT particles to the flagellar tips, and cytoplasmic dynein mediates the transport of particles to the flagellar base. If either the motors or associated proteins are disrupted, flagella either fail to assemble or, in temperature-sensitive mutants, flagellar microtubules disassemble at restrictive temperatures (Kozminski et al., 1995; Cole et al., 1998; Pazour et al., 1998; 1999; Porter et al., 1999; Marshall and Rosenbaum, 2001; Cole, 2003; Scholey, 2003; Snow et al., 2004). Using a novel kymographic method, IFT particles were discovered to undergo nearly continuous movement up and down flagella (Iomini et al., 2001).9 {/ X8 |6 L8 r/ e3 L
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Although the importance of IFT for flagellar assembly is well established, its role in flagellar length regulation is not understood. Based on an immunological analysis of IFT proteins, an "equilibrium balance" model in which the number of IFT particles in a flagellum is fixed and their rate or frequency of movement regulates flagellar length was proposed (Marshall and Rosenbaum, 2001; Marshall, 2002; Marshall et al., 2005). This model predicts that either the frequency of IFT particles that enter flagella or the rates at which IFT particles move must decrease as flagellar length increases and must increase as flagella shorten. In cells with equal length flagella, the number and frequency of IFT particles should be identical, but in cells with unequal length flagella the longer flagellum should have fewer IFT particles than does the shorter flagellum.$ p& X6 [( j) J/ Z% d, V- `; G3 ^4 A
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To test this hypothesis, the rate and frequency of IFT particle movement was examined in steady-state, growing, and disassembling flagella on Chlamydomonas cells. Flagella on three mutants with paralyzed flagella, two with abnormally long flagella, and one with unequal length flagella and bulbous, IFT particle-filled tips (Ulf mutant) were examined to determine the following questions. (1) Does the rate of anterograde and retrograde IFT change as a function of flagellar length (2) Is IFT continuous or do particles start and stop within the flagellum (3) Does the frequency or periodicity of IFT particle entry into flagella change as a function of flagellar length (4) Is the movement of IFT particles coordinated in the two flagella on a single cell (5) Is the rate or frequency of IFT affected if IFT particles are abnormally accumulated at the tip of a flagellum

The results revealed that (a) the rate of IFT is nearly constant and, with the exception of very short flagella, is independent of flagellar length; (b) IFT particle entry into flagella is periodic, but gap or pauses in particle entry occurred; (c) gaps in particle entry are not coordinated between the two flagella on a single cell; and (d) accumulations of IFT particles at flagellar tips have little effect on the rate or frequency of IFT particle transport.

Based on the widths of kymograph tracks, the diameter of anterograde and retrograde particles were 0.12 μm and 0.06 μm, respectively. Similar sized aggregates of smaller particles attached to both the microtubules and the flagellar membrane were observed in thin-sectioned flagella. When examined by negative staining, the IFT particles were found to be formed by smaller particles linked by filaments. The IFT particles are linked to microtubules by discrete structures that may be the motor proteins.
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Three different anterograde and retrograde tracks are present in flagellaThe movement of IFT particles was visualized using a modification of the kymograph method developed by Piperno et al. (1998). The pattern of IFT particle movement in a single Chlamydomonas flagellum is shown in Fig. 1 A. For most kymographs shown here, the entire flagellum is shown for a 40-s period. IFT particles are visible throughout the flagellum, although the refraction of the cell body makes it difficult to observe regions closest to the cell bodies. Because the depth of focus of the 100x NA 1.4 lens at the wavelength used was 0.3 μm, most or all particle movement within a 0.2-μm-diameter flagellum should be visible in these micrographs.

The width of individual anterograde and retrograde particle tracks remained constant throughout the length of the flagellum. Anterograde tracks were approximately twice the width of retrograde tracks. Some variation in the thickness of tracks was observed (Fig. 1 B), and occasionally tracks appeared to merge, although close examination of the tracks suggested that the particles overlapped rather than merged, as if they were moving along different microtubules (Fig. 1 C). Some particles appeared to reverse direction before reaching the distal tip (Fig. 1 B), but most tracks extended entirely to the tip or base.6 W2 E* A( g( m. R# S
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In some flagella, tracks of larger particles moved more irregularly and with significantly slower velocity than the smaller particles (Fig. 1, A and G). These particles oscillated back and forth along the flagellum, paused often, and occasionally made extended tracks. Rarely did the tracks extend completely to the flagellar tip or flagellar base. This motility is clearly different from the more regular patterns of IFT particle movement, and probably reflects extraflagellar movement of particles first described by Bloodgood (1977)./ P% O# Y9 R! T* y) _- y5 R* X

IFT particle structure and association with microtubules and membranesThe size of IFT particles was estimated by measuring the width of anterograde and retrograde particle tracks. Anterograde particle tracks averaged 0.12 ± 0.03 μm (333 tracks) and retrograde tracks averaged 0.06 ± 0.02 μm (326 tracks). There were no significant differences in the sizes of anterograde and retrograde particles in nongrowing flagellar or in flagella induced to shorten with 20 mM sodium pyrophosphate or with high salt, and in flagella regenerating after deflagellation by pH shock. Minor variations in anterograde and retrograde IFT track width (Fig. 1 B) may represent differences in particle size, packing density, or overlapping particles moving along different microtubules, each of which would alter the apparent size in differential interference contrast (DIC) images.0 T$ Z: B1 R; D5 K* }$ X
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To determine the structure of IFT particles, flagella were examined by EM (see Figs. 1–4). Thin sections of nongrowing flagella (Fig. 1, D–F; Fig. 2, A and G–J; Fig. 3, A and D) revealed the presence of structures similar to the IFT particles identified by Kozminski et al. (1993). Particles appeared either as densely packed structures or as less dense linear particle arrays. IFT particles also were linked to the membrane, most evidently shown when the membrane ballooned away from the axoneme (Fig. 2 A, arrowhead). These membrane links also were visible in newly forming cilia (Fig. 2, B–D) and at the distal microtubule tips of growing or fully-grown flagella (Fig. 2, E–I, K). The particles averaged 0.15 μm in length but could be grouped into two broad classes of large particles, 0.13–0.25 μm, and smaller particles, 0.01–0.09 μm, each of which were comparable to the large (0.12 μm) and small (0.06 μm) particles estimated from kymograph tracks.

To determine when the IFT particles first appear in flagella, pf18 cells were amputated by pH shock and were fixed and flagella regrew. Early stages of flagellar growth are shown in Fig. 2 (B–E). Flagellar tips were first filled with particles (Fig. 2, B and E), but as microtubules formed, the amorphous particles disappeared and short IFT-like particle aggregates, similar to the moving IFT particles observed by DIC, appeared (Fig. 2, D–H).% q% Y' m  J  J6 p+ Z
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In a previous study, a Chlamydomonas ulf mutant with bulged flagellar tips full of IFT particles was found to contain numerous small particles linked by filamentous structures (Tam et al., 2003). To determine if the IFT particles seen here have similar structures, flagellated cells were attached to grids, extracted with detergent, and negatively stained. As shown in Fig. 3, filamentous particle arrays were found along the sides of microtubules (Fig. 3, B, C, and E) and at the distal microtubule tips (Fig. 3 F). Occasionally these particles formed tight aggregates (Fig. 3 E), but they often spread on the grid to reveal linear particle arrays (Fig. 3, B and C) linked to microtubules by discrete structures, possibly motor proteins.: ^0 }+ b$ C8 ]8 k& ?0 m2 c
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Because these preparations were made by attaching flagellated cells to grids and extracting them with detergent, it was possible that the particle arrays were unrelated debris caused by the extraction technique. Because IFT particles are depleted in the temperature-sensitive fla10-1 cells incubated at 32°C (Kozminski et al., 1995), fla10-1 cells were extracted before and after treatment at 32°C for 60 min. As expected, the filamentous particle arrays were observed in fla10-1 at room temperature, but only rarely were observed at 31°C. Because occasional IFT particles are seen in fla10-1 cells examined by DIC microscopy after 1 h at 60°C (unpublished data), these results confirm that the filamentous particle arrays are IFT particles.
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IFT rates and particle frequency in growing and fully grown flagellaThe length control hypothesis proposed by Marshall et al. (2005) is based on immunochemical evidence that each flagellum, regardless of its length, contains a fixed number of IFT particles. Because the number of IFT particles/flagellum is fixed, then either the rate of IFT particle movement or the spacing of IFT particles along a flagellum should change as flagella grow or shorten.

To test this hypothesis, the rates of IFT particle movement and the frequency of IFT particles along a flagellum were measured from kymograms similar to those shown in Fig. 1. Rates and particle frequency were measured in nongrowing flagella and in flagella induced to shorten or grow. IFT was recorded in two paralyzed mutants, three mutants with mutations that produce abnormally long flagella, and one mutant with unequal length flagella. Greater than 23,000 individual IFT tracks were measured in 316 different flagella.

As shown in Table I, IFT rates in nongrowing flagella on different flagellar mutants varied slightly, with anterograde rates ranging from 1.6 to 1.9 μm/s and retrograde rates ranging from 2.1 to 2.8 μm/s. There were 1.2–1.4 anterograde and 1.3–1.5 retrograde particle tracks/s. The range of IFT rates and number of particle tracks within any single mutant showed less variation than was observed among different mutants. Colchicine, which blocks microtubule assembly but not the exchange of nontubulin flagellar proteins (Song and Dentler, 2001), had no effect on the IFT rate or frequency.) w" I  c* K. v( ?+ b: z

To determine if IFT rates or particle track frequencies are related to flagellar length, flagellar shortening was induced with 20 mM sodium pyrophosphate (Fig. 4) or by raising the sodium and lowering the calcium concentrations. These were chosen because they are reversible and because they partially paralyze flagella, which makes IFT easy to record. IFT also was recorded when flagella were induced to grow by removal of pyrophosphate (Fig. 4). IFT in growing flagella was observed (a) when cells were washed out of pyrophosphate; (b) in cells assembling new flagella after flagellar amputation induced by pH shock (see Fig. 6, see Table IV); and (c) in cells flagella induced to elongate by 20 mM LiCl (Tuxhorn et al., 1998).9 {! q  a% y8 @

In five different Chlamydomonas mutants, the rate and number of anterograde and retrograde particle tracks over a 40-s (600 image) time period exhibited little variation relative to flagellar length (Table I). Histograms of the rates of representative flagella, which provide a better indication in the variation and distribution of rates, are shown in Fig. 5, and histograms of flagella regenerating after pH shock are shown in Fig. 64 D+ G+ X7 A; _& m% w" k( {

Although the average IFT rates did not significantly change as flagella shortened and grew, some shifts in IFT rates did occur in very short flagella. Cells induced to shorten flagella with high salt (Lefebvre et al., 1978) exhibited frequencies of IFT similar to those in control cells (Fig. 5, compare A, B, and E with F) until flagella were shorter than 4 μm., at which length retrograde IFT rates decreased (Fig. 5, compare F and I). In 4–5-μm-long flagella, two flagella on the same cell exhibited different distributions of rates of retrograde and anterograde IFT during the 40-s recording period (Fig. 5, G and H). A slight increase in the distribution of anterograde IFT was observed during rapid flagellar growth after cells were transferred from pyrophosphate, but this returned to control rates as the flagella elongated (Fig. 5, compare C and D with A and B). Short regenerating flagella after pH shock also showed similar anterograde and retrograde IFT rates, but as flagella grew longer than 4 μm, the distribution of anterograde and retrograde rates reached those of control flagella (Fig. 6, Table IV).8 ]5 B$ g/ N% j. a
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Together, these data reveal that IFT rates and frequency, averaged over a 40-s period, are nearly constant in five different flagellar mutants, and that the rates and frequency of IFT are nearly constant in nongrowing, shortening, and growing flagella. Flagella shorter than 4 μm exhibit a slightly slower rate of retrograde IFT than do flagella longer than 4 μm, which may indicate important differences between short and longer flagella.6 Y5 C' C1 G" o5 o* ~
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IFT particle accumulations do not impede IFTMost IFT particles move completely to the distal flagellar tip, by kinesin-2, and then are transported proximally to the flagellar base by cytoplasmic dynein (Pazour et al., 1998; Porter et al., 1999). Switches that regulate motor activity are likely to be located at the distal flagellar tip. Two classes of Chlamydomonas mutants accumulate particles at flagellar tips. The tips cDhc1b flagellar mutants fill with IFT particles and disassemble. Observations of these flagella suggested that IFT particle accumulations might stimulate flagellar disassembly. By contrast, IFT particles fill the tips of unequal length (ulf) flagellar mutants, but these flagella grow more than twice the length of normal flagella, despite the accumulation of IFT particles at their tips (Tam et al., 2003). Because flagellar growth in ulf mutants is slower than that in wild-type cells, it is possible that IFT particle accumulations at the tips may alter IFT rates or alters the switches that induce retrograde transport (Tam et al., 2003; unpublished data).8 P& I& z, @& P0 d/ e- @

Surprisingly, both the rates and frequencies of IFT in ulf-2 flagella were similar to those for other cells (Fig. 7, Table I). Anterograde IFT in ulf-2 flagella was slightly slower than that measured in other flagella (Table I), as was the periodicity of IFT particles (see Table III), which suggests that the accumulation of IFT particles at the tips may slow flagellar assembly and have small effects on IFT rate and frequency; but these effects are small, relative to the rates and frequencies observed in flagella that lack such particle accumulations.

IFT particle entry into flagella is periodicIn Chlamydomonas, two flagella usually grow at the same time and are nearly equal in length, which suggests that IFT in the two flagella may be coordinated. Alternatively, the observations of ulf mutants, with unequal length flagella, the independent flagellar shortening and growth on cells with one amputated flagellum (Rosenbaum et al., 1969) and the selective shortening of long flagella on mated lf and wild-type cells (Asleson and Lefebvre, 1998) suggested that IFT in the two flagella may not be coordinated. To determine if IFT is coordinated in two flagella, IFT was recorded in both flagella on individual cells was recorded for most of the cells described here. Representative IFT tracks in both flagella are shown in Fig. 8 (also see Fig. 4 A, B, and D; Fig. 9).
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Comparison of the two flagella revealed that anterograde and retrograde tracks were not uniformly spaced, and occasionally pauses of several seconds occurred during which no IFT was observed in one flagellum while IFT proceeded normally in the sister flagellum (Fig. 8). No anterograde or retrograde IFT was observed during these pauses, which indicates that no IFT particles entered the flagellum during the pauses. These data show that IFT is not well coordinated between the two flagella on a single cell.9 C5 O: m" j. X9 K4 s- e
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The periodicity of particle entry was examined by longitudinal reinforcement of IFT track images (Dentler and Cunningham, 1977; Kim et al., 1979). These images (Fig. 4; Fig. 7, A–C) revealed that particle entry into a flagellum is periodic and that, even after a pause in particle entry into the flagellum (no IFT tracks found in the flagellum), particle entry resumed in accordance with the period of other tracks. Additionally, both anterograde and retrograde periodicities were enhanced, indicating that they are coordinated. As with the anterograde and retrograde rates, the period of particle entry did not significantly change during flagellar growth or resorption and was consistent in all cells examined. For the 199 flagella examined, the average number of starts/s was 4.2 ± 0.6 (Table II). This was greater than the average number of IFT tracks/flagellum observed for 40 s (Table I), which is consistent with periodic pauses observed in the entry of particle tracks into flagella seen in kymographs presented here.) ], W1 W$ Y+ K  {; d" T! W2 Z
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The number of IFT particles is not fixed, but is a function of flagellar lengthThe number and frequency of particle tracks do not appear to be related to flagellar growth, so the number of particles within a flagellum should be proportional to flagellar length. To confirm this, the number of particle tracks within a 1- or 2-μm x 1 min area was counted. The results (Table III) show that growing, shortening, and control flagella contain an average of 3.8 ± 0.7 particles/μm/s. The same particle number was found in short (8 r; e9 t1 \& b) f' S0 [- N- H# |) u

Discussion
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The mechanisms that regulate the lengths of eukaryotic cilia and flagella remain a mystery. Their assembly and disassembly have been well documented, as have numerous mutants with abnormally short or abnormally long flagella and cells that contain cilia with different lengths (Dentler, 1981, 1987; Lefebvre and Rosenbaum, 1986). Even within individual flagella, the regulation of microtubule length must be locally controlled. In ctenophore macrocilia, many individual axonemes are contained in a single membrane and each axoneme has its own characteristic growth rate and final length (Tamm and Tamm, 1988). Within single axonemes, there is clear evidence for independent regulation of the lengths of specific doublet microtubules (Tyler, 1979) and central microtubules (Omoto and Witman, 1981). Although mechanisms that regulate assembly are unknown, it is clear that flagellar microtubules and associated structures assemble at the distal tips (Johnson and Rosenbaum, 1992), so one site of length regulation is likely associated with these tips, possibly with microtubule capping structures (Dentler, 1980; Dentler and Rosenbaum, 1977).

Flagellar components appear to be transported to the distal tips by IFT (Kozminski et al., 1995; Cole et al., 1998; Piperno et al., 1998; Pazour and Rosenbaum, 2002; Rosenbaum and Witman, 2002; Qin et al., 2004; Snell et al., 2004). Flagellar assembly requires both kinesin-2 (Walther et al., 1994; Matsuura et al., 2002; Mueller et al., 2005) and cytoplasmic dynein (Pazour et al., 1998, 1999; Porter et al., 1999). In the temperature-sensitive kinesin-2 Chlamydomonas mutant fla10-1, both IFT and flagellar protein incorporation ceases at 32°C, and IFT (Song and Dentler, 2001; Kozminski et al., 1995; Piperno et al., 1998) and flagella disassemble, which confirms that IFT is required for assembly. The role of IFT in flagellar disassembly is less certain. At restrictive temperature, fla10-1 flagella shorten without IFT (Kozminski et al., 1995; Iomini et al., 2001), so IFT may only be necessary to return anterograde motors and IFT proteins to the cell body. Flagellar disassembly may occur by IFT-independent removal of flagellar components near the basal body (Stephens, 2000; Parker and Quarmby, 2003).# P. V2 x: @& X3 q

Based on the importance of IFT, the rate of flagellar assembly, immunoblot analysis of IFT proteins, and the exchange of flagellar proteins with a cytoplasmic pool (Gorovsky et al., 1970; Stephens, 2000; Song and Dentler, 2001), Marshall et al. (2005) proposed a "balance-point equilibrium" hypothesis in which the number of IFT particles in a flagellum is constant, regardless of flagellar length, and that the number and rate of movement of IFT particles determines flagellar length.# L% n3 @' \3 ?! j" q# C

If the number of IFT particles in a flagellum is constant, either the frequency of IFT particles along the flagellum must decrease as flagella grow or the rate of anterograde or retrograde particle movement should decrease. Conversely, as flagella shorten, the frequency of particles along flagella should increase or IFT rates must increase. In the data reported here, no significant differences in IFT rate or frequency were observed in steady-state flagella on several different Chlamydomonas mutants. The same rates and particle frequencies were observed in flagella induced to shorten by sodium pyrophosphate or high Na /low Ca2  treatment. When washed back into culture medium or Hepes buffer, flagella regrew but maintained the same IFT rates and frequencies. Similar results were observed in flagella growing after pH shock amputation of old flagella. The data reported here do not support the balance-point hypothesis.1 d% b: o8 \% f

In flagella shorter than 4 μm there was a slight reduction of the retrograde IFT rate compared with longer flagella, but this was not sufficient to support the balance-point hypothesis. This slight difference may be interesting to examine further, particularly with the discovery of two motors, moving at different rates in the proximal and distal regions of Caenorhabditis elegans cilia (Snow et al., 2004).

Examination of individual particle tracks revealed numerous gaps or pauses in IFT particle entry into flagella. Based on the number of anterograde particle tracks observed during the 40-s recordings, particles entered flagella at an average of 1.4 particles/s. When the periodicity of particle entry was examined by longitudinal reinforcement of the kymographs, particle entry appeared to be periodic, with a maximum of 4 particles/s that could enter and leave the flagellum. This indicates that particle entry is periodically regulated and that the pauses or gaps in particle entry may reflect the readiness of a particle to pass a checkpoint. Because the pauses were not coordinated between two flagella on a single cell, IFT particle entry may be regulated individually by each flagellum. The nature of the entry checkpoint is not understood but it might be associated with proteins identified by Deane et al. (2001).

IFT particle accumulations at the tips of ulf mutants (Tam et al., 2003) might be expected to interfere with either the reversal of IFT particle movement or with flagellar growth or disassembly. Flagellar assembly progressed more slowly in these mutants than in wild-type cells (Tam et al., 2003; unpublished data) and the rate of anterograde IFT was slightly reduced from those in wild-type flagella. However, retrograde transport and frequency was not reduced, so the accumulation of IFT particles at flagellar tips seem to present no major obstacle to IFT particle movement or to the switching of motors that start retrograde particle movement.9 p! U& m% q3 S2 E. E
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The kymographs also revealed that retrograde particles were approximately half the size of anterograde particles, and similar sized particles were found using electron microscopy. As deflagellated cells regenerate flagella, the particles fill the region distal to the basal body and often appear attached to the membrane and, as flagellar microtubules assemble, small particle aggregates are formed. These aggregates are linked by filamentous structures, best observed in negatively stained flagella. The particles are attached both to the microtubules, presumably by the motor proteins, and to the membrane by short structures. The membrane-attachment of IFT particles has not been described previously but they may be related to the cytoplasmic dynein-containing microtubule–membrane bridges first identified in Tetrahymena and scallop cilia (Dentler et al., 1980). Further characterization of IFT particle structure and their associations with flagellar membranes will be important.7 o+ A+ A1 H8 {

Can data presented here, showing that the number of IFT particles is a function of flagellar length, be reconciled with the balance-point hypothesis, in which the number of IFT particles recognized by antibodies in each flagellum appears to be fixed (Marshall and Rosenbaum, 2001; Marshall et al., 2005) Two models are presented in Fig. 10. Model A is consistent with data presented here, in which the number of IFT particles increases with flagellar length. This model predicts that particles in addition to those identified immunologically may remain to be discovered. Model B is based on the structure of IFT particles and indicates that some of the particle aggregates may stretch along the microtubules and produce small densities observed in the kymographs. In this model, the number of IFT particle aggregates in a flagellum would remain constant but the number of visible particles would be proportional to flagellar length. Further studies will be required to identify additional IFT components or to define ways the particle aggregates can form multiple IFT aggregates seen by DIC.) A; |' R2 ^# j
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Rather than regulating the number of particles within a flagellum, it is likely that flagellar microtubule length is regulated by the loading of flagellar proteins on IFT particles, at flagellar bases, and the unloading of proteins from IFT particles, at flagellar tips. Three proteins, mutations in which cause abnormally long flagella (LF1, LF2, LF3), form particulate structures in the cell body and may be involved in loading material onto IFT particles (Barsel et al., 1988; Asleson and Lefebvre 1998; Tam et al., 2003; Nguyen et al., 2005), and a fourth protein (LF4) is located in the flagellum (Berman et al., 2003). A Chlamydomonas aurora-like kinase (CALK) associated with flagellar disassembly has been identified (Pan et al., 2004), but the location of CALK is not understood. It is likely that these components are associated with signaling systems that determine the length of individual microtubules and, as previously suggested (Dentler, 1981), it is reasonable to suggest that the selection of components for individual microtubules from the IFT transport particles is performed by proteins associated with the capping structures at microtubule tips.

Materials and methods' ^7 O+ T! V5 ]$ Y' V0 ?

Chlamydomonas cells were cultured in minimal medium (Sager and Granick, 1953) with continuous aeration on a 12-h light/ dark cycle and were used 3–4 h after the start of the light period. Paralyzed mutants (pf18 [cc1036)], lf3-2 [13c2, from a cross between lf3 and pf16)], pf16 [13a2, from a cross between lf3 and pf16]) were used to facilitate recording IFT. Motile lf2 and ulf cells were paralyzed with 20 mM pyrophosphate (pH 7.0) or 20 mM LiCl. LF, 13c2, 13a2, and ulf mutants were obtained from L.-W. Tam and P. Lefebvre (University of Minnesota, St. Paul, MN), and pf18 from the Chlamydomonas Genetics Center.
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Light microscopy and analytical methodsFor microscopy, #0 (22 x 22 mm) and #1 (24 x 60 mm) coverslips (Gold Seal #3026 and #3323, respectively) were cleaned in deionized water and detergent, rinsed in deionized water, and oven dried. Cleaned 24 x 60-mm coverslips were attached with double-stick tape to 25 x 75 x 1-mm aluminum bars prepared with a 22 x 22-mm cutout. Cleaned 22 x 22 mm coverslips were treated with 1 mg/ml poly-L-lysine for 2–12 h and rinsed with deionized water and culture medium or HM (50 mm Hepes, pH 7.1, and 2 mM MgSO4) immediately before applying cells.

Cells were pelleted in a clinical centrifuge and gently suspended in fresh minimal medium or in HMC (HM 1 mM CaCl2). 4-ml aliquots of cells were placed in 6-well culture dishes and rotated at RT for the duration. For length measurements, 100-μl aliquots of cells were fixed with 100 μl of 2% glutaraldehyde in HMC.
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To prepare IFT chambers, 50 μl of the suspended cells were applied to poly-lysine–treated coverslips, incubated for 1–3 min, and then inverted over the mounted 24 x 60-mm coverslip. The two coverslips were separated by Parafilm strips. Excess medium was removed with filter paper and chambers were sealed with VALAP (1:1:1 Vaseline/Lanolin/Paraffin).$ I1 i* C6 z- n. w( E
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Cells were viewed at RT with a microscope (Axioplan 2ie; Carl Zeiss MicroImaging, Inc.), 100x/1.4 PlanApochromat lens, 1.4 NA condenser lens, and DIC optics. Samples were illuminated using a 100-W halogen lamp, UV and green interference filters. Cells were healthy for at least 3 h of recording. Images were projected onto a Nuvicon camera (Dage-MTI) using a 1.6x optovar (Carl Zeiss MicroImaging, Inc.) and an 8x eyepiece in a projection tube (Carl Zeiss MicroImaging, Inc.), and contrast was enhanced using Dage and Image image processors. Images were collected at 15 frames/s for 600 frames (40 s) with a Macintosh 6500 computer, and Scion frame grabber board.
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Cells were selected for the presence of straight flagella and the orientation of their flagella relative to the DIC shear. Whenever possible, cells in which IFT could be observed in both flagella were selected. Image stacks were transferred to a Macintosh G4 computer and opened in Image J (http://rsb.info.nih.gov/ij/). To produce kymographs, images were rotated to orient each flagellum vertically, with the flagellar distal tip at the top. A selection containing part or all of the flagellum was made, resliced, and Z-projected on screen. IFT rates were determined by measuring the angle of the IFT particle tracks using Image J and measurements were recorded and transferred to Excel (Microsoft). Kymographs, saved as TIFF files, were filtered using Photoshop CS (Adobe Corp.) by applying Gaussian blur (0.7) and unsharp mask (298%, 2.7 pixel radius, 1 threshold). For optical reinforcements, filtered kymographs were selected, copied to new layers, reduced to 30% transparency, and moved to generate reinforcements. The distance shifted was measured using Photoshop.! W1 t6 m8 R! K( V
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Flagellar elongation and shorteningTo induce flagellar shortening, cells were harvested and suspended in minimal medium with 20 mM sodium pyrophosphate (pH 7.0) (Lefebvre et al., 1978). This also paralyzed flagella, which facilitated IFT recordings. Flagellar regrowth was observed by harvesting cells from pyrophosphate and suspending them in fresh medium. Flagellar resorption also was induced by suspending cells medium containing low Ca2 , 25 mM NaCl, and 0.7 mM KCl (Lefebvre et al., 1978). To observe newly assembling flagella, cells were amputated by pH shock and allowed to regenerate (Lefebvre, 1995). Flagellar length in the population of cells were determined by fixing cells with an equal volume of medium containing 2.5% glutaraldehyde and measuring lengths using Image J.

Electron microscopyFor thin sections, cells were cultured as described above, gently pelleted, suspended in M medium, and were fixed by adding an equal volume of M medium containing 5% glutaraldehyde and embedding in Embed 812 (Dentler and Adams, 1992). Sections were stained with methanolic uranyl acetate followed by lead citrate.

A modification of the method described by Dentler and Rosenbaum (1977) was used for negative staining. Cells were concentrated and suspended in a small volume of HMC (10 mM Hepes, 0.1 mM CaCl2, and 1 mM MgSO4) and a drop of cells was applied to a poly--lysine treated carbon-formvar film on a copper grid. The grid, containing cells, was then inverted over a drop of HMC at 4°C followed by inversion over 0.005–0.1% Nonidet P-40 detergent in HMC for 5–20 s at 4°C. Cells then were rinsed with cold HMC, stained, with 1% aqueous uranyl acetate, and air dried. Samples were examined with a transmission electron microscope (1200 EXII; JEOL), photographed using a MegaView camera (Soft Imaging System); images were adjusted for contrast and cropped using Photoshop.

Acknowledgments

I thank Dr. David Moore-Nichols for help with Image J, Dr. Pete Lefebvre for supplying cell stocks and for critical reading of this manuscript, Drs. Sid Tamm and Lai-Wa Tam for many helpful comments, and Dr. Bill Snell for his encouragement.

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