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Vol. 17, Issue 12, 5075-5093, December 2006
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-Tubulin ComplexWellcome Trust Centre for Cell Biology, Edinburgh University, Edinburgh EH9 3JR, United Kingdom
Submitted November 3, 2005;
Revised September 8, 2006;
Accepted September 25, 2006
Monitoring Editor: Trisha Davis
| ABSTRACT |
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-tubulin complex (
-TuC). We identified three genes, gfh1+, mod21+, and mod22+, in a screen for fission yeast mutants affecting microtubule organization. gfh1+ is a previously characterized
-TuC protein weakly similar to human
-TuC subunit GCP4, whereas mod21+ is novel and shows weak similarity to human
-TuC subunit GCP5. We show that mod21p is a bona fide
-TuC protein and that, like gfh1
mutants, mod21
mutants are viable. We find that gfh1
and mod21
mutants have qualitatively normal microtubule nucleation from all types of microtubule-organizing centers (MTOCs) in vivo but quantitatively reduced nucleation from interphase MTOCs, and this is exacerbated by mutations in mod22+. Simultaneous deletion of gfh1p, mod21p, and alp16p, a third nonessential
-TuC protein, does not lead to additive defects, suggesting that all three proteins contribute to a single function. Coimmunoprecipitation experiments suggest that gfh1p and alp16p are codependent for association with a small "core"
-TuC, whereas mod21p is more peripherally associated, and that gfh1p and mod21p may form a subcomplex independently of the small
-TuC. Interestingly, sucrose gradient analysis suggests that the major form of the
-TuC in fission yeast may be a small complex. We propose that gfh1p, mod21p, and alp16 act as facultative "noncore" components of the fission yeast
-TuC and enhance its microtubule-nucleating ability. | INTRODUCTION |
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-tubulin and associated proteins that are alternatively known as gamma-complex proteins (GCPs) or gamma-ring proteins (Grips) (Zheng et al., 1995
-tubulin complexes (
-TuCs) have been identified, and these may vary in their relative abundance in different types of cells. The smaller complex is known as the
-tubulin small complex (
-TuSC) and contains two copies of
-tubulin and one copy each of GCP2 and GCP3 (Oegema et al., 1999
-tubulin ring complex (
-TuRC), contains multiple copies of
-tubulin, GCP2, and GCP3, plus the additional proteins GCP4, GCP5, and GCP6 (Fava et al., 1999
-TuRC is much more active for microtubule nucleation than the
-TuSC (Oegema et al., 1999
-TuRC has been observed to form a "lock-washer" structure that may be made up of several linked
-TuSCs, allowing the
-TuRC to act as a direct template for microtubule nucleation (Zheng et al., 1995
-TuRC and
-TuSC to microtubule nucleation inside living cells; thus, it remains an open question to what extent both large and small
-TuCs are directly involved in nucleation in vivo, and whether different complexes may be involved in different types of microtubule nucleation.
In the budding yeast Saccharomyces cerevisiae,
-tubulin (Tub4p) and the GCP2 and GCP3 homologues Spc97p and Spc98p, respectively, are all essential proteins. They form a "Tub4 complex" that is recruited to the nucleoplasmic face of the spindle pole body (SPB; the yeast centrosome equivalent) by the protein Spc110p and to the cytoplasmic face of the SPB by Spc72p (Knop and Schiebel, 1998
, and references therein). However, budding yeast homologues of GCP4, GCP5, and GCP6 have not been identified; thus, it is not clear whether budding yeast can serve as a useful model for understanding the function of the proteins that contribute to the formation of the larger
-TuRC.
Unlike budding yeast, microtubule nucleation sites in the fission yeast Schizosaccharomyces pombe are not restricted to the SPB, but rather they are also found on the nuclear envelope and on microtubules themselves during interphase (so-called interphase microtubule-organizing centers, or iMTOCs), and at the cell division site during mitosis (the so-called equatorial microtubule-organizing center, or eMTOC; Hagan, 1998
; Drummond and Cross, 2000
; Tran et al., 2001
; Sawin et al., 2004
; Zimmerman et al., 2004
; Janson et al., 2005
; Sawin and Tran, 2006
). The fission yeast homologues of
-tubulin, GCP2, and GCP3 are known as gtb1p/tug1p, alp4p, and alp6p, respectively, and all three proteins are essential for viability (Horio et al., 1991
; Stearns et al., 1991
; Vardy and Toda, 2000
). In addition, homologues of both GCP4 and GCP6 have recently been identified and characterized; these are known as gfh1p and alp16p, respectively (Fujita et al., 2002
; Venkatram et al., 2004
). Interestingly, although defects in microtubule distribution are apparent in both gfh1
and alp16
mutants, neither gfh1p nor alp16p is essential for viability. This suggests that in fission yeast, microtubule nucleation may not absolutely require an intact large
-TuC (we reserve the term "ring" complex for those complexes where a ring complex has been observed directly in the electron microscope). More generally, the presence of such proteins in fission yeast suggests that this organism may provide a useful system for understanding the function of these components of the
-TuC.
Here, we describe the isolation of a novel gene, mod21+, which we show to be the fission yeast homologue of GCP5. Characterization of the mod21
phenotype, both singly and in combination with deletion mutants of gfh1+ and alp16+, suggests that gfh1p, mod21p, and alp16p act together as "noncore" subunits of the
-TuC, promoting the ability of the complex to drive microtubule nucleation. Biochemical characterization of all three proteins suggests that gfh1p and alp16p may cooperate in the assembly of a large
-TuC in fission yeast, and this is consistent with our finding that nonadditive phenotypes are observed when gfh1+, mod21+, and alp16+ are simultaneously deleted. Importantly, however, even in this triple-deletion strain, most aspects of
-tubulindependent microtubule nucleation persist as normal. Because we find that
-tubulin in wild-type fission yeast mostly seems to exist in the form of a small complex, we suggest that
-TuCs containing noncore subunits and
-TuCs lacking noncore subunits both contribute to microtubule nucleation in fission yeast.
| MATERIALS AND METHODS |
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::hphMX and mod21
::hphMX hygromycin-resistant strains were generated by transforming gfh1
::kanMX and mod21
kanMX strains with a PCR-amplified hphMX cassette containing flanked regions of homology (to promoter and terminator regions) also found within the kanMX cassette (Hentges et al., 2005
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Immunofluorescence and Microscopy
For anti-tubulin immunofluorescence, cells were fixed in methanol at 70°C, processed as described above, and imaged by laser scanning confocal microscopy (Sawin and Nurse, 1998
; Sawin et al., 2004
). Figures show maximum projections of Z-stacks, including the entire cell volume. Live cell imaging was performed on a Nikon TE300 wide-field inverted microscope system as described previously (Snaith and Sawin, 2003
; Sawin et al., 2004
). For live cell three-channel imaging of GFP fused to
-TuC components (either alp4p, gfh1p, mod21p, or alp16p) together with sad1-dsRed and 4,6-diamidino-2-phenylindole (DAPI), eight Z-sections at 0.6-µm intervals were collected at a single time point (800-ms exposure for GFP, 400-ms exposure for sad1 and DAPI, with appropriate neutral density filters to minimize photobleaching), and maximum projections were generated. For quantitation of microtubule bundle number in live cells expressing GFP-atb2, 10 Z-sections were collected at 0.6-µm intervals at a single time point (800-ms exposure, with neutral density filters). These images were deconvolved using softWoRx (Applied Precision, Issaquah, WA), and maximum projections of Z-sections were then generated. For time-lapse two-channel imaging of GFP-atb2p and sad1-dsRed, eight Z-sections at 0.6-µm intervals were collected every 20 s (400-ms exposure for GFP and 200 ms for sad1-dsRed, with neutral density filters) and deconvolved, and maximum projections of Z-sections were generated. For display of total SPB movement in these sequences, maximum projections from all time points of a given sequence were combined into a single average "time projection." For time-lapse single-channel imaging of GFP-atb2p (assays of astral microtubule release), eight Z-sections at 0.6-µm intervals were collected every 30 s (800-ms exposure per section, with neutral density filters). After deconvolution, maximum projections were generated. For live-cell imaging of alp4-GFP in various mutant strains, eight Z-sections at 0.6-µm intervals were collected at a single time point (400-ms exposure, with neutral density filters), and maximum projections of Z-sections were generated without deconvolution.
Physiological Experiments
For morphology experiments, cell shape defects were determined by growing cells on YE5S plates for 2 d, replica plating to fresh plates, and examining cell shape after 3 h at 32°C (Snaith and Sawin, 2003
). For imaging of cell shape by differential interference contrast (DIC) microscopy, cells were washed off the plates with deionized water and immediately fixed in 3% formaldehyde.
For microtubule regrowth experiments, exponentially growing cells were chilled in an ice water bath for 30 min and transferred to 32°C for the specified time before collection by rapid filtration, fixation in methanol at 70°C, and processing for immunofluorescence and confocal imaging (Sawin et al., 2004
). For quantitation, nucleation sites were counted in at least 150 cells per strain, at the 30-s time point.
Biochemical Methods
For immunoprecipitations, native cell extracts were prepared by freezing pelleted cells in liquid nitrogen and grinding to a powder while frozen. Frozen powder was resuspended in buffer H50 (50 mM Na HEPES, pH 7.5, 75 mM KCl, 1 mM EDTA, and 0.1% Triton X-100, plus a protease inhibitor cocktail). Extracts were clarified by microfuge centrifugation (13,000 rpm) for 15 min at 4°C, and the protein concentration was adjusted to 8 mg/ml. One milliliter of each extract was incubated with 10 µl of protein G Dynabeads suspension, preloaded with 2 µg of either hemagglutinin (HA)-antibody 12CA5, or an anti-GFP antibody. After incubation with rotation for 1 h at 4°C, beads were washed six times in 1 ml of buffer H50 and resuspended in Laemmli sample buffer for SDS-PAGE and Western blotting. In all immunoprecipitation experiments, immunoprecipitation lanes were 50x overloaded relative to total extract lanes.
For sucrose gradients, clarified extracts were prepared as for immunoprecipitation by using buffer H50 also containing 1 mM
-mercaptoethanol and 0.1 mM GTP. Sucrose gradients (540%) were generated in the same buffer. Gradients were loaded with 100 µl of clarified extract and centrifuged at 50,000 rpm for 4 h at 4°C in a TLS-55 rotor. Fractions (100 µl) were collected from the top of the gradient with a cut pipette tips and analyzed by Western blotting. For higher resolution gradients (Supplemental Figure 6), 200 µl of clarified extracts was loaded onto 13.2 ml 540% sucrose gradients and centrifuged at 28,000 rpm for 20 h at 4°C in a SW40 rotor. Fractions of 550 µl were taken from the top of the gradient by using a gradient-uploader and a fraction collector. Sedimentation coefficients were determined by parallel centrifugation of sucrose gradients containing protein standards.
For sucrose-gradient analysis of higher-eukaryotic
-tubulin complexes, Xenopus egg extract was prepared as described previously (Sawin and Mitchison, 1991
) and diluted fourfold in buffer H50 containing 1 mM
-mercaptoethanol and 0.1 mM GTP before loading onto gradients. Drosophila embryo extract was prepared by homogenizing 016 h Drosophila embryos in buffer H50 containing 1 mM
-mercaptoethanol and 0.1 mM GTP. Crude extract was clarified by centrifugation in a tabletop centrifuge (13,000 rpm for 15 min at 4°C) before loading onto sucrose gradients.
| RESULTS |
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-TuC
-TuC, and mutants produce a curved cell phenotype after return-to-growth from stationary phase (Sawin et al., 2004
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-TuC proteins GCP4 and GCP5, respectively, although in both cases the sequence similarity was remarkably low (<20%, without even considering gaps; Supplemental Figures 1 and 2). Mod12p is identical to gfh1p, which has recently been identified and characterized as a homologue of GCP4 (Venkatram et al., 2004
mutants were viable, and this was also true for mod21
mutants. As in our original mutant screen, gfh1
and mod21
mutants yielded curved cells only as double mutants in combination with mod22-1 (Figure 1A). By immunofluorescence of fixed cells, relatively minor defects in interphase microtubule organization could be observed in gfh1
and mod21
single mutants during steady-state growth (Venkatram et al., 2004
mod22-1 and mod21 mod22-1 double mutants showed more abnormal microtubule distributions, including fewer, thicker microtubule bundles, and often curving of microtubule bundles around cell tips (Figure 1B and Supplemental Table 1). We also found that the double mutant gfh1
mod21
did not show a stronger defective microtubule phenotype than either single mutant, and the triple mutant gfh1
mod21
mod22-1 did not show a stronger phenotype than either gfh1
or mod21
in combination with mod22-1, indicating that gfh1p and mod21p are not redundant for microtubule function in fission yeast.
To confirm that mod21p is a bona fide component of the fission yeast
-TuC, we examined its potential associations with known proteins of the
-TuC as well as its intracellular localization. In coimmunoprecipitation experiments from fission yeast extracts, we found that Myc-tagged mod21p was physically associated with HA-tagged
-TuC proteins alp4p (GCP2 homologue) and alp6p (GCP3 homologue), in the same manner as Myc-tagged gfh1p (Figures 2, A and B, and 10; see Materials and Methods and Supplemental Tables 13 for an assessment of the functionality of these and other tagged strains).
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-TuC protein, we examined the localization of mod21-GFP in live cells coexpressing the SPB marker sad1-dsRed (Chikashige et al., 2004
-TuC. In general, the fluorescence intensity of alp4-GFP at SPBs and eMTOCs was higher than that of gfh1-GFP, mod21-GFP, and alp16-GFP. This could indicate that alp4-GFP is more abundant than gfh1-GFP, mod21-GFP, and alp16-GFP at these sites. Alternatively, it is possible that GFP-tagging might negatively affect the localization of gfh1-GFP, mod21-GFP, and alp16-GFP to SPBs and eMTOCs. Indeed, additional experiments suggest that gfh1-GFP and possibly alp16-GFP (but not mod21-GFP) may have somewhat impaired function relative to untagged proteins (see Materials and Methods and Supplemental Tables 13).
Previously it has been shown that GCP4 is likely present in more than one copy in the human
-TuC, whereas GCP5 is single-copy (Murphy et al., 2001
). We therefore performed coimmunoprecipitations from diploid strains in which the different alleles of gfh1p and mod21p were fused to both GFP- and Myc-tags. In these experiments, gfh1-GFP was able to coimmunoprecipitate both mod21-Myc and gfh1-Myc, whereas mod21-GFP was able to coimmunoprecipitate gfh1-Myc but not mod21-Myc (Supplemental Figure 3). Subject to the caveat that gfh1-GFP may have impaired function, this suggests that gfh1p may be multicopy in the fission yeast
-TuC, whereas mod21p is only single copy.
gfh1p, mod21p, and alp16p All Contribute to a Single Function in Interphase Microtubule Organization and Nucleation
Neither gfh1p nor alp16p, the fission yeast homologue of the mammalian
-TuC protein GCP6, is essential for viability, but deletion of either gene leads to defects in microtubule organization (Fujita et al., 2002
; Venkatram et al., 2004
). Because there has generally been relatively little in vivo characterization of the specific roles of GCP4, GCP5, or GCP6 in any eukaryote, we wanted to determine whether all or a subset of these proteins might be functionally redundant. Interestingly, we were able to construct a viable quadruple mutant gfh1
mod21
alp16
mod22-1 strain, as well as all possible double and triple mutants, without difficulty. We also tested in more detail whether multiple mutations in any of these genes might produce a stronger microtubule-defective phenotype than single mutations. Immunofluorescence experiments in exponentially-growing cells showed that all possible combinations of deletions of gfh1+, mod21+, and alp16+ were roughly similar to each other with regard to microtubule distribution; in addition, we found that when, and only when, any of these deletions or combination of deletions was combined with the mod22-1 mutation, the microtubule phenotype became significantly worse (Figure 1B, Supplemental Figure 4, and Supplemental Table 1; also see Figure 3).
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, mod21
, alp16
, and mod22-1 mutants. When wild-type cells are cooled to 0°C, microtubules depolymerize within a few minutes, and when these cells are rewarmed to normal culture temperature, microtubules are rapidly nucleated from multiple sites on the surface of the cell nucleus (Mata and Nurse, 1997
and mto2
mutant cells can have varying numbers of microtubule bundles before cold treatment, in mto2
mutants recovering from cold treatment, only the SPB is active for cytoplasmic microtubule nucleation, whereas in recovering mto1
mutants, all cytoplasmic nucleation is abolished, with new microtubule nucleation occurring only from the nucleoplasmic face of the SPB and microtubules eventually breaking through the nuclear envelope into the cytoplasm (Sawin et al., 2004
and mto2
mutants generally seem to be more stable than in wild-type cells (Janson et al., 2005
-TuC to the nuclear surface, brought about by the association of the
-TuC with the microtubule nucleation protein mto1p, which, unlike tubulin, does visibly redistribute to the nuclear surface as a result of cold treatment, before rewarming (Sawin et al., 2004
In all combinations of gfh1
, mod21
, alp16
, and mod22-1 mutants, we observed microtubule nucleation from multiple sites on the nuclear surface upon recovery from cold treatment, indicating that these genes are not essential for formation of the multiple, distributed nucleation sites seen in wild-type cells (Figure 3; our unpublished data). However, mutants that showed more aberrant microtubule distributions during exponential growth (e.g., mod21
mod22-1 double mutants, or gfh1
mod21
alp16
mod22-1 quadruple mutants) were also more impaired in the earliest stages of microtubule regrowth (Figure 3, D and E). In these experiments, we also quantitated the number of apparent microtubule nucleation sites at the earliest time points (Figure 4). Relative to wild-type cells, we observed reductions in the number of nucleation sites in gfh1
, mod21
and alp16
single mutants, and similar reductions in multiple mutants. Due to inherent difficulties in scoring nucleation sites at the light-microscopic level, there was some variation in the number of apparent sites in different mutants, but we did not observe any strong synthetic effects after multiple deletion of gfh1+, mod21+, and alp16+. Interestingly, when single- or multiple-deletion mutants were combined with the mod22-1 mutation, the number of nucleation sites was typically further reduced (Figure 4), whereas mod22-1 single mutants themselves were not significantly different from wild-type cells. Together, these results suggest that gfh1p, mod21p, and alp16p are likely to contribute to a single common function in microtubule behavior and/or nucleation, and that mod22+ is also important for nucleation.
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-tubulin (Ding et al., 1998
, mod21
and alp16
single mutants (i.e., in mod22+ backgrounds; Figure 5, A and B; our additional unpublished data). Although most wild-type cells contained two to four microtubule bundles per cell (Drummond and Cross, 2000
and mod21
and alp16
single mutants generally contained one to three bundles (Figure 5C). The mod22-1 mutation by itself reduced the number of bundles only very modestly, but when it was combined with any of the gfh1
, mod21
, or alp16
single mutations, a high proportion of double-mutant cells contained only a single microtubule bundle (Figure 5C), consistent with our previous observations that mod22-1 exacerbates the deletion-mutant phenotypes. We also analyzed the multiple mutant gfh1
mod21
alp16
in both mod22+ and mod22-1 backgrounds. Consistent with our previous observations of nonadditive phenotypes, the number of microtubule bundles per cell in gfh1
mod21
alp16
mutants was not further reduced relative to any of the single mutants, and as with single mutants, the mod22-1 mutation further reduced the number of bundles in the gfh1
mod21
alp16
mutants (Figures 4 and 5C).
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, mod21
, alp16
, and mod22-1 mutations do not simply "generally reduce" the average number of bundles per cell. Rather, these mutations reduce the likelihood that a cell will have more than one bundle. From a more mechanistic perspective, this could imply that the mutant cells contain one single site that is more likely than others to nucleate microtubules. Such a hypothetical site could in theory be responsible for all microtubule bundles in vivo, even in cells with more than one bundle, via mechanisms such as microtubule nucleation-and-release (Keating and Borisy, 1999
Because the most likely candidate for such a hypothetical "unique nucleation site" was the SPB, we coimaged GFP-atb2 and the SPB marker sad1-dsRed in wild-type cells; single-mutant gfh1
, mod21
, and alp16
cells; and triple-mutant gfh1
mod21
alp16
cells, both in mod22+ and mod22-1 backgrounds, by time-lapse microscopy. Interestingly, we found that in all mutants, new cytoplasmic microtubules could be nucleated at sites away from the SPB, as also occurs in wild-type cells (Figure 6, C, D, E, F, I, J, K, and L, white arrows; and Supplemental Movies 110; additional data not shown). This directly discounts the simple model that the SPB might be the only cytoplasmic microtubule nucleation site in the mutants.
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, mod21
and alp16
mutants and that although non-SPB-mediated microtubule nucleation also occurs in the mutants, it does so less frequently than in wild-type cells.
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An additional indicator of non-SPBmediated microtubule nucleation in fission yeast is the presence of iMTOC satellites on microtubules themselves (Sawin et al., 2004
; Zimmerman et al., 2004
; Janson et al., 2005
; Samejima et al., 2005
). For example, microtubule-associated satellites of GFP-tagged alp4p are visible in wild-type cells, but not in mto2
mutants, which are defective in non-SPBmediated microtubule nucleation (Janson et al., 2005
; Samejima et al., 2005
), and it has recently been observed that new microtubules can be nucleated from such satellites, although this may be difficult to detect routinely (Janson et al., 2005
). We observed alp4-GFP satellites in gfh1
and mod21
mutants, both in mod22+ and mod22-1 backgrounds (Figure 8), consistent with our observations of microtubule behavior in vivo.
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, mod21
, and Multiple Mutants Do Not Release Astral Microtubules
phenotype, we examined potential release of astral microtubules in both gfh1
and gfh1
mod22-1 cells expressing GFP-tubulin as well as in other mutants (Figure 9 and Table 3). However, we did not observe significant release of astral microtubules from SPBs in gfh1
mutants. Release from SPBs was occasionally observed (Figure 9B and Supplemental Movie 13), but this was equally rare in both wild-type and gfh1
cells and was not altered by either the mode of GFP-atb2p expression or mod22 status (Table 3 and Supplemental Movies 1115). We also examined potential release of astral microtubules in mod21
mutants, both in mod22+ and mod22-1 backgrounds, and in the gfh1
mod21
alp16
mod22-1 quadruple mutant. Again, we failed to observe a significant increase in the frequency of astral microtubule release relative to wild-type cells (Table 3 and Supplemental Movies 1619). In total, we observed either no or one astral microtubule release events in 29 eligible astral microtubule histories from wild-type cells, and between two and nine release events in 276 eligible histories from mutant cells (most events in mutant cells were questionable; see Table 3 for details). From these results, we conclude that release of astral microtubules is not an intrinsic property of gfh1
, mod21
, or alp16
mutants, either in a wild-type or mod22-1 background. In all strains, we often observed single microtubules nucleated from the eMTOC toward the end of mitosis, during the earliest stages of formation of the postanaphase array (PAA; see below). Although these might be mistaken for released astral microtubules, with appropriate time resolution they were clearly not astral microtubules but rather early PAA microtubules (Figure 9 and Supplemental Movies 1119).
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In summary, our results from both live and fixed cell experiments indicate that deletion of gfh1+, mod21+ and/or alp16+, either individually or in combination, does not affect major qualitative aspects of microtubule nucleation and dynamics, including the appearance of interphase microtubule nucleation sites, mitotic spindle assembly, astral microtubule behavior and postanaphase array formation. Rather, deletion of these genes, especially in combination with the mod22-1 mutation, leads to a more quantitative reduction in the number of apparent interphase microtubule nucleation sites or iMTOCsspecifically, non-SPB sites. We interpret this to indicate that gfh1p, mod21p, and alp16p may function to promote the efficiency of microtubule nucleation by the
-TuC, thereby increasing the number of active microtubule nucleation sites in vivo.
Organizational State of the Fission Yeast
-TuC In Vivo
One potential explanation for the nonadditive defective microtubule phenotype seen in the gfh1
mod21
alp16
multiple mutant relative to single or double mutants, in both mod22+ and mod22-1 backgrounds, is that each of the nonessential
-TuC proteins might be required for the others to be stable in vivo or for them to associate with a small
-TuC containing
-tubulin, alp4p, and alp6p. For example, in Xenopus
-TuRC reconstitution experiments, immunodepletion of GCP6 from salt-dissociated
-TuRC has been shown to prevent the reassembly of large complexes (Zhang et al., 2000
). We therefore examined association dependencies of gfh1p, mod21p, and alp16p with the
-TuC, by performing coimmunoprecipitation experiments in a variety of mutant backgrounds (Figure 10).
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-tubulin with alp4p and alp6p remain intact in these mutants.
In further experiments, we found that the coimmunoprecipitation of alp16-Myc with alp4-HA was dependent on gfh1p but not on mod21p (Figure 11A), and also that levels of alp16p were not altered in gfh1
or mod21
strains. Subject to the caveats associated with using tagged strains (see Materials and Methods and Supplemental Tables 13), we conclude from these results that association dependencies can account for at least some of the similar phenotypes seen among single and multiple deletions of gfh1+, mod21+ and alp16+, although, notably, both gfh1p and alp16p still associate with the small
-TuC proteins in mod21
mutants.
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mutants (Figure 11B), even though neither gfh1p nor mod21p would be expected to associate with the small
-TuC proteins under these conditions (Figure 10). By contrast, alp16p was not associated with mod21p in the absence of gfh1p (Figure 11C). In the same experiment, we found that alp16p did associate with gfh1p in the absence of mod21p, but we note that under these conditions, both gfh1p and alp16p are themselves associated with the small
-TuC (Figures 10B and 11, A and C). Together, these results suggest that assembly of a larger
-TuC in fission yeast may involve the interdependent association of distinct subcomplexes, including a gfh1pmod21p subcomplex, although we note in this context that the gfh1-HA allele is likely to have impaired function (see Materials and Methods and Supplemental Tables 13).
As described above, our analysis of mutant phenotypes indicates that many
-TuCdependent microtubule behaviors are essentially intact in fission yeast when multiple subunits and/or regulators of the
-TuC are absent (gfh1
, mod21
, and alp16
) or mutated (mod22-1). This led us to wonder whether these subunits might not always be tightly associated with the
-TuC in vivo; that is, whether a significant fraction of functional
-TuCs in wild-type cells might in fact be small complexes. Previous analysis of the fission yeast
-TuC by gel filtration chromatography has produced ambiguous and/or conflicting results concerning the size of wild-type and mutant complexes (Vardy and Toda, 2000
; Fujita et al., 2002
; Venkatram et al., 2004
; see Discussion). We therefore followed a complementary approach to analyze the
-TuC, by using sucrose gradient sedimentation.
Using the buffer conditions of our coimmunoprecipitation experiments, we found that nearly all
-tubulin in wild-type fission yeast extracts was present in a relatively low S-value complex,
89S, and this was not significantly altered in a gfh1
mod21
alp16
mod22-1 strain (Figure 12A). As controls, we prepared Drosophila embryo extracts and Xenopus egg extracts, using the same buffers as for fission yeast (see Materials and Methods). As reported previously, Drosophila
-tubulin sedimented in both small and large complexes, whereas Xenopus
-tubulin sedimented mostly as a large complex (Stearns and Kirschner, 1994
; Oegema et al., 1999
). Both gfh1p and mod21p also sedimented with low S-values, albeit reproducibly differently from each other (Figure 12B and Supplemental Figure 6). From these data, it could not be confirmed that either gfh1p or mod21p was comigrating with
-tubulin. Overall, our results suggest that, in contrast to
-tubulin from higher eukaryotes, most of the
-tubulin in fission yeast cell extracts is not detected in large protein complexes, even when the homologues of GCP4 (gfh1p), GCP5 (mod21p), and GCP6 (alp16p) are present. This could reflect a lower abundance of large complexes in vivo or a reduced stability of large complexes in vitro.
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-tubulin seemed to sediment in a larger complex, >20S, that occurred as a "bump" on the shoulder of the broad small S-value peak (Supplemental Figure 5, asterisk). Small amounts of gfh1p and mod21p were also reproducibly enriched at this position, and the
-tubulin bump was no longer apparent in the gfh1
mod21
alp16
mod22-1 mutant (Supplemental Figure 5). Although these results might suggest that the bump represents an intact large fission yeast
-TuC, this should be viewed with caution, because sedimentation profiles of alp4p or alp6p did not routinely show such a distinct bump (Supplemental Figure 5). Another reason for caution in interpreting such high S-value forms of
-tubulin is that in further experiments involving higher resolution gradients and longer centrifugation times, we observed not only the small 89S form of
-tubulin seen previously but also a prominent higher S-value form that seemed to be distinct from the higher S-value form observed with shorter centrifugation times (Supplemental Figure 6, asterisks). Curiously, no other
-TuC components comigrated with this new larger form, which was equally present in both wild-type cells and gfh1
mod21
alp16
mod22-1 mutants (Supplemental Figure 6). This suggests that fission yeast
-tubulin may be subject to aggregation artifacts under certain conditions in vitro. | DISCUSSION |
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-TuC contribute to its function is a major outstanding question in microtubule nucleation. Our characterization of mod21p, together with gfh1p and alp16p (Fujita et al., 2002
-TuC similar to that found in higher eukaryotes and that this complex is important for maintaining normal levels of microtubule nucleation in vivo. At the same time, however, two findings in particular lead us to propose that the nonessential proteins gfh1p, mod21p, and alp16p should be considered as noncore components of the
-TuC, in contrast to the essential core components
-tubulin, alp4p and alp6p. First, we have found that most qualitative aspects of microtubule nucleation persist in vivo when all noncore components of the
-TuC are deleted, the major observed difference being a quantitative reduction in interphase microtubule nucleation activity. This stands in marked contrast to the very strong nucleation-defective phenotypes observed upon loss of nonessential proteins that recruit the
-TuC to prospective cytoplasmic nucleation sites, such as mto1p or mto2p (Sawin et al., 2004
-TuC containing the noncore components, even in wild-type cells; rather, we observe nearly all
-tubulin in low S-value forms (see below for further discussion).
Roles of Novel Components mod21+ and mod22+
Because both gfh1p and alp16p are required for association of mod21p with the
-TuC, it is difficult to judge whether the three noncore subunits have distinct functions. However, we note that the association of both gfh1p and alp16p with the
-TuC is independent of mod21p, whereas the association of mod21p with the
-TuC depends on both gfh1p and alp16p, and the loss of mod21p phenocopies simultaneous loss of all three noncore subunits. In this light, mod21p may merit special attention as the most "peripheral" and the least "architectural" of the noncore subunits. Further mutational analysis of noncore components will help to address these issues.
In this work, we also identified genetically an additional regulator of
-TuC function, mod22+. The identification of mod22-1 was not only fortuitous but also essential to our identification of mod21+ in a morphological mutant screen. Because the mod22-1 phenotype is strongest when noncore components are deleted, it seems plausible that mod22+ may function to promote the nucleation efficiency of a small core
-TuC. Although mod22+ has not yet been cloned, our results to date indicate that mod22 is not allelic to any known components of the
-TuC or to any of the three tubulin genes in fission yeast (our unpublished data).
Function of gfh1p, mod21p, and alp16p in Microtubule Nucleation and Organization
Our analysis of the noncore subunits suggests that they can be treated together as a single functional class in relation to regulating microtubule behavior. In the area of microtubule nucleation, we have shown that loss of one, two, or all three noncore subunits does not disrupt microtubule nucleation from any of the three different types of MTOCs normally present in vivo. This in turn indicates that an intact large
-TuC is broadly dispensable for microtubule nucleation in fission yeast (Fujita et al., 2002
; Venkatram et al., 2004
). It is possible that the reduced iMTOC nucleation observed in deletion mutants is due to the loss of a specific but as yet unrecognized subclass of iMTOCs; further higher-resolution work will be required to address this.
Altered microtubule dynamics have been observed in many fission yeast mutants affecting microtubule nucleation, particularly
-TuC mutants (Paluh et al., 2000
; Vardy and Toda, 2000
; Fujita et al., 2002
; Sawin et al., 2004
; Venkatram et al., 2004
, 2005
; Janson et al., 2005
; Zimmerman and Chang, 2005
). In all of our mutants, microtubules within bundles were seen to turn over, but the bundles themselves had longer lifetimes than in wild-type cells, accompanied by oscillations of SPBs. The mechanistic reasons for these differences in bundle behavior and/or structure are not yet clear. Such differences could be an indirect consequence of reduced microtubule nucleation (Sawin et al., 2004
; Samejima et al., 2005
), driven, for example, by a higher ratio of bundling proteins relative to bundles. Alternatively, if microtubule minus-ends were normally capped by
-TuCs in wild-type fission yeast, but not in our mutants, minus-ends might be more free to elongate and become bundled. Although we observed the
-TuC marker alp4-GFP associated with microtubules in our mutants, we do not know whether its localization may be subtly altered.
In our experiments, we did not quantitate parameters of dynamic instability of individual microtubules, partly because important dynamic instability transitions may occur deep within bundles rather than at the ends of bundles (making them very difficult to observe) and also because the bundles in mutant cells may themselves have a different polarity and/or organization relative to wild-type cells. It is still unclear whether the alterations in dynamics that have been observed in microtubule-nucleation mutants arise primarily as an indirect consequence of nucleation defects or whether nucleation complexes themselves play a more direct role in modulating microtubule dynamics (Paluh et al., 2000
; Sawin et al., 2004
; Zimmerman and Chang, 2005
). Further work is needed to resolve this important issue.
In contrast to the previous results of Venkatram et al. (2004)
, we did not observe significant release of astral microtubules from SPBs during mitosis in any of our mutants. The reason for this discrepancy is not clear. Very early PAA microtubules that translocate from their nucleation sites could be mistaken for released astral microtubules, but we observed such microtubules equally frequently in wild-type and mutant cells. The results of Venkatram et al. (2004)
could be due to aberrantly high levels of GFP-tubulin expression. In their work, GFP-atb2p was expressed from a multi-copy plasmid, using the very high-strength nmt1 promoter under fully derepressed conditions (Venkatram, personal communication), whereas we used two integrated versions of GFP-atb2p, expressed at near to or slightly lower than physiological levels. In previous work, we demonstrated that some mutant strains defective in microtubule nucleation can be supersensitive to GFP-tubulin levels (Sawin et al., 2004
).
The Fission Yeast
-TuC in Relation to Higher Eukaryotes
In spite of extensive biochemical studies of the
-TuC in several different organisms, there are still questions as to which form(s) of the complex may be active for nucleation in vivo, and in what contexts. In budding yeast, where homologues of GCP4, GCP5 and GCP6 have not been identified, the active form of
-TuC is thought to be the
11S Tub4 complex, anchored to the SPB (Knop et al., 1997
; Vinh et al., 2002
). In metazoan cells, both small and large
-TuCs can be identified in cell extracts to varying extents, the
3035S
-TuRC being a much more potent nucleator in vitro than the smaller
10S
-TuSC subcomplex, perhaps by 2 orders of magnitude (Oegema et al., 1999
). Because the
-TuRC has been seen to form a cap on nucleated microtubules (Moritz et al., 2000
) and is by far the predominant form of
-tubulin in vertebrate cells, a general view has emerged that the
-TuRC is the primary microtubule nucleator in higher eukaryotes, for both centrosomal and noncentrosomal nucleation. However, while our paper was under review, Verrolet et al. (2006)
published a study on the role of the Drosophila homologues of GCP4, GCP5, and GCP6 in microtubule nucleation in vivo (Verollet et al., 2006
). In this work,
-tubulin targeting and microtubule nucleation at the centrosome were still preserved after combined RNA interference knockdowns of these three
-TuRCspecific proteins, suggesting that the
-TuSC is sufficient for at least some aspects of microtubule nucleation in higher eukaryotes. However, it is unclear whether
-TuSCmediated nucleation would normally function alongside
-TuRCmediated nucleation in untreated cells (Verollet et al., 2006
).
What is the situation in fission yeast? Our sucrose gradient data suggest that a large proportion of the
-TuC in wild-type fission yeast may be in the form of small complexes, with perhaps only a very small fraction in larger, canonical complexes containing noncore subunits. How can we reconcile this with our phenotype analysis showing that cells without noncore subunits nucleate microtubules reasonably well from all types of MTOCs but are nevertheless partially defective in interphase nucleation? One interesting, albeit speculative, possibility is that there may be a "division of labor" between large and small
-TuCs in fission yeast (Figure 13). According to this view, wild-type cells may contain a relatively small number of large
-TuCs, which contain noncore subunits and are highly active for microtubule nucleation, and a much greater number of small
-TuCs, which lack noncore subunits and are less active for nucleation. In this manner, the two pools of
-TuCs could each contribute a significant amount of the total interphase microtubule nucleation activity. In relation to other systems, this view would put fission yeast somewhere "in between" higher eukaryotes, which rely primarily or exclusively on the
-TuRC (possibly because of the need to nucleate hundreds of microtubules), and budding yeast, which have only the equivalent of the small
-TuSC. Because budding yeast nucleate cytoplasmic microtubules only from the SPB, it is also noteworthy that loss of noncore components in fission yeast does not restrict cytoplasmic nucleation to the SPB, because this indicates that the differences between budding and fission yeast with regard to nucleation are not simply explained by the presence/absence of noncore components. Further work will be necessary to test these ideas in detail.
|
-TuC in vivo is not yet certain. In particular, Fujita et al. (2002)
-TuC behaved as a very large complex by gel filtration, and its size was unaffected by alp16
(Fujita et al., 2002
-TuCs exceed the exclusion limit of the column used by both groups (Superose 6). In these experiments, the use of low ionic strength buffers containing both glycerol and ATP could have led to unintentional aggregation of a small
-TuC. Indeed, in our own experiments, we found conditions that seemed to aggregate
-tubulin artificially, and changes in buffer conditions have also been noted to alter the size of the budding yeast Tub4 complex on sucrose gradients (Vinh et al., 2002
-TuRC. Thus, at minimum, it is likely that an association of
-TuC noncore components with core-components is less robust in fission yeast than in higher eukaryotes. It remains to be seen whether such a weaker association would be constitutive or perhaps regulated by labile posttranslational modifications (e.g., phosphorylation), which might not survive cell extraction.
| ACKNOWLEDGMENTS |
|---|
| Footnotes |
|---|
This article was published online ahead of print in MBC in Press (http://www.molbiolcell.org/cgi/doi/10.1091/mbc.E05-11-1009) on October 4, 2006.
Address correspondence to: Kenneth E. Sawin (ken.sawin{at}ed.ac.uk)
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