Human Molecular Genetics, 2000, Vol. 9, No. 5 703-712
© 2000 Oxford University Press
Doublecortin mutations cluster in evolutionarily conserved functional domains
Department of Molecular Genetics, 1Electron Microscopy Unit and 2Department of Materials and Interfaces, The Weizmann Institute of Science, 76100 Rehovot, Israel and 3Institut Cochin de Genetique Moleculaire, INSERM U129, CHU Cochin-Port-Royal, 24 rue du Faubourg Saint-Jacques, 75014 Paris, France
Received 29 November 1999; Revised and Accepted 25 January 2000.
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
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Mutations in the X-linked gene doublecortin (DCX) result in lissencephaly in males or subcortical laminar heterotopia (‘double cortex’) in females. Various types of mutation were identified and the sequence differences included nonsense, splice site and missense mutations throughout the gene. Recently, we and others have demonstrated that DCX interacts and stabilizes microtubules. Here, we performed a detailed sequence analysis of DCX and DCX-like proteins from various organisms and defined an evolutionarily conserved Doublecortin (DC) domain. The domain typically appears in the N-terminus of proteins and consists of two tandemly repeated 80 amino acid regions. In the large majority of patients, missense mutations in DCX fall within the conserved regions. We hypothesized that these repeats may be important for microtubule binding. We expressed DCX or DCLK (KIAA0369) repeats in vitro and in vivo. Our results suggest that the first repeat binds tubulin but not microtubules and enhances microtubule polymerization. To study the functional consequences of DCX mutations, we overexpressed seven of the reported mutations in COS7 cells and examined their effect on the microtubule cytoskeleton. The results demonstrate that some of the mutations disrupt microtubules. The most severe effect was observed with a tyrosine to histidine mutation at amino acid 125 (Y125H). Produced as a recombinant protein, this mutation disrupts microtubules in vitro at high molar concentration. The positions of the different mutations are discussed according to the evolutionarily defined DC-repeat motif. The results from this study emphasize the importance of DCX–microtubule interaction during normal and abnormal brain development.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
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The lissencephaly syndromes in humans involve abnormal cortical lamination and are medically categorized as neuronal migration defects (1,2). The various human lissencephalies are classified according to morphology or putative etiology (3,4). Two types of lissencephaly have been defined (5,6). In type I, also known as classical lissencephaly, the cortex consists of four layers instead of the normal six, whereas in type II, also known as cobblestone lissencephaly the cortex is unlayered (4). Two lissencephaly type I disease genes have been identified. The first lissencephaly gene cloned was LIS1 (7) (recently reviewed in ref. 8). Mutations in one allele of this gene (7,9) are sufficient to cause lissencephaly type I. LIS1 interacts with tubulin and influences microtubule dynamics (10). It has also been cloned independently as a non-catalytic subunit of platelet-activating factor acetylhydrolase (11). A second lissencephaly type I gene was mapped to the X chromosome (12,13). It was cloned and termed doublecortin (DCX) (14,15). Mutations in the X-linked DCX gene result in lissencephaly in males or subcortical laminar heterotopia (SCLH), i.e. ‘double cortex’, in females (14,15).
It has been hypothesized that due to random X-inactivation, affected females heterozygous for the X-linked mutation show a milder phenotype, though so far this has not been conclusively shown and other mechanisms may also be involved. The milder phenotype consists of a brain with bilateral plates or bands of gray matter located beneath the cortex and ventricle but separated from both, hence the descriptive term double cortex, also known as SCLH (16). The clinical severity of SCLH varies strikingly from asymptomatic clinical presentation with heterotopic bands assessed by magnetic resonance imaging, to severe mental impairment with intractable epilepsy. The relative thickness of the heterotopic band seems to correlate with the phenotype, as patients with thicker bands have more severe mental retardation and seizures (17). To date, 39 various mutations were identified resulting in nonsense, splice site and missense mutations throughout the gene (14,15,18–21). Recently mutations both in LIS1 and DCX that result in SCLH in male patients have been reported (22). No clear correlation was observed between the clinical severity and mutation profiles (18). However, it has been noticed that amino acid substitution mutations were much more common in inherited lissencephaly (19). Single amino acid substitution mutations (19 described so far) in DCX cluster in two regions: amino acids 43–125 and 178–253 (19). Among these 19 amino acids, two have been independently substituted to different amino acids: tyrosine 125 to histidine or aspartic acid, and isoleucine 250 to threonine or asparagine. Initially, the sequence of DCX revealed similarity to a cDNA from human brain (KIAA0369) (23). The deduced amino acid sequence of human KIAA0369 protein contains two domains: an N-terminal segment similar to Doublecortin (85% similarity) and a C-terminal domain nearly identical to the previously discovered kinase CPG16 in rat (24–27). Therefore, we suggested naming this protein Doublecortin-like kinase (DCLK) (28). Human KIAA0369 cDNA has been sequenced and mapped to human chromosome 13q12.3 (29,30). So far no neurological disorders have been mapped to this region. Recently, we and others have defined the first function for DCX as a microtubule-associated protein that stabilizes microtubules (31–33). Our results demonstrated that the first 213 amino acids of DCX are sufficient to bind microtubules, whereas the region from amino acid 110 to the C-terminus did not (33).
In order to gain further insight on protein function, we performed an advanced computer analysis of proteins with DC-like domains from vertebrates, insects, worms and fungi. The analysis identified an 80 amino acid region that typically appears as two repeats in the N-termini of the proteins. In order to study the function of the repeats we have expressed each of the DC-domain repeats and both of them (including an intervening sequence) in vitro and in vivo. To study the functional consequences of DCX mutations, we overexpressed seven of the reported mutations in DCX (14,15) in COS-7 cells. Overexpression of several of the mutations resulted in bundling of microtubules similar to the wild-type protein. However, some of the mutated proteins aggregated in the cells and disrupted the microtubule cytoskeleton. Mutation Y125H had the most striking phenotype when overexpressed and was further subjected to in vitro analysis. In this paper, we define the DC domain region and its conserved motifs in various organisms and proteins and show that DCX mutations can result in different functional consequences. We discuss our experimental results in the context of the conserved domains.
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RESULTS |
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TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
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Conserved domains in DCX
Database searches with DCX and DCLK (28) (also known as KIAA0369) identified a number of other proteins with the DC domain (Fig. 1A). Some of these were only available as EST fragments and probably represent partial gene sequences. The domain was found in genes from human, mouse, rat, Caenorhabditis elegans, Drosophila and Dictyostelium. The human and some of the C.elegans sequences were previously reported (34). However, we could not confirm the presence of a DC domain in a Schizosaccharomyces pombe protein reported in that work.
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A multiple alignment analysis of the protein sequences identified a conserved region of ~80 amino acids that appears in one or two tandemly repeated copies in the N-terminal ends of the proteins. Vertebrate DCX and DCLK (28), also known as KIAA0369 (23), ORP1 from human and mouse (34), a C.elegans homolog of DCLK and the Dictyostelium protein all have two copies of the region separated by 40–95 amino acids (Fig. 1A). In this work, we designated the first part of human DCX as pep1, the second as pep2 and both including intervening sequences as pep(1+2) (Fig. 1A and B). It is possible that the other proteins are of partial sequence and also have a second DC region. The position of the 19 reported lissencephaly-causing amino acid substitution mutations described so far (14,15,18–22) are indicated on the sequence (Fig. 1B), and the large majority (17 in total) fall within the designated region. All 15 repeats shown in Figure 1A were used for multiple sequence alignment. The DC region consists of four ungapped conserved motifs (A–D, where their positions within the sequence of DCX are indicated in Fig. 1B) that can be confidently aligned. It is clear that some amino acid residues are more conserved than others (Fig. 1C), for example amino acids 8–11 in the A domain are in most repeats RNGD.
Expression of repeated domains
In vitro.
Computational sequence analysis of the human DCX protein identified in it a DC domain made up of a region repeated in amino acids 52–133 and 179–257. We expressed them as glutathione S-transferase (GST) fusion recombinant proteins: pep1 (amino acids 51–135), pep2 (amino acids 178–259) and pep(1+2) (amino acids 51–259) (Fig. 1B). We examined whether the peptides have the capability of binding to pre-assembled microtubules as shown previously with the full-length protein DCX (33). As can be seen in Figure 2A, pep1 and pep2 did not bind to pre-assembled microtubules; however, pep(1+2) is found both in the soluble and in the insoluble pellet bound to microtubules. Treatment with nocodazole resulted in complete solubilization of the pellet fraction of pep(1+2) (Fig. 2A). Next, we examined whether the peptides interact with tubulin subunits. In a pull-down assay using brain extract, pep1 and pep(1+2) pulled down a significant amount of tubulin, whereas pep2 pulled down less tubulin (Fig. 2B). However, the results obtained using purified tubulin demonstrated that only pep(1+2) pulled down a significant amount of tubulin (Fig. 2C). This assay was performed under conditions that do not support microtubule assembly (cold incubation and low protein concentration). The different results in these assays using pep1 may suggest that this peptide is able to recruit additional protein(s) from brain extract that facilitate the interaction with tubulin.
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In order to examine whether the peptides may affect microtubule formation, we measured the assembly rate of tubulin using a light-scattering assay (Fig. 3). This assay is based on an increase in optical scattering as microtubules polymerize, measured as an effective optical density. Addition of pep1 or pep(1+2) to tubulin without DCX increased the assembly rate of tubulin (Fig. 3). Addition of pep2 by itself to tubulin had the lowest effect on increase of the assembly (Fig. 3 and data not shown). Addition of pep1 or pep(1+2) to DCX and tubulin had an additive effect on microtubule assembly whereas pep2 reduced the effect of the normal protein. Previously, we have shown that addition of DCX to tubulin resulted in microtubule bundling (33). We examined the effect of the peptides on microtubule bundling effect by electron microscopy. In the presence of pep(1+2) microtubule bundles were formed (Fig. 4, compare A with B). We could not assess bundling activity of the individual repeat units (pep1 or pep2; data not shown).
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In vivo.
The three peptides composed of pep1, pep2 and pep(1+2) of DCLK were expressed transiently in COS-7 cells using PECE–FLAG expression vector. Similar to the in vitro experiments that were done with DC repeats, pep1 and pep2 did not bind microtubules in cells. However, pep(1+2) did bind microtubules to some extent. We used the well established protocol of gentle cell extraction with non-ionic detergent (0.5% Triton X-100) that removes lipids and soluble proteins, leaving intact the detergent-insoluble matrix composed of the nucleus, the cytoskeleton framework and cytoskeleton-associated proteins. Gentle detergent extraction showed that the pep1 and pep2 were in the soluble fraction (Fig. 5A); however, pep(1+2) was also in the insoluble fraction (Fig. 5A, two right lanes). Immunostaining of cells confirmed the biochemical fractionation and, although the immunostaining of pep1 or pep2 seems cytoplasmic, immuno- staining of pep(1+2) reveals staining of cytoskeletal structures resembling microtubules (Fig. 5B–D). This cytoskeletal staining was not completely identical with staining of cells transfected with the full-length DCLK (Fig. 5E), as the fibers appear thinner. Nevertheless, pep(1+2) cytoskeletal staining was disrupted by nocodazole treatment (Fig. 5F) that disrupts microtubule staining (Fig. 5G).
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Mutated DCX expression in COS cells
In order to define the intracellular localization of mutated DCX, we transiently transfected COS-7 epithelial cells with FLAG-tagged DCX constructs. For this analysis we used seven mutations (15,18). All the DCX mutated proteins were readily expressed in COS-7 cells demonstrated by western blot analysis (Fig. 6). Biochemical fractionation of exogenous expressed protein did not suggest any significant difference between the mutated DCX and normal DCX. In transfected COS-7 cells, the exogenous DCX (recognized by FLAG tag) appeared mainly in the detergent-insoluble fraction (Fig. 6).
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One of the key questions in understanding the function of DCX concerns its intracellular localization. Our previous analysis demonstrated that DCX colocalizes with the microtubule cytoskeleton and stabilizes the polymerized microtubules. Immunostaining of transfected COS-7 cells allowed assaying for, and to distinguish between, different effects of the DCX mutations. Overexpression of mutation R192W did not change cell morphology and this mutated DCX colocalized with microtubules (data not shown). Another group of DCX mutations (T203R, R59L, S47R) where the overexpressed protein colocalized to microtubules caused microtubule bundling and cell morphology was changed (Fig. 7). This is the general effect previously observed with overexpression of the wild-type DCX protein. The change in cell morphology can be appreciated when looking at two cells stained with anti-tubulin antibodies in Figure 7b. The transfected cell (compare with Fig. 7a) is considerably smaller and the microtubules are clearly bundled in comparison with the well spread untransfected cells with a nicely developed cytoskeleton. The microtubules in the cells transfected with these mutations (T203R, R59L, S47R) are stable as determined by staining with anti-acetylated-tubulin antibodies (Fig. 7e, h and l). The overall cellular structure of overexpression of this group of mutated DCX proteins revealed a very similar pattern as overexpressing the wild-type protein; i.e. colocalization with the microtubule cytoskeleton as observed by immuno- staining (Fig. 7c, f, i and l).
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The last group of DCX mutated proteins appeared aggregated in COS-7 cells, and did not convincingly colocalize with microtubules (D246X, Y125H, D62N) (Fig. 8). The morphology of these cells was affected, and most of the cells appeared smaller. Microtubules of these cells seemed to be disrupted especially where mutated DCX aggregates appeared. In the case of mutation D246X and D62N, high levels of overexpression resulted in different cell morphology. However, in cells with relatively low levels of overexpression, the microtubule cytoskeleton was not significantly disturbed (data not shown). Mutation Y125H was the most severe mutation, and the morphology of most of the cells changed. Therefore, we decided to investigate the effects of this mutation using in vitro studies.
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Recombinant Y125H protein and microtubules
Our in vivo experiments suggested that the levels of overexpression as well as the type of the mutation expressed determine the effect on the cell cytoskeleton. To study how different concentrations of mutated DCX (Y125H) affect tubulin polymerization, we used differential interference contrast (DIC) microscopy. Enhancement of microtubule assembly on introduction of low concentration of Y125H was observed (Fig. 9). When the concentrations of Y125H were equal to or higher than the tubulin concentration the picture completely changed. The protein formed aggregates and the filaments of microtubules were disrupted (Fig. 9). Taking into consideration the disrupted microtubule cytoskeleton in cells overexpressing this mutation and the fact that these aggregates did not appear in the absence of tubulin (Fig. 9), we assume that the aggregates result from microtubule severing.
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
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Many different mutations occur in the DCX gene and all of them can result in SCLH. Point mutations are most common in males with lissencephaly (14,15,18–21). Rare cases with missense mutations in DCX or LIS1 that result in SCLH have been described recently (22). Our results suggest that different mutations can yield different functional disturbances and result in either SCLH or lissencephaly. Our analysis focused mainly on missense mutations, although one (D246X) was a truncation mutation. Interestingly, the large majority of point mutations cluster within the conserved DC motifs that we have defined. The multi-alignment analysis performed reveal that some of the missense mutations are dramatic and are likely to disturb protein function. For example the eighth amino acid of pep1 and pep2 is highly conserved among species and is either arginine or lysine in all the DC domains known to date. In DCX there is an arginine in this position and there are lissencephaly-causing mutations both in the first (R59L) and second (R186C) repeats. Other mutations may be considered to be less severe, in some cases the amino acid substitution is a conserved change that naturally occurs in other repeats (for example, T203R where R is found in the same position in the first repeat). Our experimental results suggest that pep1 and pep2 are not identical. Furthermore, comparing the repeats as independent units, it is apparent that the order of the repeats is important and the first repeats from several genes are more similar to each other than to the second repeats (data not shown). Thus, it is likely that a duplication leading to the DC domain repeat structure occurred before the divergence of the different genes containing tandemly repeats of DC domains. We speculate that the function of the repeats is conserved in evolution, though this hypothesis remains to be tested in a more rigorous fashion. Nevertheless, the results shown here demonstrate some similarities between DCX and DCLK. The first DC repeat, pep1, binds tubulin more strongly and increases tubulin polymerization as measured by optical density. Addition of the first repeat with DCX to tubulin increased the assembly rate whereas addition of the second repeat decreased the assembly rate. It has been shown that charge is important in tubulin and microtubule-associated protein interactions. However, the differences between DCX pep1 and pep2 cannot be explained by difference in charge. There is no obvious difference in the isoelectric points: the pI of pep1 is 9.23 and the pI of the pep2 is 10.16, the pI of the DC motif including the intervening sequence is 10.24.
There are several striking similarities between DCX and Tau. Tau is a neuronal microtubule-associated protein that promotes microtubule assembly and bundling in axons (35–37). Tau contains three to four tandem repeats, and the repeat domain enhances microtubule assembly. In vitro studies using peptides from the repeat domain showed binding and assembly activity especially by the first repeat but with much lower affinities than the intact protein (38,39). In a similar fashion DC repeat motifs do not mimic all DCX–microtubule-related activity. Only when both repeats are expressed do they partly localize to microtubules in vivo, partly bind to pre-assembled microtubules in vitro and cause bundling of microtubules. Studies of the tau protein revealed that the inter-repeat region also has microtubule-binding capacity (40) and regions flanking the microtubule-binding domain play important regulatory roles in enhancing the binding affinity of the repeats (41–43). The results obtained in this study and our previous results (33) suggest that the DCX N-terminal region (amino acids 1–52) is important for the interaction with microtubules. This may be a direct or indirect effect, as this region may also bind the microtubule itself or may simply be involved in proper folding of the whole DCX protein, respectively. Naturally occurring lissencephaly-causing mutations also suggest the importance of this region, as there are lissencephaly-causing missense mutations in the first 52 amino acids. The variability seen in our system indicates that there is more than one way to alter the function of the DCX protein; disruption of microtubules is probably one of them. This is not the case with disease-causing mutations in tau. These mutations which result in inherited dementia typically involve one of the microtubule-binding domains of Tau (44). The mutated tau protein products have weaker binding to microtubules (45,46). In a similar fashion, functional characterization of mutations found in the MID1 gene, which is mutated in Opitz syndrome (multiple congenital anomaly involving midline structures, developmental delay and mental retardation), revealed that association with microtubules is compromised (47,48).
The outcome of DCX mutations is clearly more variable, there are mutations that may have less or equal microtubule-bundling activity, some may have higher activity, and the most dramatic may disrupt microtubules altogether. Microtubule disruption quite similar to the effect seen with the DCX mutation Y125H was seen with overexpression of MARK protein kinases that phosphorylate microtubule-associated proteins (49). The site of this mutation (Y125H) may interfere in phosphorylation of the predicted Abl phosphorylation site (Y70). The variability seen in our experiments suggests the existence of additional functions for DCX that are not yet discovered.
We have defined here a new evolutionarily conserved motif that may be functionally conserved as well. Most disease-associated point mutations cluster in this region. We have found that this region is involved in DCX–microtubule function, therefore indirectly implying that DCX–microtubule function is important during brain development. Under- standing the outcome of DCX mutations will expand the knowledge about the pathophysiology of lissencephaly and processes that are important during normal brain development.
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MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
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Computational sequence analysis
Sequences were retrieved from the NCBI and Sanger Centre databases. Database searches were performed on these databases with the BLAST program (50,51). Local multiple alignment was done using the BlockMaker (52) and MACAW (53) programs as previously described (54,55). Although no alignment position is absolutely conserved, the resulting blocks were significantly sensitive and selective in distinguishing proteins with DC domains from all other proteins. Searching the SwissProt database release 37 (78 000 sequences) augmented with 14 DC domain proteins with the DC blocks using the BLIMPS (52) program gave perfect and almost perfect (12/14) separation of the true positives and true negatives, giving equivalence values (56) of 0 and 2 and receiver operating curves (57) of 1 and 0.999.
Cell culture
COS-7 cells (58) were grown at 37°C with 5% CO2 and 95% air in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 4 mM glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin. Cultures were split using standard trypsinization procedures. COS-7 cells were transfected using DEAE transfection procedure (59) with 20 µg of DNA in the absence of serum in the media. Four hours after transfection the media was aspirated and 10% DMSO was added for 2 min. The cells were washed and fresh standard growth media added. Transfected cells were then analyzed at various times for expression of exogenous protein. Efficiency of transfections was estimated using a green fluorescent protein (GFP) expression vector (Clontech, Palo Alto, CA).
Plasmid construction
Wild-type DCX was cloned in the pRSET vector (Qiagen, Hilden, Germany), using two EcoRI sites and single-strand DNA was prepared. The mutations were introduced using site-directed mutagenesis (59). The oligonucleotides used were:
D246X, 5'-gactcggcattctgttttccatc-3', T
R amino acid 203;
5'-gagtgggctCtcttcttgttc-3', RW amino acid 192;
5'-cagccttccAaggcttcacc-3', YH amino acid 125;
5'-ctgaggaacaCACGTGgctttcccc-3', DN amino acid 62;
5'-gaagtagcggtTcccattgcg-3', RL amino acid 59;
5'-gtccccattgAggtagaaacg-3', S to R amino acid 47;
5'-cttctcattacGcagtgcctg-3'.
All of the mutations were verified by sequencing. The EcoRI fragments containing the mutated DCX coding regions were then cloned into pECE (60) with the FLAG epitope at their N-terminus.
DC repeats from DCX and DCLK (28) were cloned using PCR with the following primers:
Pep1 mouse DCLK, 5'-cgGaattcAAAGCCAAGAAGGTTC-3';
Pep2 mouse Pep1 mouse DCLK, 5'-cgGaattcAAAGCCAAGAAGGTTC-3';
Pep2 mouse DCLK, 5'-CgGaattcCGACCCAAGCTGGTC-3';
PEP1 DCX, 5'-cgGaattcAAAGCCAAGAAGGTAC-3';
PEP2 DCX, 5'-cgGAATTCCGCCCCAAGCTGGTTAC-3';
PEP1 Mouse 3' DCLK, 5'-CGTCTAGATCACTTAAAGGGCTCGAT-3';
PEP2 Mouse 3' DCLK, 5'-CGTCTAGATCAACGGAACTTCTCTGG-3';
PEP1 3' DCX, 5'-CGTCTAGATCATTTAAAGAAGTTGTC-3';
PEP2 3' DCX, 5'-CGTCTAGATCAGCGAAATTTTTCAGG-3'.
Plasmids with inserts derived from PCR were completely sequenced. The corresponding fragments were cloned into PECE–FLAG or pGEX4T1.
Proteins
Recombinant DCX and mutated DCX were cloned in pRSET and transfected to Escherichia coli strain BL21, recombinant protein isolated on NiNTA columns according to the manufacturer’s recommendations (Qiagen). Tubulin was prepared from bovine brain extract as described (10). GST fusion peptide plasmids were transfected to E.coli strain BL21, and recombinant protein was isolated using glutathione–agarose beads (Sigma, Rehovot, Israel).
Antibodies
Anti-
tubulin (monoclonal, clone DM1A), or anti-acetylated tubulin (monoclonal, clone no. 6-11B-1) were purchased from Sigma. Anti-doublecortin polyclonal antibodies J74 were produced against a mixture of peptides (described in ref. 31).
Anti-FLAG M2 monoclonal antibodies
All secondary antibodies are from Jackson Immunoresearch (West Grove, PA): peroxidase-conjugated affinipure goat anti-mouse IgG (H+L), lissamine rhodamine-conjugated affinipure goat anti-mouse IgG (H+L), Cy3-conjugated affinipure goat anti-rabbit IgG (H+L), FITC-conjugated affinipure goat anti-mouse and anti-rabbit IgG (H+L).
GST pull-down assay
E18 brain extract or purified proteins were prepared in T-T buffer (20 mM Tris–HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.1% Triton-X), supplemented with protease inhibitors (Sigma). Proteins were incubated with 10 µg of GST–DCX, –PEP1, –PEP2, –PEP(1+2) and GST as control, at 4°C for 3–15 h. Glutathione beads (30 µl) in 300 µl of T-T buffer were added to the protein mixture and rotated for 30 min at room temperature. After four washes with T-T buffer, 2x sample buffer was added and the beads were boiled and ran on an SDS–PAGE gel. Western blot was performed with -tubulin antibodies (monoclonal, clone DM1A).
Immunostaining
Briefly, transfected cells were plated on glass coverslides. After 48 h they were washed twice with phosphate-buffered saline (PBS), then fixed and permeabilized simultaneously in cold methanol for 10 min. After fixation the cells were incubated with 30 µl of the first antibody for 60 min at room temperature, then washed three times in PBS and incubated for 30 min with 30 µl of fluorescent-conjugated secondary antibodies. The coverslips were washed three times in PBS, drained and mounted. The immunostaining was visualized using an Olympus microscope (IX50 model; Hamburg, Germany) using the appropriate filters. Photography was with Kodak 160T film.
Detergent extraction assay
This was performed essentially as described by Cohen et al. (61) and Horesh et al. (33).
Microtubule assembly in vitro
Rate measurements.
Tubulin was purified as described (10). The assembly rate of tubulin to form polymers was monitored using a light-scattering assay (62,63). Purified tubulin was diluted in PEM buffer (100 mM PIPES pH 6.9, 1 mM MgSO4, 1 mM EGTA) supplemented with 1 mM GTP, to a final concentration of 16 µM. Recombinant proteins were dialyzed against PEM buffer prior to their addition to the tubulin solution. Absorbance was measured at 350 nm at 1 min intervals in a uvicon spectrophotometer equipped with temperature-controlled cells. Switching the temperature to 37°C induced assembly.
Microscopy of microtubules.
The effect of recombinant pro- teins on microtubule bundling was visualized by video-enhanced DIC microscopy. A solution (10 µl) containing phosphocellulose-purified tubulin and recombinant proteins, in PEM buffer supplemented with 1 mM GTP at indicated molar ratio was allowed to polymerize by incubation in an Eppendorf tube for 30 min at 26°C. A sample of the tube contents was transferred to microscope slides with coverslips mounted over parafilm spacers, and sealed with wax. DIC microscopy was performed using a Zeiss microscope equipped with a temperature-controlled oil immersion objective (Fluor 100/1.3).
Electron microscopy
Samples were prepared as described for DIC microscopy using tubulin at a concentration of 15 µM with or without the addition of 9 µM of EcoRV 1–213 fragment and incubated for 15 min at 37°C. Eight microliters of each sample was applied to a carbon-coated copper 400-mesh electron microscope grid, which had been previously glow-discharged to render the carbon surface hydrophilic. The grid was then rinsed with water, and 10 µl of uranyl acetate stain (1% in water) was applied. The grid was blotted after 30 s. Samples were examined with a Philips CM12 electron microscope operating at 100 kV.
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ACKNOWLEDGEMENTS |
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This work was supported in part by the HFSP grant no. RG283199, Minerva Foundation, Germany, and the Minna James Heineman Foundation (to O.R.). O.R. is an incumbent of the Aser Rothstein Career Development Chair in Genetic Diseases. M.E. is an incumbent of the Delta Career Development Chair, and acknowledges support from the Israel Academy of Sciences and the Gerhard M.J. Schmidt Minerva Center for Supramolecular Architecture. S.P. acknowledges support from the Helen and Milton Kimmelman Center, supported by a research grant from the Kekst Family Center for Medical Genetics, the Forchheimer Center and the Crown Human Genome Center of the Weizmann Institute.
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FOOTNOTES |
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+ To whom correspondence should be addressed. Tel: +972 8 9342319; Fax: +972 8 9344108; Email: lvreiner@wicc.weizmann.ac.il
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REFERENCES |
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