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Vol. 19, Issue 7, 3124-3137, July 2008
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*Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom; Section of Microbiology, University of California, Davis, Davis, CA 95616; and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200
Submitted November 19, 2007;
Revised April 16, 2008;
Accepted April 29, 2008
Monitoring Editor: Tim Stearns
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONREFERENCES |
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONREFERENCES |
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; Dutcher, 1995; Ostrowski et al., 2002; Pazour et al., 2005) that are synthesized in the cytoplasm. For accurate flagellar assembly, these flagellar constituents need to be transported from the cell body and assembled at the distal flagellar tips (Binder et al., 1975). Flagellar assembly and maintenance is achieved through the continuous and bidirectional movement of large proteinaceous particles (rafts) from the base of the flagellum to the distal flagellar tip (originally described in Kozminski et al., 1993 and reviewed recently in Rosenbaum and Witman, 2002 and Scholey, 2003). This mechanism, known as intraflagellar transport (IFT), ensures the delivery of axonemal building blocks to the distal flagellar tips. The first observations of IFT particles moving anterogradely along the flagellum were seen in the unicellular alga Chlamydomonas reinhardtii using differential interference contrast (DIC) microscopy (Kozminski et al., 1993). The mechanism and regulation of IFT has since been well characterized in experimental systems such as Chlamydomonas and Caenorhabditis elegans (reviewed in Rosenbaum and Witman, 2002; Scholey, 2003).
Beyond the well-studied role of IFT in the assembly and maintenance of motile flagella, proper IFT functioning is essential for sensory transduction during mating in Chlamydomonas (Pan and Snell, 2002), assembly of primary (9 + 0) cilia in the kidney (Lin et al., 2003), vision (Pazour et al., 2002), and chemosensory behavior in metazoans (Perkins et al., 1986; Starich et al., 1995). Recently identified links between proper flagellar function and human ciliary diseases such as polycystic kidney disease (Pazour et al., 2000; Haycraft et al., 2001; Lin et al., 2003) and Bardet-Biedl syndrome (Li et al., 2004; Snell et al., 2004) highlight the importance of understanding both the components and cellular control of flagellar length dynamics (Sloboda, 2002).
The kinesin-2 heterotrimeric complex, which includes two kinesin-2 homologues as well as the kinesin-associated protein (KAP; Wedaman et al., 1996), powers the anterograde movement of IFT proteinaceous rafts along the outer doublet of axonemes. The retrograde movement of rafts toward the cell body is mediated by cytoplasmic dynein 1b (Signor et al., 1999). The kinesin-2 heterotrimeric complex was initially identified biochemically from sea urchin eggs (Cole et al., 1993; Wedaman et al., 1996), and its role in axoneme assembly has since been confirmed in diverse flagellated eukaryotes. To illustrate, the disruption of kinesin-2 function has been shown to result in severe inhibition of flagellar or cilia assembly in diverse eukaryotes including C. reinhardtii (Walther et al., 1994; Kozminski et al., 1995), Tetrahymena thermophila (Brown et al., 1999), and a variety of metazoan lineages and cell types (Shakir et al., 1993; Yamazaki et al., 1995; Morris and Scholey, 1997; Han et al., 2003; Sarpal et al., 2003). Aside from its role in IFT, kinesin-2 has also been suggested to have a role in intracellular transport (Yang et al., 2001), ER–Golgi transport (Stauber et al., 2006), and chromosome segregation (Miller et al., 2005).
Although flagellated protists represent a significant fraction of microbial eukaryotic diversity (Patterson et al., 1999), the role of kinesin motors in basic cellular processes such as flagellar assembly and function has only been studied in depth in a handful of protists, including the green alga C. reinhardtii, the trypanosomes (Leishmania major and Trypanosoma brucei) and the ciliate T. thermophila (reviewed recently in Scholey, 2008). One such multiflagellated parasitic protist, Giardia intestinalis, is a widespread and understudied parasite of humans and animals (Savioli et al., 2006). The interphase microtubule cytoskeleton of Giardia is characterized by eight canonical 9 + 2 axonemes (see Figure 5, a and b) as well as several unique microtubular structures—the median body and the ventral disk (Elmendorf et al., 2003). The "ventral disk," an overlapping spiral microtubule array, is critical to virulence as it mediates the attachment of Giardia trophozoites to the intestinal microvilli (Elmendorf et al., 2003).
Flagellar motility is required for Giardia to complete cell division and cytokinesis (Adam, 2001; Elmendorf et al., 2003; Nohynkova et al., 2006; Tumova et al., 2007), and the eight axonemes are distinctive in possessing long, cytoplasmic (non-membrane-bound) regions. All eight axonemes then exit the cell body as conventional membrane-bound axonemes. The eight basal bodies are in close proximity to the two nuclei. Each flagellar pair likely possesses a unique molecular identity based on the unique associations with ancillary structures that remain generally uncharacterized beyond their ultrastructure (Elmendorf et al., 2003). In support, several proteins have been shown to localize to different pairs of cytoplasmic and external portions of axonemes including: GASP-180, a member of a novel family of coiled-coil proteins (Elmendorf et al., 2005), and several 
-giardins (Szkodowska et al., 2002; Weiland et al., 2005). It has recently been suggested that during giardial division, daughter flagella undergo a maturation process in which the flagella migrate and transform to different flagellar types (Nohynkova et al., 2006).
Because of the evolutionary divergence of Giardia, it is important to study the structure, as well as the in vitro and in vivo functions of giardial kinesins. Within the kinesin gene family, kinesin-2 homologues are perhaps the most conserved kinesin motors within their group (Wickstead and Gull, 2006) and are present in the majority of eukaryotes that have a flagellum during their life cycle (Richardson et al., 2006; Wickstead and Gull, 2006). The Giardia genome contains all components of the kinesin-2 heterotrimeric complex including two kinesin-2 homologues (Wickstead and Gull, 2006) and one KAP homolog (Briggs et al., 2004; Morrison et al., 2007); however, the Giardia genome does not contain homologues of the homodimeric OSM-3 complex found in both metazoans and ciliates (Wickstead and Gull, 2006). IFT has been inferred from phylogenomic analyses (Briggs et al., 2004; Morrison et al., 2007), but has not been empirically demonstrated in Giardia. Yet, in principle, IFT would only be required to maintain the lengths of membrane-bound, or noncytoplasmic, portions of axonemes. Although many IFT raft proteins and motors are conserved across diverse taxa, some eukaryotes have cytoplasmic axoneme assembly that is IFT-independent, including both the malaria parasite Plasmodium falciparum (Avidor-Reiss et al., 2004) and Drosophila sperm (Han et al., 2003; Sarpal et al., 2003). Given the central importance of flagellar biology to Giardia's pathogenic life style, flagellar proteins, such as kinesin-2, may make excellent targets for antigiardial drugs.
In this study, we have solved the crystal structures of the catalytic core of a kinesin-2 homolog (GiKIN2a) and its hydrolysis-deficient mutant from G. intestinalis. These are the first high-resolution structures of a kinesin-2 motor. The structural fold of the kinesin motor domain is remarkably conserved and provides insights into the nucleotide coordination within its active site. We have also confirmed the ancient and conserved role of kinesin-2 as a plus-end–directed IFT motor in Giardia. To determine whether giardial kinesin-2 function is conserved in vivo, we overexpressed a green fluorescent protein (GFP)-tagged kinesin-2 rigor construct (GiKIN2aT104N), demonstrating that the majority of cells had dramatic shortening of external axoneme length. Thus, as in other organisms, this kinesin-2 rigor mutant also acts as a dominant negative and supports our inference that IFT-mediated assembly and maintenance of axoneme length is an ancient and conserved process. Cytoplasmic axoneme length was unaffected in this mutant, and we propose that cytoplasmic regions of giardial axonemes do not require kinesin-2 for their assembly.
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MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONREFERENCES |
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) within 13-ml screwcap tubes (Fisher Scientific, Pittsburgh, PA). For the analysis of tetracycline-inducible mutants, strains were incubated without doxycycline (EMD Chemicals Inc., San Diego, CA) for 24 h to induce the dominant negative kinesin-2 phenotype.
Bacterial Expression and Protein Purification
The sequence corresponding to the motor domain (1-1053 nt) of GiKIN2a (XP_001064328) was amplified from Giardia genomic DNA by PCR using KOD polymerase (Novagen, Madison, WI). Two oligonucleotide primers were used for PCR (forward 5'-gactaccatatgtcgagcgacaacatcaaggttat-3' and reverse 5'-gactacggtaccctaatgtggatggtgatggtggcgaatctgcgcatccttcgggtct-3'), producing a fragment with encoded 6xHis-tag and unique restriction sites NdeI (5'-end) and KpnI (3'-end). After digestion and DNA purification (Qiagen, Chatsworth, CA), the fragment was cloned into the pET17b vector (Novagen) and subsequently verified by sequencing. The vector-containing insert was transformed into BL21 (DE3) competent cells (Novagen) and grown in 12L of 2xTY, containing 100 µg/ml ampicillin. The cell culture was initially grown at 37°C and expression was induced at OD600 0.6 with 0.5 mM IPTG; after induction the incubation temperature was changed to 22°C. The expressed protein contained 357 amino acids and had a molecular weight of 39.6 kDa.
Cells were harvested and frozen in liquid nitrogen. Lysis of cells was achieved by thawing cell pellets in lysis buffer, with subsequent sonication; lysis buffer: 50 mM PIPES, pH 7.5, 150 mM NaCl, 3 mM dithiothreitol (DTT), 2 mM MgCl2, 1 mM ATP, protease inhibitor tablets (1 per 70 ml; Roche Diagnostics, Alameda, CA), 0.1 mg/ml lysozyme (Sigma, St. Louis, CA), 40 µg/ml DNAaseI (Sigma). The supernatant was loaded onto two consecutive 5-ml HisTrapHP columns (GE Healthcare, Waukesha, WI). After an extensive wash with 50 mM PIPES, pH 7.5, 150 mM NaCl, 3 mM DTT, 2 mM MgCl2, 1 mM ATP, and 20 mM imidazole, the protein was eluted with 300 mM imidazole, 50 mM PIPES, pH 7.5, 150 mM NaCl, 3 mM DTT, 2 mM MgCl2, and 1 mM ATP. Peak fractions were loaded onto MonoQ-column (GE Healthcare), the column was washed with buffer C (50 mM PIPES, pH 7.5, 3 mM DTT, 2 mM MgCl2, and 1 mM ATP), and the protein was eluted with buffer C with 150 mM NaCl added. Peak fractions were pooled and concentrated before being loaded onto a 16/60 Sephacryl S-200 column (GE Healthcare) pre-equilibrated in buffer C with 100 mM NaCl and 1 mM NaN3. The protein was eluted as a single peak and was concentrated at 4°C in Vivaspin concentrators (10,000 MWCO, Vivascience, Westford, MA) to 12 mg/ml before storage in liquid nitrogen at –70°C.
Design of GiKIN2aT104N Mutant for Structural Analysis
QuickChange site-directed mutagenesis (Stratagene, La Jolla, CA) was performed according to the manufacturer's instructions. The plasmid containing the GiKIN2a motor domain was used as the template DNA to obtain the GiKIN2aT104N mutant. The mutagenesis primers were as follows: GiNF: 5'-agacaggtgccggaaagaaattggacgatgggaggtaa-3' and GiNR: 5'-ttacctcccatcgtccaattctttccggcacctgtct-3'. The altered nucleotides are underlined. The plasmid was sequenced to confirm that only the desired mutation had been introduced.
Crystallization and Data Collection
Purified GiKIN2a motor domain protein at 10 mg/ml was crystallized by the sitting-drop vapor diffusion technique. The crystallization buffer for the wild-type and mutant GiKIN2a protein was 100 mM bicine, pH 9.0, and 30% (wt/vol) PEG 6000. Before crystallization trials, 1 mM ATP and 2 mM MgCl2 were added to the protein. Crystals were grown at 18°C and were used when they were between 2 d and 1 wk old. Before data collection, the crystals were harvested in mother liquor with 25% (wt/vol) PEG 400 and frozen directly into liquid N2.
Data were collected to 1.6 Å resolution on beam-line ID14-3 at the European Synchrotron Radiation Facility (ESRF) in Grenoble (France). Crystals of wild-type and mutant GiKIN2a belong to space group P1 and have two molecules in the asymmetric unit; the cell dimensions are given in Table 1.
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). The structure of GiKIN2a was solved by molecular replacement using PHASER (Storoni et al., 2004) and the Neurospora crassa kinesin (PDB entry 1GOJ) as the search model. Crystallographic refinement was carried out using CNS (Brunger et al., 1998) with Engh and Huber (1991) parameters. Water molecules were initially added automatically with the program CNS and subsequently were corrected by visual inspection of the difference map. All manual model building for GiKIN2a was carried out using MAIN (Turk, 1992) and for GiKIN2aT104N using Coot (Emsley and Cowtan, 2004). The stereochemistry of the model was verified using the program PROCHECK (Laskowski et al., 1993). The parameters of the final models are summarized in Table 2.
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) followed by phosphocellulose chromatography (Mandelkow et al., 1985). Two hundred fifty microliters of 10 mg/ml pig brain β tubulin (80 mM PIPES, pH 6.9, 1 mM MgSO4, 1 mM EGTA, and 1 mM DTT) and 300 µl of 10 mg/ml GiKIN2aT104N were incubated on ice together for 30 min, centrifuged briefly, and injected into a Superose 12 HR10/30 gel filtration column (GE Healthcare). The column was eluted at 0.5 ml/min with 80 mM PIPES, pH 6.8, 1 mM MgCl2, and 1 mM EGTA, and 500-µl fractions were collected and analyzed by 12.5% SDS-PAGE. Protein bands were stained with Coomassie Blue. The elution profile of the protein complex was compared with the elution profiles of the individual proteins as well as with known molecular-weight standards (data not shown).
Cloning and Transformation of GFP-tagged and Rigor Mutant Strains
The kinesin-2 homolog GiKIN2a (XP_001064328), with AscI/AgeI sites for subcloning and 
80 base pairs upstream of the start codon to include the native promoter, was amplified from Giardia genomic DNA by PCR using the oligonucleotide primers K2aF: 5'ggcgcgccaatgctgccctcaggtgctcagaagaactggccag3' and K2aR: 5'accggtagttcataggtgtctatttgagagtagaacatttgtagctgtgt3' (restriction sites are underlined). The PCR amplicon was then subcloned into the pMCS.pac vector (Sagolla et al., 2006) to produce a C-terminal kinesin-2 GFP fusion. To create an inducible dominant negative kinesin-2 construct, GiKIN2a was PCR amplified from Giardia genomic DNA (using TK2GF: 5'ggcgcgccatgtcgagcgacaacatcaaggttatcgtgcgttgc3' and TK2GR: 5'accggtagttcataggtgtctatttgagagtagaacatttgtag3') and was cloned downstream of the ran promoter and associated tetO elements in pTetGFPC.pac (Dawson et al., 2007). The kinesin-2 rigor construct GiKIN2aT104N was generated by site-directed mutagenesis (Stratagene) of the previous construct using the oligonucleotide primers k2DNF: 5'acaggtggcggaaagaattggacgatgggaggt3' and k2DNR: 5'acctcccatcgtccaattctttccgccacctgt3' and confirmed by DNA sequencing.
For the other giardial kinesin-2 homolog (GiKIN2b) as well as the two GFP-tagged IFT Complex A (IFT140) and Complex B (IFT81) proteins (see Figure 6), we used a similar strategy as above to PCR amplify genes from the Giardia genome and cloned the amplicons into the pMCS.pac vector using the AscI/AgeI restriction sites. The two IFT complex proteins were clear homologues in the Giardia Genome Database. We used the following oligonucleotide primers for the PCR amplifications of the GiKIN2b, IFT81, and IFT140 genes (restriction sites are italicized): K2bF: 5'attaggcgcgccgtgccaatattcactagctatctcgccatc3'; K2bR: 5'atcgaaccggtagaccgaaaccagccatgccacggtgtgacttttggg3'; IFT81F: 5'atcgggcgcgccgtgtttgaaaagttcgacatgtgcggacgtgtcag3' IFT81R: 5'aattaccggt aggttggttattctaattttgtccatacgcatctcggc3'; IFT140F: 5'tactggcgcgccgcctctatcttgtcataaagcctcagtatttg3'; IFT140R: 5'gctccccgggaggtgatcgctcttttcggctgttaggtctatatc3'.
To create GFP-tagged and inducible kinesin rigor mutant strains, G. intestinalis strain WBC6 was electroporated with roughly 50 µg of plasmid DNA (above) using the GenePulserXL (Bio-Rad, Richmond, CA) with previously described conditions (Sagolla et al., 2006). Episomes were maintained in transformants by antibiotic selection using 50 µg/ml puromycin (Davis-Hayman and Nash, 2002). Tetracycline repression of the kinesin rigor mutant was maintained with 10 µg/ml doxycycline (Sigma).
Quantitation of GinKIN2a Overexpression Using Quantitative PCR
The de-repression and overexpression of episomal constructs (after removal of doxycycline) was confirmed using quantitative PCR (qPCR) of the GFP-tagged rigor mutant (GiKIN2aT104N), the GiKIN2a (both native and mutant forms), and actin as an internal relative standard (Supplementary Figure S2). Previously we have observed the maximal induction of transgenes at 1–8 h after removal of doxycycline, and these levels of induction continued after the removal of doxycycline for over 48 h (Dawson et al., 2007). Total RNA was isolated from 6-ml cultures of the uninduced or overexpressed GiKIN2aT104N rigor mutant strain using the Cells-to-cDNA kit (Ambion, Austin, TX). Cells were sampled at 0.25, 0.5, 1, 8, 16, 24, and 48 h after induction. For quantitative analysis of expression using qPCR, 1-µl aliquots of the cDNA synthesis reaction were used in actin-specific (actF 5'cctgaggcccccgtgaatgtggtgg3' and actR 5'gcctctgcggctcctccggagg3'), GFP-specific (GFPF5'gagctgttcaccggggtggtgccc3' and GFPR5'cgggcatggcggacttgaagaagtcgtgc3'), and GiKIN2a-specific (qKIN2aF 5'ggagccacgcacataccataccg3' and qKIN2aR 5'ccgagcaatgtggtctcttagctggc3') PCR amplifications in DyNamo HS SYBR Green pPCR Master Mix (Finnzymes, Espoo, Finland). qPCR was performed with the Opticon 2 system (Bio-Rad). To demonstrate that RNA samples were not contaminated with DNA, PCR amplifications were also performed with control cDNA synthesis reactions that lacked reverse transcriptase. GiKIN2aT104N overexpression was compared using the relative method of quantification (Livak and Schmittgen, 2001), and GFP expression and kinesin-2 levels were normalized to the actin gene. Overexpression was determined from comparisons of normalized GFP expression in induced time points to uninduced controls (see Supplementary Figure S2).
Immunofluorescence Microscopy and Image Data Analysis
Immunostaining of the GFP-tagged strains was performed as described previously (Sagolla et al., 2006). Briefly, trophozoites were gently fixed in 1% paraformaldehyde and cytoskeletal buffer (PEM) for 15 min, and later permeabilized in 0.1% TritonX-100/PEM before immunostaining. This preserved both native GFP fluorescence and cytoskeletal structure. To measure the membrane-bound regions of axonemes, we coimmunostained microtubules and axonemes with both -tubulin and 14-giardin antibodies (see Figure 7). 14-giardin has been previously shown to localize only to membrane-bound (not cytoplasmic) regions of all eight axonemes (Szkodowska et al., 2002). Images were collected using an Olympus IX70 wide-field inverted fluorescence microscope (Melville, NY) with an Olympus UPlanApo 100x, NA 1.435, oil immersion objective and Photometrics CCD CH350 camera cooled to –35°C (Roper Scientific, Tucson, AZ). Serial sections were acquired at 0.2-µm intervals (30 total sections on average) and deconvolved using the SoftWoRx deconvolution software (Applied Precision, Issaquah, WA). Two-dimensional (2D) projections were created from the 3D data sets using SoftWorX for presentation purposes. Flagellar length measurements (based on immunostaining of axonemes in the GiKIN2aT104N strain) were calculated from 3D image stacks using the Imaris software package (BitPlane, Zurich, Switzerland). Over 100 axonemes were measured for each treatment, with roughly 30 axonemes from each flagellar pair type, i.e., caudal, ventral, posteriolateral, and anterior.
Transmission Electron Microscopy and Scanning Electron Microscopy of Trophozoites
To determine the flagellar ultrastructure and prepare samples for transmission electron microscopy trophozoites were first attached to sapphire discs and then were high-pressure frozen as described in with a few adjustments (Sawaguchi et al., 2003). Cells were attached to cleaned sapphire discs at 37°C. Cells were then frozen using the Baltech high-pressure freezer, and freeze substituted using the Leica freeze substitution apparatus (Deerfield, NY). Cells were embedded with Epon resin and serial-sectioned on a Ultracut E. Sections were stained with uranyl acetate in 70% methanol and lead citrate and viewed on JEOL 1200 transmission electron microscope (TEM; Tokyo, Japan).
For scanning electron microscopy (SEM), trophozoites were first allowed to attach to either to Aclar or track membrane filters and subsequently were fixed for 1 h in 2% glutaraldehyde in cacodylate buffer. Then, cells were postfixed with 2% OsO4, dehydrated in ethanol, critically pointed-dried, and coated with the MED 020 Bal-tec high-vacuum coating system (Zurich, Switzerland) using iridium. Images were taken using the Hitachi S5000 FESEM (Brisbane, CA) at 10 Kv.
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RESULTS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONREFERENCES |
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; Morrison et al., 2007), Giardia has two kinesin-2 homologues (GiKIN2a and GiKIN2b). The GiKIN2a motor domain and its mutant GiKIN2aT104N were cloned into the pET17b vector (Novagen) and expressed as C-terminal histone 6–tagged protein (His6)-tagged protein in BL21 (DE3) cells (Novagen). The proteins were purified over a Ni -NTA column, followed by anion exchange chromatography and gel filtration chromatography. Crystals were grown for both proteins from nearly identical crystallization conditions (0.1 M bicine, pH 9.0, 30%, wt/vol, PEG 6000).
The high-resolution crystal structures of G. intestinalis wild-type kinesin GiKIN2a (at 1.6 Å resolution) and its mutant GiKIN2aT104N (at 1.8 Å resolution) in complex with ADP and Mg2+ (Table 1) were solved. The crystallographic model for the wild-type GiKIN2a was refined with R/Rfree values of 0.20 and 0.22 and for the model of mutant GiKIN2aT104N with R/Rfree values of 0.22 and 0.26 (Table 2). Both crystals belonged to space group P1 with two molecules in an asymmetric unit (Table 1). The root-mean-square (RMS) deviation of the wild-type GiKIN2a structure from the mutant structure was 0.284 Å, indicating that both structures are very similar in overall conformation. The structure of GiKIN2a (Figure 1) reveals a kinesin motor domain in the ADP-bound state with eight β-strands and six -helices characteristic for the kinesin catalytic core (Sack et al., 1999). The active site in the crystal structure of the wild-type GiKIN2a motor domain (Figure 2a) shows that the Mg2+ ion (a purple sphere) is coordinated in an octahedral geometry by T104, an oxygen from the β-phosphate of ADP, and four water molecules (blue spheres).
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). As in classic GTPases and other kinesin structures in the ADP state, the GiKIN2a's closed pocket is defined by the characteristic distance (5.86 Å) between P-loop Gly97 and Gly244 of the switch II region. A typical distance of around 5.7 Å for the closed state has been reported for other kinesins that have been crystallized with bound ADP (e.g., rat kinesin-1, PDB, and 2KIN; Sack et al., 1999).
Contrary to the majority of kinesin structures in the ADP state, a salt bridge between Arg211 of switch I and E246 of switch II, which has been hypothesized to stabilize the closed confirmation of the motor domain in analogy to myosin, is not observed in GiKIN2a (distance between Arg211 and E246 is 4.3 Å). A similar phenomenon has been described for PDB:KIF1A (Kull and Endow, 2002). Based on results from ATPase activation assays, Yun et al. (2001) suggested that this salt bridge between the switch I and switch II region is essential for the ATPase activation of the kinesin motor by microtubules.
As visible in Figure 2b, the mutation T104N did not introduce any major overall conformational changes in the motor domain of GiKIN2aT104N and did not cause dissociation or movement in the position of the ADP nucleotide. The most notable difference we observed was in the coordination of Mg2+ induced by the mutation, which disrupted an almost perfect octahedral coordination around the magnesium ion because N104 is no longer involved in its stabilization (Figure 2). In the mutant, residue D241 is directly involved in Mg2+ coordination, resulting in a shift of its position away from the O atom of the β-phosphate of the ADP nucleotide (2.17 Å in wild type vs. 2.71 Å in the mutant). This shift strengthens the direct interaction between the magnesium ion and residue D241 and thus inhibits the release of the magnesium ion from the active site.
In the motor domain of the GiKIN2aT104N, the salt bridge between Arg211 and E246, with a distance of 3.6 Å, appears to be preserved. Neither Arg211 nor E246 underwent a conformational change in the hydrolysis deficient mutant.
Crystal structures of GiKIN2a and GiKIN2aT104N (Figure 2, a and b) show that the aromatic ring of Trp105 forms a 
-stacking interaction with the adenine ring of the ADP nucleotide. This tryptophan residue is unique to the motor domain of GiKIN2a among the kinesin-2 family, as can be seen in the multiple sequence alignment (Supplementary Figure S1).
The superposition of GiKIN2a with monomeric human kinesin, which has two bound sulfate anions as well as ADP (PDB:1MKJ; Sindelar et al., 2002; Figure 3a) shows high overall structure similarity with the RMS deviation of 1.0 Å over 294Ca atoms, despite the evolutionary distance between the proteins. A stretch of twelve amino acids following the catalytic core, referred to as a neck-linker, is suggested to be involved in the kinesin movement and force generation (Chikashige et al., 1997). The docked state of the neck linker is favored for kinesins with ATP bound in the active site, whereas the undocked state is predominant for kinesins with ADP bound (Rice et al., 1999). The neck linker is normally disordered when ADP is bound and is therefore not visible in crystal structures, but the presence of sulfate ions is thought to be responsible for the docked state in 1MKJ (Sindelar et al., 2002). Surprisingly, the ADP-bound GiKIN2a also crystallized with the neck-linker in the docked state. Figure 3b displays the close superposition of the neck-linker region of the human (1MKJ) and Giardia (GiKIN2a) kinesins, branching off at Glu334 of 1MKJ and Asp344 of GiKIN2a.
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. The mutated residue T104N in the Giardia kinesin-2 homolog corresponds to the T93N mutation of the rat kinesin-1. To examine in vitro the irreversible binding of the kinesin-2 GiKIN2aT104N rigor mutant to β-tubulin heterodimers, gel filtration chromatography was used (see Materials and Methods). As shown in Figure 4a, β-tubulin eluted from the Superose 12 HR10/30 gel filtration column (GE Healthcare) as a single peak at 13 ml, and the salt appears at 20.5 ml. The profile of β-tubulin was consistent with previous work (Hung et al., 2004), suggesting that β-tubulin predominantly gel filtrated as heterodimer under the conditions used. When a mixture of the GiKIN2aT104N kinesin motor and β-tubulin with no added nucleotide was gel filtrated, the kinesin monomer bound tightly to the tubulin heterodimers and eluted as a complex larger than the tubulin heterodimer (Figure 4, a and b). The excess GiKIN2aT104N eluted at 14.5 ml and the salt peak trailed at 20.5 ml. The presumed binding stoichiometry is one GiKIN2aT104N monomer per microtubule heterodimer (Figure 4b) based on the 1:1 stoichiometry of kinesin-tubulin binding observed with SDS-PAGE (Figure 4b) and reported in previous studies (Crevel et al., 2004).
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; Smith and Yang, 2004; Nicastro et al., 2006), with few exceptions (Schrevel and Besse, 1975; Prensier et al., 1980). Compared with many other flagellated protists, Giardia is somewhat unique in that all eight axonemes possess long cytoplasmic regions and exit at specialized structures on the plasma membrane termed flagellar pores (reviewed recently in Elmendorf et al., 2003). We used TEM to confirm the conserved 9 + 2 structure of the giardial axonemes in both cytoplasmic and membrane bound regions, particularly around the basal bodies and flagellar pore region. This ultrastructural analysis indicated that the transition zones of all eight axonemes are restricted to small regions proximal to the basal bodies (as in other flagellates like Chlamydomonas), rather than to the entire cytoplasmic axoneme (Figure 5). Finally, electron-dense structures or "collars" at the points are present where each flagellum exits the cell body (Figure 5, e and f).
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; Morrison et al., 2007). To determine whether IFT was required for the assembly of all regions of giardial axonemes, we localized both kinesin-2 homologues (GiKIN2a and GiKIN2b) in trophozoites using C-terminal GFP fusions expressed in cells using their native promoters and fixed under conditions that preserve GFP fluorescence (see Materials and Methods). All images are presented as 2D projections of 3D data sets. Although it is possible to distinguish the external and internal axonemes in these projections relative to the GFP-labeled IFT proteins, the complex organization and density of microtubules in the peripheral cytoplasm does not permit the discrete visualization of some of the other microtubule structures in the cell such as the funis (see Materials and Methods). The GiKIN2a:GFP fusion localized along the length of external regions of all eight axonemes (Figure 6, a–h) concentrating at the eight exit points from the cell body or at flagellar pores (Elmendorf et al., 2003) and at all eight distal flagellar tips. In contrast to other flagellated protists such as Chlamydomonas (Vashishtha et al., 1996), we observed no significant localization of kinesin-2 to the region between the two nuclei where the basal bodies are located. Cytoplasmic regions of the posteriolateral and ventral axonemes and each flagellar pore region were particularly enriched in the GiKIN2a:GFP fusion. To visualize the localization of proteins of the IFT complex A and B raft complexes, we GFP-tagged giardial homologues of IFT140 and IFT81 (GiardiaDB open reading frames [ORFs] 17251 and 15428, respectively). Both IFT proteins localized to the membrane-bound regions of axonemes, concentrating at the distal flagellar tips and the flagellar pore regions (Figure 6, i–p, and see inset for localization of foci on membrane bound axonemes). As with the kinesin-2 localization, we observed some cytoplasmic localization of the IFT81 and IFT140 GFP fusions, mainly to posteriolateral axonemes.
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; Lin-Jones et al., 2003), we generated an inducible ectopic rigor kinesin-2 mutant. After demonstrating that GiKIN2aT104N remained bound to tubulin heterodimers in vitro (above), we confirmed that this rigor kinesin-2 mutant acted as a dominant negative in vivo (Materials and Methods and Figure 7). After de-repression of this construct by the removal of doxycycline from the medium, we quantified levels of the wild-type GiKIN2a, GiKIN2aT104, and actin (used as a relative control) using qPCR. Overexpression of the dominant negative construct is minimally 2–5-fold greater than the wild-type GiKIN2a, beginning at 15 min and reaching a maximal level of 25-fold overexpression at 24 h (Supplementary Figure S2). Twenty-four hours after the removal of doxycycline repression, we immunostained cells with both anti--tubulin to stain all microtubule arrays and anti-14-giardin (Figure 7), which localizes and marks only membrane-bound regions of axonemes (Szkodowska et al., 2002). Using these axonemal markers (Figure 7g), we quantified the lengths of external regions of axonemes (from cell body to distal tips) in each flagellar pair (more than 100 flagella measured for each treatment). We found that the majority of cells had flagellar length defects. In particular, there was a clear and statistically significant decrease in the length of membrane-bound regions of axonemes (30% shorter in caudal flagella and 15% shorter in both ventral and posteriolateral flagella), relative to uninduced controls (see Figure 7g). We were not able to detect a significant shortening of the anterior axonemes or shortening of cytoplasmic axoneme region after induction of the dominant negative GiKIN2aT104N, however. The anti-14-giardin antibody clearly marks all noncytoplasmic regions of axonemes (Figure 7, a–f). In extreme cases (roughly 5% of cells), the cytoplasmic regions of the axonemes were curled or bent and apparently were unable to exit the cell body (data not shown). We qualitatively monitored flagellar beat in live induced cells and noticed no substantial defects (data not shown); however, a more comprehensive analysis of flagellar beating in the GiKIN2aT104N strain (particularly in the ventral or posteriolateral flagellar pairs) would be instructive to compare with prior studies of flagellar beat patterns (Campanati et al., 2002).
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONREFERENCES |
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; Snell et al., 2004). The study of Giardia flagellar biology has obvious clinical relevance in terms of parasitology, as well as nonclinical relevance in terms of basic flagellar cell biology and cytoskeletal evolution (Elmendorf et al., 2003). Each pair of giardial axonemes is differentiated, and each pair contributes to various modes of flagellar motility (Campanati et al., 2002). Motility is required for Giardia to find suitable sites to attach and detach from surfaces including the intestinal villi (Campanati et al., 2002). Thus, flagellar motility is critical for the completion of Giardia's life cycle in the mammalian host both during interphase and during late stages of cytokinesis.
The Structures of G. intestinalis Kinesin GiKIN2a and GiKIN2aT104N
Although the giardial kinesin-2 motor, GiKIN2a, has a low sequence identity to other kinesin-2 homologues, there are no striking differences observed in kinesin-2 structure as compared with that of eukaryotes such as metazoans. Similar to the structure of both the rat kinesin K349 and the human kinesin K349 (Sindelar et al., 2002), the new high-resolution crystal structures of GiKIN2a and GiKIN2aT104N contain ADP in the active site accompanied by a docked neck linker (residues 331-344).
This high-resolution crystal structure of the GiKIN2aT104N rigor mutant afforded the opportunity to visualize the mutated residue within the active site and assess the impact of this mutation on nucleotide binding. The overall confirmation of the rigor mutant GiKIN2aT104N was the same as for the wild-type motor, yet the coordination of the magnesium ion was disturbed. It is known from previous work (Ma and Taylor, 1997) that in the absence of microtubules the release of ADP from the kinesin active site requires the stripping of the magnesium ion. In the wild-type kinesin the aspartate residue D241 in the switch 2 region (DLAGSE) indirectly coordinates the magnesium ion through a water molecule (Figure 2a), whereas the conserved threonine residue T104 (GKTWT) directly coordinates the magnesium ion. In the structure of the GiKIN2aT104N rigor mutant (Figure 2b) the asparagine residue N104 is too distant to be involved in the direct coordination of the magnesium ion, which has moved closer to aspartate D241. In case of aspartate D241, the binding affinity of the highly negatively charged oxygen (pKa = 3.9) of its acid group for the magnesium ion is much stronger than the affinity provided by threonine's side chain oxygen (pKa = 16). Therefore, the enhanced stabilization of the magnesium ion through D241 as seen in Figures 2, 3, and 5b most likely prevents the ADP release.
It is possible that even in the presence of microtubules, a similar magnesium coordination could be observed in GiKIN2aT104N. It is known from previous work (Ma and Taylor, 1997) that in the absence of microtubules the release of ADP from the kinesin active site requires the stripping of the magnesium ion from the active site with EDTA or apyrase, whereby the magnesium exchange limits ADP exchange. Before obtaining a high-resolution crystal structure of the GiKIN2aT104N rigor mutant, it was thought that the mutation would result in a weakly binding magnesium ion that would exchange very quickly and thereby promote the release of the nucleotide. Thus, we expected to obtain a crystal structure of GiKIN2aT104N with an empty nucleotide-binding pocket. However, the comparison of wild-type and rigor mutant kinesin structures demonstrated that the magnesium ion in GiKIN2aT104N appeared to be held in place through the direct interaction with D241 as seen in Figure 2b. Most likely the altered coordination slows down the magnesium ion and ADP release, thereby keeping the motor bound to the microtubules. However, proof of this hypothesis and a more intricate understanding of the complex interplay of the motor domain, neck-linker and microtubule would require a crystal structure of β-tubulin in complex with the rigor mutant.
Cytoplasmic Regions of Axonemes Are Not Elongated Transition Zones
The observation that the eight giardial axonemes possess long cytoplasmic regions before exiting at flagellar pores (Elmendorf et al., 2003) might indicate that cytoplasmic axonemes are essentially elongated "transition zones." Previous work has demonstrated that cytoplasmic regions of axonemes, particularly the nonmotile caudal pair, have a conserved flagellar ultrastructure and retain radial spokes, dynein arms, and the central microtubule pair (Clark and Holberton, 1988; Elmendorf et al., 2003; Carvalho and Monteiro- Leal, 2004). There has been no prior study that has empirically shown that IFT is required for the assembly of both cytoplasmic and membrane bound portions of the giardial axonemes. It has been suggested, however, that both IFT-mediated and non-IFT-mediated assembly of axonemes can occur simultaneously in the same cell (Han et al., 2003; Briggs et al., 2004).
Using TEM, we confirmed that the 9 + 2 structure of the giardial axonemes is present in both cytoplasmic and membrane-bound regions (Figure 5). Further, the transition zones of all eight axonemes are restricted to small regions proximal to the basal bodies (as in other flagellates like Chlamydomonas), rather than to the entire cytoplasmic region (Figure 5, e and f). Electron-dense structures are present at the regions where each flagellum exits; the cell body and SEM imaging also showed "collars" in the vicinity of the flagellar pores (see Figure 5).
Giardial IFT Components Localize to Cytoplasmic and Membrane-bound Regions of Axonemes
Homologous components of both the retrograde and anterograde IFT complexes (A and B), and the kinesin-2 motors are present in the genome, yet IFT has not been empirically demonstrated in Giardia. Both giardial kinesin-2:GFP fusions (GiKIN2a and GiKIN2b) localized along the length of axonemes, concentrating in foci at the flagellar tips and the flagellar pore regions of all eight axonemes (Figure 6 and Supplementary Figure S3), the same area where electron-dense structures were observed using electron microscopy (Figure 5, e and f). The cytoplasmic regions of two pairs of axonemes—the posteriolateral and ventral—were also seen to accumulate significant GiKIN2a:GFP and GiKIN2b:GFP signals, possibly indicating that IFT particles dock on cytoplasmic portions of axonemes and accumulate at flagellar pore regions.
In Chlamydomonas, the kinesin-2 homolog FLA10 and plus-end–tracking protein EB1, accumulate both at the flagellar tips and at the flagellar basal bodies (Vashishtha et al., 1996; Pedersen et al., 2003). The basal body/transition zone region has thus been suggested as a docking site for the organization of IFT particles, based on such immunolocalization data of kinesin-2 homologues and IFT proteins to basal bodies (Deane et al., 2001) and the disruption of basal body localization in either kinesin-2 mutants (Vashishtha et al., 1996; Cole et al., 1998) or KAP mutants (Mueller et al., 2005). There was no significant localization of kinesin-2:GFP to the eight basal bodies (localized between the two nuclei), which is similar to Tetrahymena IFT localization (Brown et al., 1999, 2003) and is contrary to Chlamydomonas, trypanosomes (Absalon et al., 2008), and mammals (Follit et al., 2006), where the basal body transitional fibers have been shown to be the docking site for IFT particles (Vashishtha et al., 1996; Brazelton et al., 2001; Deane et al., 2001).
The notion that IFT particles assemble and dock on the cytoplasmic regions of axonemes needs to be confirmed using live analysis of IFT particle movement on both cytoplasmic and membrane-bound regions of axonemes, however. For this initial investigation, we cautiously interpret that the exit point and distal tip regions of giardial axonemes represent the beginning and end points of the IFT pathways; future investigation of IFT particle assembly and movement are required to resolve whether IFT functions in the assembly and maintenance of cytoplasmic axonemes in Giardia.
Is IFT Required for the Assembly and Maintenance of Both Cytoplasmic and Membrane-bound Regions of Giardial Axonemes?
Kinesin-2 disruption mutants commonly do not extend axonemes beyond the transition zone of the basal bodies in diverse flagellated organisms (Perkins et al., 1986; Starich et al., 1995; Nonaka et al., 1998; Brown et al., 1999; Marszalek et al., 1999; Takeda et al., 1999; Pan and Snell, 2002; Pazour et al., 2002; Lin et al., 2003). To test that the giardial kinesin-2 rigor mutant had a dominant negative phenotype (as has been shown in other flagellated organisms; Gelfand et al., 2001; Lin-Jones et al., 2003; Betley et al., 2004; Fan and Beck, 2004; Brown et al., 2005), we overexpressed the rigor kinesin-2 mutant (GiKIN2aT104N) and monitored flagellar length in each flagellar pair (exit points to distal tips; Materials and Methods and Figure 7). The overexpressed kinesin-2 rigor mutant resulted in significantly shorter flagellar lengths in the membrane-bound regions of axonemes (between 15 and 30% in the caudal, ventral, and posteriolateral flagellar pairs; see Figure 7). Therefore, we propose that GiKIN2a is required for IFT-mediated assembly of external or "membrane-bound" regions of axonemes and that the GiKIN2aT104N mutant acts as a dominant negative in vivo. Although giardial IFT particles might assemble on cytoplasmic regions of axonemes (Figure 6), IFT-mediated axoneme assembly would only be required for the external or membrane-bound regions of axonemes. The lack of a complete inhibition of IFT-mediated axoneme assembly, however, could be due to the fact that only one member of the kinesin-2 heterotrimeric complex was disrupted as has been seen in Tetrahymena, where the kinesin-2 complex may be able to function as a homodimer (Brown et al., 1999).
An IFT-independent mode of flagellar morphogenesis, however, may be responsible for cytoplasmic axonemal assembly and possibly for the membrane-bound regions of the anterior axonemes. In contrast to the caudal, posteriolateral, and ventral flagellar pairs in Giardia, we found that anterior flagellar length was unaffected in the dominant negative kinesin-2 mutant. This observation is consistent with prior findings that anterior flagellar length is less affected by microtubule drugs than the other flagellar pairs (Dawson et al., 2007). An alternative explanation is that anterior axonemes assemble at a different, likely slower rate than the other axonemal pairs. IFT-independent assembly of axonemes has some precedent in other organisms. For example, IFT is required in Drosophila for the assembly and maintenance of sensory neurons, but IFT is not required for the assembly and function of Drosophila sperm flagella (Han et al., 2003). Similarly the malarial parasite P. falciparum lacks kinesin-2 homologues (Briggs et al., 2004) and Plasmodium basal bodies/centrioles form and nucleate axoneme assembly in only the microgamete cytoplasm, rather than in the somatic stages (reviewed recently in Morrissette and Sibley, 2002). This hypothesis needs to be further confirmed using additional experimental methods for disrupting IFT or kinesin-2 function.
Giardia Flagellar Function and the Evolution of Flagellar Assembly Mechanisms
Despite the extensive cytoplasmic regions of the axonemes, there is no empirical evidence suggesting that the giardial axonemes are aberrant in terms of either molecular architecture or function, compared with more commonly studied axonemes in experimental systems such as Chlamydomonas. Further, Giardia possesses a full complement of microtubule-associated proteins, such as 24 kinesins from the majority of kinesin families including the kinesin-2 homologues studied here (Wickstead and Gull, 2006). Although prior contentions that Giardia is a "derived" or "degenerate" parasite (Knight, 2004), the flagellar assembly mechanisms involving IFT (Briggs et al., 2004) are likely to be as highly conserved as the structure of the giardial axoneme. "Derived" is a relative term, and the ultrastructural state of flagella in Giardia would need to be compared with a closely related nonparasitic species for this designation to have any relevance. In support of this notion, we have shown here that the giardial kinesin-2 homolog GiKIN2a has no striking differences in its structure compared with other kinesins, and GiKIN2a retains a conserved function as the anterograde motor for intraflagellar transport and axoneme assembly. It is clear that mechanisms for eukaryotic flagellar assembly are highly conserved throughout eukaryotic evolution.
Functional and structural studies of cytoskeletal and flagellar proteins in diverse protists (Brugerolle, 1991) provide a unique evolutionary and comparative perspective to cytoskeletal mechanisms in other well-studied experimental systems. For these reasons, the study of giardial flagellar length dynamics could serve as an additional experimental system with which to elucidate fundamental flagellar assembly and maintenance mechanisms in other eukaryotes. Giardia has been proposed to be a member of one of the earliest diverging branches of eukaryotes in single or multigene eukaryotic phylogenies when an archaeal outgroup is included (Sogin et al., 1989; Best et al., 2004; Ciccarelli et al., 2006; Morrison et al., 2007). In many cases, the Giardia genome contains fewer homologues of cytoskeletal proteins (unlike metazoans or plants), providing perhaps a more ancestral or simpler model for experimental studies of flagellar biology (Morrison et al., 2007). Importantly, the conservation of flagellar assembly mechanisms in Giardia illustrates the ancient origins of these mechanisms in the evolutionary history of the Eucarya.
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ACKNOWLEDGMENTS |
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Footnotes |
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These authors contributed equally to this work. 
Address correspondence to: Scott Dawson scdawson{at}ucdavis.edu)
Abbreviations used: GiKIN2a, Giardia intestinalis kinesin 2a homolog; GiKIN2b, Giardia intestinalis kinesin 2b homolog; GiKIN2aT104N, ATP hydrolysis-deficient mutant strain of GiKIN2a gene; IFT, intraflagellar transport; DIC, differential interference contrast microscopy; KAP, kinesin-associated protein; GASP, novel Giardia coiled-coil protein; OSM-3, "osmotic avoidance-3" C. elegans kinesin-2 homolog that functions as a homodimer; pET17b, Novagen cloning vector; BL21 (DE3), E. coli strain for expression of recombinant proteins; IPTG, isopropyl β:D:1:thiogalactopyranoside; PEG, polyethylene glycol; CCP4, Collaborative Computational Project Number 4; IFT140, intraflagellar transport protein, Complex A, subunit 140; IFT81, intraflagellar transport protein, Complex B, subunit 81; GFP, green fluorescent protein; qPCR, quantitative PCR; His6, histone 6–tagged protein; Ni-NTA, nickel-charged affinity resin for purification of His-tagged proteins.
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