The GTP-binding peptide of beta-tubulin. Localization by direct photoaffinity labeling and comparison with nucleotide-binding proteins

Mechanism of the Initial Tubulin Nucleation Phase

Tubulin nucleation is a highly frequent event in microtubule (MT) dynamics but is poorly understood. In this work, we characterized the structural changes during the initial nucleation phase of dynamic tubulin. Using size-exclusion chromatography-eluted tubulin dimers in an assembly buffer solution free of glycerol and tubulin aggregates enabled us to start from a well-defined initial thermodynamic ensemble of isolated dynamic tubulin dimers and short oligomers. Following a temperature increase, time-resolved X-ray scattering and cryo-transmission electron microscopy during the initial nucleation phase revealed an isodesmic assembly mechanism of one-dimensional (1D) tubulin oligomers (where dimers were added and/or removed one at a time), leading to sufficiently stable two-dimensional (2D) dynamic nanostructures, required for MT assembly. A substantial amount of tubulin octamers accumulated before two-dimensional lattices appeared. Under subcritical assembly conditions, we observed a slower isodesmic assembly mechanism, but the concentration of 1D oligomers was insufficient to form the multistranded 2D nucleus required for MT formation.

Structure and Energetics of GTP- and GDP-Tubulin Isodesmic Self-Association

Tubulin self-association is a critical process in microtubule dynamics. The early intermediate structures, energetics, and their regulation by fluxes of chemical energy, associated with guanosine triphosphate (GTP) hydrolysis, are poorly understood. We reconstituted an in vitro minimal model system, mimicking the key elements of the nontemplated tubulin assembly. To resolve the distribution of GTP- and guanosine diphosphate (GDP)-tubulin structures, at low temperatures (∼10 °C) and below the critical concentration for the microtubule assembly, we analyzed in-line size-exclusion chromatography-small-angle X-ray scattering (SEC-SAXS) chromatograms of GTP- and GDP-tubulin solutions. Both solutions rapidly attained steady state. The SEC-SAXS data were consistent with an isodesmic thermodynamic model of longitudinal tubulin self-association into 1D oligomers, terminated by the formation of tubulin single rings. The analysis showed that free dimers coexisted with tetramers and hexamers. Tubulin monomers and lateral association between dimers were not detected. The dimer-dimer longitudinal self-association standard Helmholtz free energies were -14.2 ± 0.4 k_BT (-8.0 ± 0.2 kcal mol^-1) and -13.1 ± 0.5 k_BT (-7.4 ± 0.3 kcal mol^-1) for GDP- and GTP-tubulin, respectively. We then determined the mass fractions of dimers, tetramers, and hexamers as a function of the total tubulin concentration. A small fraction of stable tubulin single rings, with a radius of 19.2 ± 0.2 nm, was detected in the GDP-tubulin solution. In the GTP-tubulin solution, this fraction was significantly lower. Cryo-TEM images and SEC-multiangle light-scattering analysis corroborated these findings. Our analyses provide an accurate structure-stability description of cold tubulin solutions.

Dual Impact of a Benzimidazole Resistant β-Tubulin on Microtubule Behavior in Fission Yeast

The cytoskeleton microtubule consists of polymerized αβ-tubulin dimers and plays essential roles in many cellular events. Reagents that inhibit microtubule behaviors have been developed as antifungal, antiparasitic, and anticancer drugs. Benzimidazole compounds, including thiabendazole (TBZ), carbendazim (MBC), and nocodazole, are prevailing microtubule poisons that target β-tubulin and inhibit microtubule polymerization. The molecular basis, however, as to how the drug acts on β-tubulin remains controversial. Here, we characterize the S. pombe β-tubulin mutant nda3-TB101, which was previously isolated as a mutant resistance to benzimidazole. The mutation site tyrosine at position 50 is located in the interface of two lateral β-tubulin proteins and at the gate of a putative binging pocket for benzimidazole. Our observation revealed two properties of the mutant tubulin. First, the dynamics of cellular microtubules comprising the mutant β-tubulin were stabilized in the absence of benzimidazole. Second, the mutant protein reduced the affinity to benzimidazole in vitro. We therefore conclude that the mutant β-tubulin Nda3-TB101 exerts a dual effect on microtubule behaviors: the mutant β-tubulin stabilizes microtubules and is insensitive to benzimidazole drugs. This notion fine-tunes the current elusive molecular model regarding binding of benzimidazole to β-tubulin.

Identification of a 42-kDa Group IV cPLA2-activating protein, cPLAPγ, as a GTP-binding protein in the bovine brain

Brain tissue contains multiple forms of Phospholipase A(2) (PLA(2)) whose activities are involved in intracellular and intercellular signalling related to normal functions such as long-term potentiation, neurotransmitter release, cell growth and differentiation. Among them, we focused on regulatory mechanism of cPLA(2)α (Group IVA cytosolic PLA(2)) in brain tissue. In the present study, we report the identification of a cPLA(2)-activating protein (cPLAP) in the bovine brain. cPLAP activity appeared as two major peaks with molecular masses of 200 and 42 kDa in a Superose 12 gel filtration FPLC column. The 42-kDa form of cPLAP, designated cPLAPγ, was further purified using a Mono S FPLC column to near homogeneity and characterized to as a GTP-binding protein (G protein). Metabolic labelling and immunoprecipitation studies revealed that cPLAPγ associates with cPLA(2) in vitro and co-immunoprecipitates with [(35)S]-cPLA(2). Notably, cPLAPγ rendered cPLA(2) fully activated at submicromolar concentrations of Ca(2+). These results suggest that cPLAPγ may act as a G protein, activating cPLA(2)α prior to reaching full intracellular Ca(2+) concentrations.

Intracellular beta-tubulin/chaperonin containing TCP1-beta complex serves as a novel chemotherapeutic target against drug-resistant tumors

In the present study, treatment of HEK-293 cells with the synthetic small molecule N-iodoacetyl-tryptophan (I-Trp) at submicromolar concentrations efficiently induced cell apoptosis as judged from the accumulation of sub-G(0) cells and intracellular DNA fragmentation. Activation of all intracellular caspases, except caspase-1, was detected in I-Trp-treated cells. Proteomic analysis revealed that beta-tubulin acted as a specific intracellular target of I-Trp. Protein fingerprinting analysis indicated that the Cys(354) residue in the peptide fragment TAVCDIPPR of beta-tubulin, which is located at the binding interface with chaperonin containing TCP1-beta (CCT-beta), was alkylated by I-Trp. Moreover, site-directed mutagenesis of Cys(354) (Cys-Ala) abolished the incorporation of I-Trp into beta-tubulin, suggesting Cys(354) is indeed the targeting site of I-Trp. Immunoprecipitation showed that the beta-tubulin/CCT-beta complex was constitutively formed but disrupted after treatment with I-Trp. Overexpression of the truncated beta-tubulin (T351-S364) or treatment with I-Trp or the synthetic peptide Myr-TAVCDIPPRG caused more severe cell apoptosis in multidrug-resistant MES-SA/Dx5 cancer cells due to higher levels of CCT-beta relative to wild-type MES-SA cancer cells. Silencing the expression of CCT-beta rendered MES-SA/Dx5 cells less sensitive to I-Trp-induced apoptotic cell death. These findings suggest that the beta-tubulin/CCT-beta complex may serve as an effective chemotherapeutic target for treating clinical tubulin-binding agent-resistant or CCT-beta-overexpressing tumors.

Evidence for a distinct ligand binding site on tubulin discovered through inhibition by GDP of paclitaxel-induced tubulin assembly in the absence of exogenous GTP

GDP inhibits paclitaxel-induced tubulin assembly without GTP when the tubulin bears GDP in the exchangeable site (E-site). Initially, we thought inhibition was mediated through the E-site, since small amounts of GTP or Mg(2+), which favors GTP binding to the E-site, reduced inhibition by GDP. We thought trace GTP released from the nonexchangeable site (N-site) by tubulin denaturation was required for polymer nucleation, but microtubule length was unaffected by GDP. Further, enhancing polymer nucleation reduced inhibition by GDP. Other mechanisms involving the E-site were eliminated experimentally. Upon finding that ATP weakly inhibited paclitaxel-induced assembly, we concluded that another ligand binding site was responsible for these inhibitory effects, and we found that GDP was not binding at the taxoid, colchicine, or vinca sites. There may therefore be a lower affinity site on tubulin to which GDP can bind distinct from the E- and N-sites, possibly on alpha-tubulin, based on molecular modeling studies.

The molecular nature of benzimidazole resistance in helminths

The economic importance of benzimidazole (BZ) resistance has resulted in the isolation of resistant populations of helminths and their study (see pp 127-129 this issue). Recent research indicates that BZs act by binding to free beta-tubulin in the cell and inhibiting the formation of microtubules. The effects of BZs on other processes in the cell, such as transport and anaerobic metabolism, probably result from the inhibition of one or more of the functions of tubulin (see pp 112-115, this issue). In this article, Marleen Roos examines the evidence for changes in the beta-tubulin structure and the rate of its synthesis in BZ-resistant parasitic nematodes.

Relating molecular flexibility to function: a case study of tubulin

Microtubules (MT), along with a variety of associated motor proteins, are involved in a range of cellular functions including vesicle movement, chromosome segregation, and cell motility. MTs are assemblies of heterodimeric proteins, alpha beta-tubulins, the structure of which has been determined by electron crystallography of zinc-induced, pacilitaxel-stabilized tubulin sheets. These data provide a basis for examining relationships between structural features and protein function. Here, we study the fluctuation dynamics of the tubulin dimer with the aim of elucidating its functional motions relevant to substrate binding, polymerization/depolymerization and MT assembly. A coarse-grained model, harmonically constrained according to the crystal structure, is used to explore the global dynamics of the dimer. Our results identify six regions of collective motion, comprised of structurally close but discontinuous sequence fragments, observed only in the dimeric form, dimerization being a prerequisite for domain identification. Boundaries between regions of collective motions appear to act as linkages, found primarily within secondary-structure elements that lack sequence conservation, but are located at minima in the fluctuation curve, at positions of hydrophobic residues. Residue fluctuations within these domains identify the most mobile regions as loops involved in recognition of the adjacent regions. The least mobile regions are associated with nucleotide binding sites where lethal mutations occur. The functional coupling of motions between and within regions identifies three global motions: torsional and wobbling movements, en bloc, between the alpha- and beta-tubulin monomers, and stretching longitudinally. Further analysis finds the antitumor drug pacilitaxel (TaxotereR) to reduce flexibility in the M loop of the beta-tubulin monomer; an effect that may contribute to tightening lateral interactions between protofilaments assembled into MTs. Our analysis provides insights into relationships between intramolecular tubulin movements of MT organization and function.

Nucleoside triphosphate specificity of tubulin

We have determined the binding affinity for binding of the four purine nucleoside triphosphates GTP, ITP, XTP, and ATP to E-site nucleotide- and nucleoside diphosphate kinase-depleted tubulin. The relative binding affinities are 3000 for GTP, 10 for ITP, 2 for XTP, and 1 for ATP. Thus, the 2-exocyclic amino group in GTP is important in determining the nucleotide specificity of tubulin and may interact with a hydrogen bond acceptor group in the protein. The 6-oxo group also makes a contribution to the high affinity for GTP. NMR ROESY experiments indicate that the four nucleotides have different average conformations in solution. ATP and XTP are characterized by a high anti conformation, ITP by a medium anti conformation, and GTP by a low anti conformation. Possibly, the preferred solution conformation contributes to the differences in affinities. When the tubulin E-site is saturated with nucleotide, there appears to be little difference in the ability of the four nucleotides to stimulate assembly. The critical protein concentration is essentially identical in reactions using the four nucleotides. All four of the nucleotides were hydrolyzed during the assembly reaction, and the NDPs were incorporated into the microtubule. We also examined the binding of two gamma-phosphoryl-modified GTP photoaffinity analogues, p(3)-1, 4-azidoanilido-GTP and p(3)-1,3-acetylanilido-GTP. These analogues are inhibitors of the assembly reaction and bind to tubulin with affinities that are 15- and 50-fold lower, respectively, than the affinty for GTP. The affinity of GTP is less sensitive to substitutions at the gamma-phosphoryl position that to changes in the purine ring.

Sequence analysis and immunofluorescence study of alpha- and beta-tubulins in Reticulomyxa filosa: implications of the high degree of beta2-tubulin divergence

We have cloned and sequenced 2 alpha- and 2 beta-tubulin isoforms from the giant freshwater amoeba Reticulomyxa filosa. The microtubules of this organism exhibit some unusual properties, including the highest rates of assembly and disassembly known and the inability to be stabilized by taxol. The cloned alpha-tubulins show a high degree of identity when compared to an alpha-tubulin consensus sequence. The beta-tubulins, however, are more divergent, the beta2-tubulin being the most unusual beta-tubulin found so far. The deduced amino acid sequence of beta2 shows 55% identity to a beta-tubulin consensus sequence. It also features 51 unique exchanges which cluster in the C-terminal half of the molecule. Several unique exchanges and two insertions occur in regions adjacent to, or directly implicated in, conserved beta-tubulin functions. A phylogenetic analysis places the beta-tubulins of R. filosa in the vicinity of beta-tubulins from fungi and slime molds. Monoclonal and polyclonal antibodies raised against R. filosa tubulins show that the electrophoretic mobility of alpha- and beta-tubulins is reversed with respect to tubulins from most other sources. Immunofluorescence experiments reveal a ubiquitous distribution of both beta-tubulins in the amoebal network. Our observations suggest possible links between the aberrant primary structure of the beta2-tubulin and the unusual properties of R. filosa microtubules.

Phospholipase C-delta1 is activated by capacitative calcium entry that follows phospholipase C-beta activation upon bradykinin stimulation

To characterize the regulatory mechanism of phospholipase C-delta1 (PLC-delta1) in the bradykinin (BK) receptor-mediated signaling pathway, we used a clone of PC12 cells, which stably overexpress PLC-delta1 (PC12-D1). Stimulation with BK induced a significantly higher Ca(2+) elevation and inositol 1,4,5-trisphosphate (IP(3)) production with a much lower half-maximal effective concentration (EC(50)) of BK in PC12-D1 cells than in wild type (PC12-W) or vector-transfected (PC12-V) cells. However, BK-induced intracellular Ca(2+) release and IP(3) generation was similar between PC12-V and PC12-D1 cells in the absence of extracellular Ca(2+), suggesting that the availability of extracellular Ca(2+) is essential to the activation of PLC-delta1. When PC12-D1 cells were treated with agents that induce Ca(2+) influx, more IP(3) was produced, suggesting that the Ca(2+) entry induces IP(3) production in PC12-D1 cells. Furthermore, the additional IP(3) production after BK-induced capacitative calcium entry was detected in PC12-D1 cells, suggesting that PLC-delta1 is mainly activated by capacitative calcium entry. When cells were stimulated with BK in the presence of extracellular Ca(2+), [(3)H]norepinephrine secretion was much greater from PC12-D1 cells than from PC12-V cells. Our results suggest that PLC-delta1 is activated by capacitative calcium entry following the activation of PLC-beta, additively inducing IP(3) production and Ca(2+) rise in BK-stimulated PC12 cells.

Paclitaxel resistance in non-small-cell lung cancer associated with beta-tubulin gene mutations

PURPOSE

The mechanisms that cause chemoresistance in non-small-cell lung cancer (NSCLC) patients have yet to be clearly elucidated. Paclitaxel is a tubulin-disrupting agent that binds preferentially to beta-tubulin. Tubulins are guanosine triphosphate (GTP)-binding proteins. Beta-tubulin is a GTPase, whereas alpha-tubulin has no enzyme activity. We reasoned that polymerase chain reaction (PCR) and DNA sequencing of the beta-tubulin gene could reveal more information regarding the connection between beta-tubulin mutations and primary paclitaxel resistance.

PATIENTS AND METHODS

Constitutional genomic DNA and paired tumor DNA were isolated from 49 biopsies from 43 Spanish and six American stage IIIB and IV NSCLC patients who had been treated with a 3-hour, 210 mg/m(2) paclitaxel infusion and a 24-hour, 200 mg/m(2) infusion, respectively. Oligonucleotides specific to beta-tubulin were designed for PCR amplification and sequencing of GTP- and paclitaxel-binding beta-tubulin domains.

RESULTS

Of 49 patients with NSCLC, 16 (33%; 95% confidence interval [CI], 20.7% to 45.3%) had beta-tubulin mutations in exons 1 (one patient) or 4 (15 patients). None of the patients with beta-tubulin mutations had an objective response, whereas 13 of 33 (39.4%; 95% CI, 22.8% to 56%; P = 0.01) patients without beta-tubulin mutations had complete or partial responses. Median survival was 3 months for the 16 patients with beta-tubulin mutations and 10 months for the 33 patients without beta-tubulin mutations (P =.0001).

CONCLUSION

We have identified beta-tubulin gene mutations as a strong predictor of response to the antitubulin drug paclitaxel; these mutations may represent a novel mechanism of resistance and should be examined prospectively in future trials of taxane-based therapy in NSCLC.

Direct photoaffinity labeling of cysteine-295 of alpha-tubulin by guanosine 5'-triphosphate bound in the nonexchangeable site

The alphabeta-tubulin heterodimer has two high affinity guanosine 5'-triphosphate binding sites, so that purified tubulin usually contains two molecules of bound guanosine nucleotide. Half this nucleotide is freely exchangeable with exogenous guanine nucleotide, and its binding site has been readily localized to the beta-subunit. The remaining nonexchangeable guanosine 5'-triphosphate can only be released from tubulin by denaturing the protein. We replaced the exchangeable site nucleotide of tubulin with 2'-deoxyguanosine 5'-diphosphate, exposed the resulting tubulin to ultraviolet light, degraded the protein, and isolated ribose-containing peptide derived from the nonexchangeable site. A large cyanogen bromide peptide was recovered, and its further degradation with endoproteinase Glu-C established that cysteine-295 of alpha-tubulin was the major reactive amino acid cross-linked to guanosine by ultraviolet irradiation.

Crystal structure of the bacterial cell-division protein FtsZ

Bacterial cell division ends with septation, the constriction of the cell wall and cell membranes that leads to the formation of two daughter cells. During septation, FtsZ, a protein of relative molecular mass 40,000 which is ubiquitous in eubacteria and is also found in archaea and chloroplasts, localizes early at the division site to form a ring-shaped septum. This septum is required for the mechanochemical process of membrane constriction. FtsZ is a GTPase with weak sequence homology to tubulins. The nature of FtsZ polymers in vivo is unknown, but FtsZ can form tubules, sheets and minirings in vitro. Here we report the crystal structure at 2.8 A resolution of recombinant FtsZ from the hyperthermophilic methanogen Methanococcus jannaschii. FtsZ has two domains, one of which is a GTPase domain with a fold related to one found in the proteins p21ras and elongation factor EF-Tu. The carboxy-terminal domain, whose function is unknown, is a four-stranded beta-sheet tilted by 90 degrees against the beta-sheet of the GTPase domain. The two domains are arranged around a central helix. GDP binding is different from that typically found in GTPases and involves four phosphate-binding loops and a sugar-binding loop in the first domain, with guanine being recognized by residues in the central connecting helix. The three-dimensional structure of FtsZ is similar to the structure of alpha- and beta-tubulin.

Structure of the alpha beta tubulin dimer by electron crystallography

The alphabeta tubulin heterodimer is the structural subunit of microtubules, which are cytoskeletal elements that are essential for intracellular transport and cell division in all eukaryotes. Each tubulin monomer binds a guanine nucleotide, which is nonexchangeable when it is bound in the alpha subunit, or N site, and exchangeable when bound in the beta subunit, or E site. The alpha- and beta-tubulins share 40% amino-acid sequence identity, both exist in several isotype forms, and both undergo a variety of posttranslational modifications. Limited sequence homology has been found with the proteins FtsZ and Misato, which are involved in cell division in bacteria and Drosophila, respectively. Here we present an atomic model of the alphabeta tubulin dimer fitted to a 3.7-A density map obtained by electron crystallography of zinc-induced tubulin sheets. The structures of alpha- and beta-tubulin are basically identical: each monomer is formed by a core of two beta-sheets surrounded by alpha-helices. The monomer structure is very compact, but can be divided into three functional domains: the amino-terminal domain containing the nucleotide-binding region, an intermediate domain containing the Taxol-binding site, and the carboxy-terminal domain, which probably constitutes the binding surface for motor proteins.

A putative beta-tubulin phosphate-binding motif is involved in lateral microtubule protofilament interactions

We have investigated the role of a putative GTP-binding beta-tubulin motif in microtubule polymerization. A peptide containing residues 126-142 of the beta-tubulin subunit (peptide G) was synthesised and an antibody against it raised. Peptide G prevents the binding of GTP to tubulin and also microtubule polymerization but not the formation of vinblastine-induced tubulin spirals, suggesting that it may prevent lateral but not longitudinal tubulin-tubulin interactions. The antibody to peptide G shows little reaction with the interphase microtubule network, mitotic spindles or midbody of cultured cells, whereas it clearly reacts with vinblastine-induced paracrystals. These results suggest that this putative phosphate-binding site present in beta-tubulin could be involved in the lateral tubulin-tubulin interactions along the microtubule structure.

Tubulin secondary structure analysis, limited proteolysis sites, and homology to FtsZ

The far-ultraviolet circular dichroism spectrum of the alpha beta-tubulin dimer analyzed by six different methods indicates an average content of approximately 33% alpha helix, 21% beta sheet, and 45% other secondary structure. Deconvolution of Fourier transform infrared spectra indicates 24% sheet, 37% (maximum) helix, and 38% (minimum) other structure. Separate alignments of 75 alpha-tubulin, 106 beta-tubulin, and 14 gamma-tubulin sequences and 12 sequences of the bacterial cell division protein FtsZ have been employed to predict their secondary structures with the multiple-sequence method PHD [Rost, B., & Sander, C. (1993a) J. Mol. Biol. 232, 584-599]. The predicted secondary structures average of 33% alpha helix, 24% beta sheet, and 43% loop for the alpha beta dimer. The predictions have been compared with sites of limited proteolysis by 12 proteases at the surfaces of the heterodimer and taxol-induced microtubules [de Pereda, J. M., & Andreu, J. M. (1996) Biochemistry 35, 14184-14202]. From 24 experimentally determined nicking sites, 18 are at predicted loops or at the extremes of secondary structure elements. Proteolysis zone A (including acetylable Lys40 and probably Lys60 in alpha-tubulin and Gly93 in beta-tubulin) and proteolysis zone B (extending between residues 167 and 183 in both chains) are accessible in microtubules. Proteolysis zone C, between residues 278 and 295, becomes partially occluded in microtubules. The alpha-tubulin nicking site Arg339-Ser340 is at a loop following a predicted alpha helix in proteolysis zone D. This site is protected in taxol microtubules; however, a new tryptic site appears which is probably located at the N-terminal end of the same helix. Zone D also contains beta-tubulin Cys354, which is accessible in microtubules. Proteolysis zone E includes the C-terminal hypervariable loops (10-20 residues) of each tubulin chain. These follow the two larger predicted helical zones (residues 372-395 and 405-432 in beta-tubulin), which also are the longer conserved part of the alpha- and beta-tubulin sequences. Through combination of this with other biochemical information, a set of surface and distance constraints is proposed for the folding of beta-tubulin. The FtsZ sequences are only 10-18% identical to the tubulin sequences. However, the predicted secondary structures show two clearly similar (85-87 and 51-78%) regions, at tubulin positions 95-175 and 305-350, corresponding to FtsZ 65-135 and 255-300, respectively. The first region is flanked by tubulin proteolysis zones A and B. It consists of a predicted loop1-helix-loop2-sheet-loop3-helix-loop4-sheet fold, which contains the motif (KR)GXXXXG (loop1), and the tubulin-FtsZ signature G-box motif (SAG)GGTG(SAT)G (loop3). A simple working model envisages loop1 and loop3 together at the nucleotide binding site, while loops 2 and 4 are at the surface of the protein, in agreement with proteolytic and antigenic accessibility results in tubulin. The model is compatible with studies of tubulin and FtsZ mutants. It is proposed that this region constitutes a common structural and evolutionary nucleus of tubulins and FtsZ which is different from typical GTPases.

Site-directed mutagenesis of Saccharomyces cerevisiae beta-tubulin: interaction between residue 167 and benzimidazole compounds

Benzimidazoles are widely used as anthelmintic agents and systemic fungicides. In susceptible organisms, benzimidazoles bind to beta-tubulin and block microtubule polymerization. To further characterize this interaction, site-directed mutagenesis followed by gene replacement was used to change Saccharomyces cerevisiae beta-tubulin residue Phe-167 to Tyr. Consistent with previous studies, this mutation resulted in at least 3-4-fold decreased sensitivity to the benzimidazole derivatives carbendazim and nocodazole. The Tyr-167 mutant was cold sensitive, implying a direct effect on benzimidazole binding rather than a nonspecific increase in microtubule stability. Surprisingly, the mutant had 8-fold increased sensitivity to the derivative benomyl, which is structurally identical to carbendazim except at position 1. This suggests that residue 167 interacts with benzimidazoles in the vicinity of the 1-position.

Adenylyl cyclase and G-proteins in Phytomonas

Phytomonas sp. membranes have an adenylyl cyclase activity which is greater in the presence of Mn2+ than with Mg2+. The Mg2+ and Mn2+ activity ratio varies from one membrane preparation to another, suggesting that the adenylyl cyclase has a variable activation state. A[35S]GTP-gamma-S-binding activity with a Kd of 171 nM was detected in Phytomonas membranes. Incubation of these membranes with activated cholera or pertussis toxin and [adenylate 23P]NAD+ led to incorporation of radioactivity into bands of about 40-44 kDa. Crude membranes were electrophoresed on SDS-polyacrylamide gels and analyzed, by Western blotting, with the 9188 anti-alpha[s] antibody and the AS/7 antibody (anti-alpha[i], anti-alpha[i1], and anti-alpha[i2]. These procedures resulted in the identification of polypeptides of approximately 40-44 kDa. Phytomonas adenylyl cyclase could be activated by treatment of membrane preparations with cholera toxin, in the presence of NAD+, while similar treatment with pertussis toxin did not affect this enzyme activity. These studies indicate that in Phytomonas, adenylyl cyclase activity is coupled to an unknown receptor entity through G alpha[s] proteins.

Identification of two new members of the tubulin family

Analysis of the delta- and epsilon-tubulin sequences indicates that they both consist of two structural domains of which the N-terminal domain can bind to alpha/beta heterodimers while the C-terminal domain probably binds to a non-tubulin protein. Both additional tubulins probably bind GTP but lack GTPase activity, while their synthesis requires the TCP1 chaperonine but is not autoregulated. Although these properties resemble those of gamma-tubulin, the low sequence identity (Table I) demonstrates that the gamma-, delta-, and epsilon-proteins should be classed as different members of the tubulin family. The identification of these additional members is unexpected. Examination of the cellular expression and distribution of the delta- and epsilon-tubulins, and whether other organisms contain homologous genes, may reveal further features of the eukaryotic cytoskeleton.

Neuropeptide Y promotes GTP photo-incorporation into a 55 kDa protein

Incubation of bovine hippocampal membranes with [alpha-32P]GTP and exposure to ultraviolet light resulted in the labelling of seven species with apparent molecular masses of 200, 74, 55, 53, 50, 43 and 40 kDa. Labelling of the 55 kDa species was greatly enhanced in the presence of carboxyl terminal fragments [neuropeptide Y-(18-36)] of neuropeptide Y. Labelling occurred with [alpha-32P]GTP but not [alpha-32P]ATP. A group of putative direct G protein activating peptides including mastoparan, melittin, substance P and adrenocorticotropic hormone (ACTH)-(1-24), were also able to stimulate the labelling of this protein. Labelling of the 55 kDa protein could be demonstrated in bovine brain but not peripheral tissues. Western blot analysis using an antibody against the common alpha subunit of G proteins recognized a protein co-migrating with the 55 kDa GTP-binding protein. These findings demonstrate the existence of a previously uncharacterized neuronal protein, with an apparent molecular mass of 55 kDa, that binds GTP in response to neuropeptide Y and other peptides.

Photoaffinity labelling of cardiac membrane GTP-binding proteins in response to insulin

Plasma membranes from rat cardiac ventricular tissue and insulin receptors partially purified by wheat-germ-agglutinin chromatography were subjected to direct photoaffinity labelling with [alpha-32P]GTP in order to elucidate the presence of insulin-receptor-coupled GTP-binding proteins. In plasma membranes three proteins have been identified that exhibit an enhanced photolabelling with the nucleotide in response to insulin. The apparent molecular masses of these proteins were found to be 56, 60 and 74 kDa. Photolabelling of partially purified insulin receptors showed the copurification of the 60-kDa species, whereas the 56-kDa and 74-kDa proteins could not be detected. Furthermore, the 60-kDa G-protein was found to be specifically co-immunoprecipitated with the insulin receptor. Incubation of insulin receptors with insulin increased the labelling of the 60-kDa band to 205 +/- 27% (n = 5) of control. Immuno- and ligand-blotting experiments revealed the additional presence of a 39-kDa G(o)-like protein and two G-proteins with molecular masses of 24 and 26 kDa in the receptor preparation. Under basal conditions the insulin receptor and the 60-kDa G-protein exhibited an apparent inverse distribution between plasma and microsomal membranes with the G-protein being extensively labelled in the microsomal fraction. In conclusion, our data show that, in its native environment, the cardiac insulin receptor couples to at least three GTP-binding proteins. Out of these, a 60-kDa species of microsomal origin, copurifies with the insulin receptor. It is suggested that this G-protein is associated with the insulin receptor and may be involved in insulin receptor signalling in target cells.

Role of the carboxy terminal region of beta tubulin on microtubule dynamics through its interaction with the GTP phosphate binding region

The dynamic instability of microtubules depends on the GTP binding to tubulin, the rate of hydrolysis of GTP bound to tubulin molecules, at the microtubule caps, and on the affinity and exchange rate of tubulin for GTP versus GDP. It has been demonstrated that the binding of microtubule-associated proteins (MAPs) such as Tau or MAP2 notably enhances microtubule stability in vivo. These MAPs bind to the tubulin carboxy terminal domain. Consequently, an attractive hypothesis to explain the modulation of microtubule dynamics by MAPs is that the carboxy terminal domain of tubulin interacts with a region close to the GTP binding site, preventing the binding of GTP or exchange of GDP for GTP. By carrying out a combined analysis of crosslinking and limited proteolysis, an intramolecular interaction between the carboxy terminus and the tubulin region containing the GTP binding site in beta tubulin has been observed. It is proposed that this interaction modifies the binding of GTP to the tubulin beta-subunit and, therefore, affects tubulin assembly dynamics. This suggests a molecular explanation for the effect of MAPs in facilitating tubulin polymerization through the regulation of the interaction of GTP.

Molecular cloning and sequencing analysis of a beta-tubulin gene from Lupinus albus

Genomic lambda-Dash library constructed from Lupinus albus nuclear DNA was screened using a fragment of the beta-tubulin cDNA (beta 8-31) clone of Chlamydomonas reinhardtii as probe. One of the positive recombinant phages was isolated, subcloned and analysed by sequencing. We present here nucleotide and derived amino acid sequences of the beta-tubulin gene, designated as L beta 1 and identified by similarity with other beta-tubulins. The L beta 1-encoded protein reveals a very high degree of similarity with other plant tubulins and contains consensus sequences for binding guanine base, phosphate and Mg2+. Northern analysis of total RNA isolated from roots, leaves, flowers and pools revealed that Lupinus albus beta-tubulin genes are constitutively expressed in all studied plant tissues.

The gamma-tubulin gene of the malaria parasite Plasmodium falciparum

By screening of cDNA and genomic libraries of Plasmodium falciparum with a DNA probe derived from the cognate beta-tubulin gene, gene Pf gamma tub has been identified that codes for gamma-tubulin, a newly discovered member of the tubulin superfamily that is indispensible for nuclear division and microtubule assembly [12]. Gene Pf gamma tub is not interrupted by introns and only present as a single-copy in the parasite genome. Its encoded amino acid sequence (452 amino acids; M(r) 50,560) has a 63% similarity to the gamma-tubulins encoded by Aspergillus nidulans, Schizosaccharomyces pombe, Drosophila melanogaster, Xenopus laevis and Homo sapiens. This figure is significantly (approx. 8%) lower than the average identity between the gamma-tubulins of the latter five species suggesting that during evolution the genes have been exposed to different selection pressures. The identity of gamma-tubulin to the Plasmodium falciparum encoded alpha- and beta-tubulins is 30 and 33%, respectively.

G protein binding and G protein activation by nucleotide transfer involve distinct domains on tubulin: regulation of signal transduction by cytoskeletal elements

Cytoskeletal proteins have been demonstrated to interact with elements which mediate neuronal signal transduction. This laboratory has shown that tubulin forms complexes with certain G proteins and transfers GTP to them, and such nucleotide transfer correlates well with the inhibition of adenylyl cyclase. A previous study showed that tubulin-G protein complex formation occurred at regions of tubulin which were likely to be involved in binding to other tubulin dimers during the process of microtubule polymerization [Wang, N., & Rasenick, M. M. (1991) Biochemistry 30, 10957-10965]. This study represents an attempt to investigate the regions of tubulin which orchestrate the transfer of GTP from tubulin to G protein. It is demonstrated that two monoclonal antibodies, with determinants in similar regions of alpha (DM1a) or beta (DM1b) tubulin, blocked (by 70-80%) the ability of tubulin dimers (with GppNHp bound) to promote a stable inhibition of adenylyl cyclase. Under the same conditions, a polyclonal antitubulin antibody caused only a slight reduction in adenylyl cyclase inhibition. None of the antibodies altered the inhibition of adenylyl cyclase induced by GppNHp in the absence of tubulin. Under conditions where tubulin-GppNHp inhibited synaptic membrane adenylyl cyclase, tubulin dimers with the photoaffinity GTP analog azidoanilido-GTP (32P-AAGTP) bound transferred that nucleotide to G alpha i1 on the membrane. DM1a and DM1b blocked this nucleotide transfer. Similarly, tubulin-AAGTP transferred AAGTP to purified G proteins in solution and DM1a and DM1b blocked this process as well. Despite their ability to block the activation of Gi1 by tubulin, neither antibody altered the ability of tubulin to bind to native Gi alpha affixed to nitrocellulose.(ABSTRACT TRUNCATED AT 250 WORDS)

Isolation and characterization of a beta-tubulin-encoding gene from Colletotrichum gloeosporioides f. sp. aeschynomene

Colletotrichum gloeosporioides f. sp. aeschynomene (C.g.a.) is a fungal pathogen of legumes and is used as a commercial mycoherbicide for rice and soybeans. As an initial study to potentially improve the utility of this fungus and develop a gene transfer system, a beta-tubulin (beta Tub)-encoding gene (TUB1) was isolated, cloned and sequenced. The coding sequence and deduced amino acid sequence of the C.g.a. TUB1 gene was highly homologous to the TUB1 gene of Colletotrichum graminicola. Southern hybridizations, using the C.g.a. TUB1 and C. graminicola TUB2 genes as probes, suggest that C.g.a. contains two TUB genes. Variation in both the restriction pattern and the number of TUB genes present in different formae specialis of C. gloeosporioides was evident. These observations are relevant for assessing relationships among formae specialis of C. gloeosporioides.

Identification of heterotrimeric and low molecular weight GTP-binding proteins in rabbit skeletal muscle longitudinal sarcoplasmic reticulum

Direct photoaffinity labeling of proteins of longitudinal sarcoplasmic reticulum (LSR) of rabbit skeletal muscle with [32P]GTP revealed GTP-binding proteins of about 52, 45 and 30 kDa. ADP-ribosylation with [32P]NAD in the presence of cholera toxin (CTX) or pertussis toxin (PTX) indicates the existence of a CTX substrate (about 45 kDa); no PTX substrates were observed. Western blots of LSR probed with RM/1, an antiserum against a decapeptide from the C-terminus of Gs alpha, showed an immunoreactive band at about 45 kDa. [32P]GTP overlays of Western blots of LSR showed a heavily-labeled protein of about 29 kDa and one or more additional slightly smaller proteins that were more weakly labeled. When LSR was subjected to mild trypsin hydrolysis, the Western blot overlay revealed three bands at about 23, 25 and 29 kDa. Western blots of LSR proteins showed no significant immunoreactivity with the anti-(pan)-ras monoclonal antibodies 142-24E05 and Ras 11. ADP-ribosylation of LSR with [32P]NAD in the presence of C3 exoenzyme of Clostridium botulinum yielded a labeled band at about 23 kDa. Our results indicate the presence in rabbit LSR of a Gs alpha, the absence of Gi and G(o), and the presence of several low molecular weight GTP-binding proteins, distinct from p21 ras, one of which belongs to the rho or rac family.

Should the tubulins be members of the GTPase superfamily?

The beta-subunit of the alpha/beta tubulin heterodimer resembles other members of the GTPase superfamily in that: it binds GTP, the GTP is hydrolysed to GDP on microtubule assembly and this induces a conformational change; it exhibits a similar nucleotide stereospecificity; aluminium and beryllium fluorides inhibit this hydrolysis-dependent conformational change; and beta-tubulin contains peptides which are similar to the consensus motifs characteristic of the GTPase superfamily proteins. By contrast, UV photo-cross-linking and other binding studies have identified peptides which may contribute to the GTP-binding site but which are absent from the GTPase superfamily proteins. We suggest that beta-tubulin has a 'dual personality', with the characteristics of the GTP-binding site depending upon the precise conformation of the protein and upon whether the experimental assays probe nucleotide binding or the hydrolytic mechanism. We suggest that the hydrolytic mechanism of beta-tubulin resembles that of the other members of the GTPase superfamily, although the differences within the consensus motifs dictate that the architecture of the GTP pocket cannot be identical.

The beta-tubulin gene from rat and human isolates of Pneumocystis carinii

The development of new drugs for treating Pneumocystis carinii infections in AIDS patients is hampered by the lack of long-term culture systems, and by our generally limited knowledge of this organism. Recently, however, we observed significant activity of various benzimidazoles against growth of this organism in short-term cultures. Benzimidazoles inhibit microtubule polymerization; there is strong evidence that the primary target is the beta-tubulin subunit. To understand the basis for benzimidazole activity against P. carinii, and to examine the apparent relatedness of this organism to fungi, we have cloned and sequenced the single beta-tubulin gene from a rat P. carinii isolate. There was 89-91% identity at the amino acid level to beta-tubulins from filamentous fungi, but only 79-82% identity to yeast and protozoal beta-tubulins. Also, eight introns were distributed throughout the P. carinii beta-tubulin gene in a pattern characteristic of filamentous fungi. Specific residues previously implicated in benzimidazole sensitivity were conserved in P. carinii beta-tubulin. The polymerase chain reaction was used to amplify a segment of P. carinii beta-tubulin DNA from bronchoalveolar lavages obtained from two patients with AIDS. There was considerable divergence at the DNA level between the human and rat sequences, but 100% identity at the amino-acid level.

Cloning, sequence and expression of a beta-tubulin-encoding gene in the homobasidiomycete Schizophyllum commune

The beta-tubulin (beta Tub)-encoding gene (tub-2) of Schizophyllum commune is the first tubulin gene isolated, cloned and sequenced from higher filamentous fungi (homobasidiomycetes). The S. commune tub-2 gene is organized into nine exons and eight introns. The introns vary from 48 to 107 nt in length, and are distributed throughout the gene. The tub-2 exons code for a protein of 445 amino acids (aa), which shows great homology with beta Tubs of filamentous ascomycetes, plants, and animals, but less homology with yeasts. The codon usage of tub-2 from S. commune is biased, as it is in most beta Tub-encoding genes of filamentous fungi. The S. commune beta Tub shows a conserved aa sequence in the C-terminal domain, which is suggested to interact with microtubule-associated proteins in animals. In contrast, the S. commune beta Tub deviates from most known beta Tubs by having a Cys165 residue, which might be significant for the insensitivity of S. commune haploid strains to the antimicrotubule drug, benomyl. In tub-2 of different haploid strains, sequence polymorphisms occur in the 5' and 3' flanking regions. The expression of tub-2 is high in young mycelium, which has a high number of extending apical cells, but decreases with the aging of the mycelium. No significant difference in the hybridization signal intensity for the tub-2 transcripts was recorded either during intercellular nuclear migration at early mating, or in mycelia with a mutation in the B mating-type gene.(ABSTRACT TRUNCATED AT 250 WORDS)

Site-directed mutagenesis of the GTP-binding domain of beta-tubulin

Tubulin binds guanine nucleotides with high affinity and specificity. GTP, an allosteric effector of microtubule assembly, requires Mg2+ for its interaction with beta-tubulin and binds as the MgGTP complex. In contrast, GDP binding does not require Mg2+. The structural basis for this difference is not understood but may be of fundamental importance for microtubule assembly. We investigated the interaction of beta-tubulin with guanine nucleotides using site-directed mutagenesis. Acidic amino acid residues have been shown to interact with nucleotide in numerous nucleotide-binding proteins. In this study, we mutated seven highly conserved aspartic acid residues and one highly conserved glutamic acid residue in the putative GTP-binding domain of beta-tubulin (N-terminal 300 amino acids) to asparagine and glutamine, respectively. The mutants were synthesized in vitro using rabbit reticulocyte lysates, and their affinities for nucleotide determined by an h.p.l.c.-based assay. Our results indicate that the mutations can be placed in six separate categories on the basis of their effects on nucleotide binding. These categories range from having no effect on nucleotide binding to a mutation that apparently abolishes nucleotide binding. One mutation at Asp224 reduced the affinity of beta-tubulin for GTP in the presence but not in the absence of Mg2+. The specific effect of this mutation on nucleotide binding is consistent with an interaction of this amino acid with the Mg2+ moiety of MgGTP. This residue is in a region sharing sequence homology with the putative Mg2+ site in myosin and other ATP-binding proteins. As a result, tubulin belongs to a distinct class of GTP-binding proteins which may be evolutionarily related to the ATP-binding proteins.

Tubulin structure and biochemistry

In the past year, much has been learned about structure-function correlations in the tubulin molecule, and specifically about the nature and roles of post-translational modifications and tubulin isotypes. The interactions between tubulin and its ligands--both microtubule-associated proteins and anti-mitotic drugs--are becoming clearer at the molecular level.

Microtubule functions

Microtubules, with intermediate filaments and microfilaments, are the components of the cell skeleton which determinates the shape of a cell. Microtubules are involved in different functions including the assembly of mitotic spindle, in dividing cells, or axon extension, in neurons. In the first case, microtubules are highly dynamic, while in the second case microtubules are quite stable, suggesting that microtubule with different physical properties (stability) are involved in different functions. Thus, to understand the mechanisms of microtubule functions it is very important to understand microtubule dynamics. Historically, tubulin, the main component of microtubules, was first characterized as the major component of the mitotic spindle that binds to colchicine. Afterwards, it was found that tubulin is particularly more abundant in brain than in other tissues. Therefore, the roles of microtubules in mitosis, and in neurons, have been more extensively analyzed and, in this review, these roles will be discussed.

Microtubule assembly protects the region 28-38 of the beta-tubulin subunit

Polyclonal antibodies have been raised against the peptide 28-38 of the beta-subunit of the tubulin heterodimer in order to study the accessibility of this region in the tubulin heterodimer and in various tubulin assemblies. These antibodies were specific for all beta-tubulin subunits, except for beta'-tubulin isotypes, and did not recognize the alpha-tubulin subunit. The 28-38 region does not play a role in the interaction between the alpha- and beta-subunits since it was accessible to the antibodies on the native heterodimer. The accessibility of the antibodies was not modified by several microtubular poisons. In contrast, in all tubulin assemblies obtained in the presence of microtubular associated proteins, the region 28-38 was not available to the antibodies. These antibodies did not react with microtubules or tubulin spirals assembled either from microtubule proteins or from pure tubulin when these tubulin assemblies were probed in the absence of free tubulin after centrifugation on glass coverslips. In addition, antibodies failed to interact with the microtubule cytoskeleton in cultured Ptk2 cells indicating that the 28-38 region of beta-tubulin is also protected in cellular structures. These observations suggest that the 28-38 region of the beta-tubulin subunit is either located in a zone of interaction between two successive tubulin dimers within a protofilament or hidden by an allosteric conformational change which occurs during tubulin assembly.

Identification of a GTP-binding protein in the contact sites between inner and outer mitochondrial membranes

Whilst investigating whether GTP hydrolysis may be required for the import of preproteins into mitochondria we have found that a GTP-binding protein is located at the contact sites between mitochondrial inner and outer membranes. When mitochondrial outer membranes purified from rat liver were UV-irradiated in the presence of [alpha-32P]GTP, a 52 kDa protein was radiolabelled, whereas [alpha-32P]ATP did not label this protein. GTP-binding proteins were also labelled in the cytosolic and microsomal fractions, but the 52 kDa protein was concentrated in mitochondrial membranes and was the only protein specifically labelled by GTP in these membranes. Fractionation of mitochondrial membrane vesicles into outer membranes, inner membranes and contact sites between outer and inner membranes showed that the GTP-binding activity was highly enriched in contact sites, the location at which preprotein import is believed to occur. A protein of almost identical size was also found to be labelled in mitochondria from yeast.

Tubulin-G protein interactions involve microtubule polymerization domains

It has been suggested that elements of the cytoskeleton contribute to the signal transduction process and that they do so in association with one or more members of the signal-transducing G protein family. Relatively high-affinity binding between dimeric tubulin and the alpha subunits of Gs and Gi1 has also been reported. Tubulin molecules, which exist in solution as alpha beta dimers, have binding domains for microtubule-associated proteins as well as for other tubulin dimers. This study represents an attempt to ascertain whether the association between G proteins and tubulin occurs at one of these sites. Removal of the binding site for MAP2 and tau from tubulin by subtilisin proteolysis did not influence the association of tubulin with G protein, as demonstrated in overlay studies with [125I]tubulin. A functional consequence of that association, the stable inhibition of synaptic membrane adenylyl cyclase, was also unaffected by subtilisin treatment of tubulin. However, ring structures formed from subtilisin-treated tubulin were incapable of effecting such inhibition. Stable G protein-tubulin complexes were formed, and these were separated from free tubulin by Octyl-Sepharose chromatography. Using this methodology, it was demonstrated that assembled microtubules bound G protein quite weakly compared with tubulin dimers. The alpha subunit of Gi1 and, to a lesser extent, that of Go were demonstrated to inhibit microtubule polymerization. In aggregate, these data suggest that dimeric tubulin binds to the alpha subunits of G protein at the sites where it binds to other tubulin dimers during microtubule polymerization. Interaction with signal-transducing G proteins, thus, might represent a role for tubulin dimers which is independent of microtubule formation.

Resistance to antimitotic agents as genetic probes of microtubule structure and function

Much of our knowledge about microtubules has come from detailed morphological, biochemical, and cell biological studies. As more is learned about these organelles, questions regarding the in vivo regulation of their expression and function become increasingly important. Genetics provides an approach to address these more subtle questions in the living cell. Mammalian mutants with microtubule alterations have been isolated using selections for resistance to the cytotoxic effects of a number of antimitotic drugs. A subset of these mutants have clearly defined alterations in alpha- or in beta-tubulin, and these have been used to explore the mechanisms by which mammalian cells acquire resistance to this class of drugs. In addition, the mutants are providing valuable insights into how tubulin expression is regulated, into what factors determine the extent of microtubule assembly in living cells, into the domains of tubulin that are involved in assembly, and into the role of microtubules in essential cellular processes.

Direct photoaffinity labeling of gizzard myosin with vanadate-trapped adenosine diphosphate

The active-site topology of smooth muscle myosin has been investigated by direct photoaffinity-labeling studies with [3H]ADP. Addition of vanadate (Vi) and Co2+ enabled [3H]ADP to be stably trapped at the active site (t1/2 greater than 5 days at 0 degrees C). The extraordinary stability of the myosin.Co2+.[3H]ADP.Vi complex allowed it to be purified free of excess [3H]ADP before irradiation began and ensured that only active-site residues became labeled. Following UV irradiation, approximately 10% of the trapped [3H]ADP became covalently attached at the active site. All of the [3H]ADP incorporated into the 200-kDa heavy chain, confirming earlier results using untrapped [alpha-32P]ATP [Maruta, H., & Korn, E. (1981) J. Biol. Chem. 256, 499-502]. After extensive trypsin digestion of labeled subfragment 1, HPLC separation methods combined with alkaline phosphatase treatment allowed two labeled peptides to be isolated. Sequence analysis of both labeled peptides indicated that Glu-185 was the labeled residue. Since Glu-185 has been previously identified as a residue at the active site of smooth myosin using [3H]UDP as a photolabel [Garabedian, T. E., & Yount, R. G. (1990) J. Biol. Chem. 265, 22547-22553], these results provide further evidence that Glu-185, located immediately adjacent to the glycine-rich loop, is located in the purine binding pocket of the active site of smooth muscle myosin.