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

On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment

This article is dedicated to the memory of Michael G. Rossmann. Dating back to the last universal common ancestor, P-loop NTPases and Rossmanns comprise the most ubiquitous and diverse enzyme lineages. Despite similarities in their overall architecture and phosphate binding motif, a lack of sequence identity and some fundamental structural differences currently designates them as independent emergences. We systematically searched for structure and sequence elements shared by both lineages. We detected homologous segments that span the first βαβ motif of both lineages, including the phosphate binding loop and a conserved aspartate at the tip of β2. The latter ligates the catalytic metal in P-loop NTPases, while in Rossmanns it binds the nucleotide's ribose moiety. Tubulin, a Rossmann GTPase, demonstrates the potential of the β2-Asp to take either one of these two roles. While convergence cannot be completely ruled out, we show that both lineages likely emerged from a common βαβ segment that comprises the core of these enzyme families to this very day.

Isolation and sequence analysis of a beta-tubulin gene from arbuscular mycorrhizal fungi

A full-length beta-tubulin gene has been cloned and sequenced from Gigaspora gigantea and Glomus clarum, two arbuscular mycorrhizal fungi (AMF) species in the phylum Glomeromyota. The gene in both species is organized into five exons and four introns. Both genes are 94.9% similar and encode a 447 amino acid protein. In comparison with other fungal groups, the amino acid sequence is most similar to that of fungi in the Chytridiomycota. The codon usage of the gene in both AMF species is broad and biased in favor of an A or a T in the third position. The four introns varied in length from 87 to 168 bp for G. gigantea and from 90 to 136 bp for G. clarum. Of all fungi in which full-length sequences have been published, only AMF do not have an intron before codon 174. The introns positioned at codons 174 and 257 in AMF match the position of different introns in beta-tubulin genes of some Zygomycete, Basidiomycete, and Ascomycete fungi. The 5' and 3' splice site consensus sequences are similar to those found in introns of most fungi. Sequence analysis from single-strand conformation polymorphism analysis confirmed the presence of two beta-tubulin gene copies in G. clarum, but only one copy was evident in G. gigantea based on Southern hybridization analysis.

Expression of recombinant β-tubulin alleles from Cylicocyclus nassatus (Cyathostominae)

Small strongyles (Cyathostominae) are common nematode parasites of horses that have developed resistance to the benzimidazole anthelmintics used to control their populations. Evidence suggests that the principal mechanism of resistance involves a phenylalanine-to-tyrosine mutation at codon 200 in the beta-tubulin proteins that are components of microtubules. Other works, however, suggest that a phenylalanine-to-tyrosine mutation at codon 167, or alternative mechanisms, may be involved. As part of an ongoing project examining the role that these two beta-tubulin mutations may play in benzimidazole resistance, we have cloned the wild-type allele and the two alleles with the phenylalanine-to-tyrosine mutations at codons 167 and 200 of the beta-tubulin isotype 1 gene from the small strongyle Cylicocyclus nassatus. In this work, we describe the construction of expression vectors containing these alleles and their expression in Escherichia coli.

Detection of codon for amino acid 200 in isotype 1 beta-tubulin gene of Wuchereria bancrofti isolates, implicated in resistance to benzimidazoles in other nematodes

Albendazole, anthelmintic benzimidazole (BZ) is being co-administered with an antifilarial drug, diethylcarbamazine (DEC), in lymphatic filariasis (LF) elimination programmes. But this drug is known to result in the faster development of drug resistance and hence it is necessary to monitor drug sensitivity among populations of Wuchereria bancrofti. In vitro toxicity assays to detect drug sensitivity are not available for this parasite and hence alternative techniques such as PCR assays need to be developed, for which information on genetic basis for drug sensitivity/resistance is necessary. Such information is lacking in the case of W. bancrofti, but available for nematode parasites of farm animals wherein it has been established that replacement of phenylalanine with tyrosine at amino acid position 200 of beta-tubulin isotype 1 conferred BZ-resistance. Using this information we examined the polymorphism in the codon of this residue in W. bancrofti populations representing geographically distant areas of India, through sequencing exon 5 region of beta-tubulin isotype 1 gene. The nucleotide sequence data showed that W. bancrofti isolates from wide geographic areas of India had codon for Phe (TTC) at position 200 of the beta-tubulin isotype 1 gene suggesting that the parasite might be genetically sensitive to BZ.

Analysis of the interaction of FtsZ with itself, GTP, and FtsA

The interaction of FtsZ with itself, GTP, and FtsA was examined by analyzing the sensitivity of FtsZ to proteolysis and by using the yeast two-hybrid system. The N-terminal conserved domain consisting of 320 amino acids bound GTP, and a central region of FtsZ, encompassing slightly more than half of the protein, was cross-linked to GTP. Site-directed mutagenesis revealed that none of six highly conserved aspartic acid and asparagine residues were required for GTP binding. These results indicate that the specificity determinants for GTP binding are different than those for the GTPase superfamily. The N-terminal conserved domain of FtsZ contained a site for self-interaction that is conserved between FtsZ proteins from distantly related bacterial species. FtsZ320, which was truncated at the end of the conserved domain, was a potent inhibitor of division although it expressed normal GTPase activity and could polymerize. FtsZ was also found to interact directly with FtsA, and this interaction could also be observed between these proteins from distantly related bacterial species.

Bacterial cell division and the Z ring

Bacterial cell division occurs through the formation of an FtsZ ring (Z ring) at the site of division. The ring is composed of the tubulin-like FtsZ protein that has GTPase activity and the ability to polymerize in vitro. The Z ring is thought to function in vivo as a cytoskeletal element that is analogous to the contractile ring in many eukaryotic cells. Evidence suggests that the Z ring is utilized by all prokaryotic organisms for division and may also be used by some eukaryotic organelles. This review summarizes our present knowledge about the formation, function, and evolution of the Z ring in prokaryotic cell division.

Entamoeba histolytica encodes a highly divergent beta-tubulin

The microtubules of the amitochondrial parasite Entamoeba histolytica are atypical in certain respects. Consistent with this, we report that E. histolytica encodes the most divergent beta-tubulin identified to date, with only 54% to 58% identity to beta-tubulins from various species. A similarly divergent beta-tubulin is encoded by the related Entamoeba invadens; single gene copies appear to be present in both organisms. The Entamoeba sequences were compared with a database of 101 beta-tubulins, including the highly divergent sequence from another amitochondrial protozoan, Trichomonas vaginalis. A total of 81 residues were universally conserved, and 76 residues varied only once. Correlations with previous studies indicate that microtubule function is altered when most, but not all, conserved residues are mutated.

Mutations in the Caenorhabditis elegans beta-tubulin gene mec-7: effects on microtubule assembly and stability and on tubulin autoregulation

We have sequenced 45 mutations in mec-7, a beta-tubulin gene required for the production of 15-protofilament microtubules in the nematode Caenorhabditis elegans, and have correlated sequence alterations with mutant phenotypes. The expression patterns of most alleles have also been determined by in situ hybridization and immunocytochemistry. Most (12/16) complete loss-of-function alleles, which are recessive, result from nonsense mutations, insertions, or deletions; three others disrupt a putative GTP-binding domain. Three of the four loss-of-function, missense mutations result in elevated mec-7 message levels, suggesting a defect in tubulin autoregulation that may be attributable to a loss in the ability to form heterodimers. Most (8/9) mild alleles are caused by missense mutations. Two mild alleles appear to increase microtubule stability and lead to the elaboration of ectopic neuronal processes in mec-7-expressing cells. Most (15/23) mutations that cause severe dominant or semidominant phenotypes are clustered into three discrete domains; four others occur in putative GTP-binding regions. Many of these dominant mutations appear to completely disrupt microtubule assembly.

Guanine nucleotide-dependent assembly of FtsZ into filaments

FtsZ is an essential cell division protein that is localized to the leading edge of the bacterial septum in a cytokinetic ring. It contains the tubulin signature motif and is a GTP binding protein with a GTPase activity. Further comparison of FtsZ with eukaryotic tubulins revealed some additional sequence similarities, perhaps indicating a similar GTP binding site. Examination of FtsZ incubated in vitro by electron microscopy revealed a guanine nucleotide-dependent assembly into protein filaments, supporting the hypothesis that the FtsZ ring is formed through self-assembly. FtsZ3, which is unable to bind GTP, does not polymerize, whereas FtsZ2, which binds GTP but is deficient in GTP hydrolysis, is capable of polymerization.

Thermodynamics of ligand-induced assembly of tubulin

The equilibrium assembly of purified GDP-tubulin into microtubules induced by taxol and Taxotere has been studied as a function of solution variables, ligand, and nucleotide, in 10 mM sodium phosphate buffers. Assembly is coupled to the binding of one taxoid molecule per tubulin heterodimer, while binding to the unassembled protein is not detected within ligand solubility limits. Linked functions analysis has indicated that two Mg2+ and no more H+ ions are bound per tubulin-taxoid polymerized, and the heat capacity change is negligible within experimental error (determined by van't Hoff analysis and by differential scanning calorimetry), in contrast with drug-free control microtubule assembly and with the abnormal polymerization of the tubulin-colchicine complex. The apparent enthalpy change is ca. 240 kJ mol-1 (calorimetry), and the process is entropy driven. The apparent standard free energy change of taxoid-induced elongation at 2 mM free Mg2+, pH 6.1-6.7, and 37 degrees C is -29.5 +/- 0.4 (taxol) or -31.5 +/- 0.4 kJ mol-1 (Taxotere). This is independent of taxoid excess, which has indicated that the process measured corresponds to the elongation equilibrium of the fully liganded protein. Comparison to elongation in the absence of drug suggests an apparent linkage free energy change of binding and polymerization of -11.3 +/- 1.2 kJ mol-1. The taxoid-induced elongation of GTP-tubulin proceeds with an increment of apparent free energy change of -2.5 +/- 0.4 kJ mol-1 over GDP-tubulin. It is proposed that the taxoid binding changes the conformation of GDP-tubulin from inactive to active, allowing productive binding and elongation at the microtubule end. Among several possible model mechanisms discussed, it is particularly attractive to think of taxoids as double-sided ligands, which bind to tubulin at the microtubule end and participate in a lateral contact interface with the newly added tubulin molecule. In the kinetic pathway of assembly, these ligands should bind first to inactive Mg(2+)-induced linear GDP-tubulin oligomers and transform them into active bidimensional polymerization nuclei.

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.

Site-directed mutagenesis of alpha-tubulin. Reductive methylation studies of the Lys 394 region

Previous studies have implicated at least two regions in alpha-tubulin that are important for the regulation of microtubule assembly. These regions include a cluster of basic residues consisting of Arg 390, His 393, and Lys 394 and the highly acidic carboxyl terminus. Lys 394 is highly reactive to HCHO and NaCNBH3. The reductive methylation of Lys 394 by these reagents is thought to be responsible for the profound inhibitory effects of low concentrations of HCHO on microtubule assembly (cf. Szasz J., M. B. Yaffe, M. Elzinga, G. S. Blank, and H. Sternlicht. 1986. Biochemistry. 25:4572-4582). In this study we reexamined the basis for this inhibition. Lys 394 in a human keratinocyte alpha-tubulin (k alpha 1) was replaced by a glutamic acid residue using site-directed mutagenesis. The mutant K394E was synthesized in vitro using rabbit reticulocyte lysates, and its ability to coassemble with bovine brain microtubule protein (MTP) before and after reaction with HCHO and NaCNBH3 was compared with that of wild-type. No differences in the coassemblies of the unmethylated proteins were detected suggesting that Lys 394 is not essential for microtubule assembly. However, methylated K394E prepared at low HCHO concentrations (< 1 mM) incorporated into microtubules to a greater extent (approximately 30-40%) than methylated wild-type. This result is consistent with the hypothesis that methylation of Lys 394 interferes with microtubule assembly. However, the extent of protection afforded by the replacement of Lys 394 with Glu 394 was less than half as large as that predicted from the earlier studies. We tentatively conclude that another residue(s) besides Lys 394 contributes significantly to the assembly-inhibition observed with low concentrations of HCHO. Since this residue(s) is less reactive than Lys 394, it would have to inhibit assembly substoichiometrically when methylated. Potential candidates for this residue include bulk lysyl residue(s), a lysyl residue(s) with intermediate reactivity toward HCHO, and the NH2-termini. The NH2-termini are especially attractive candidates since they appear to have a structural role in microtubule assembly.

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.