The two beta-tubulin genes of Chlamydomonas reinhardtii code for identical proteins

The relatively large beta-tubulin gene family of Arabidopsis contains a member with an unusual transcribed 5' noncoding sequence

We have characterized the beta-tubulin gene family of Arabidopsis thaliana. Five distinct genes were cloned and analyzed by restriction enzyme mapping and cross-hybridization studies. Three of the genes appear to be dispersed, whereas two others are linked within 1.5 kb of one another. The two linked genes are closely related and appear to have resulted from a fairly recent duplication. The three dispersed genes do not cross-hybridize to one another or to the two linked genes under highly stringent hybridization conditions, suggesting that they arose from more ancient duplications. From Southern analysis we estimate that there are a total of between six and ten beta-tubulin genes in Arabidopsis. Additional analyses indicate that the gene family is equal in size or larger than those in other plants, but significantly smaller than those in related Brassica species. Sequence determination of one of the Arabidopsis genes revealed a highly unusual transcribed leader sequence. The leader contains two fairly long tracks of adenines. One is located toward the 5' end of the mRNA and the other is just before the initiation codon. A track of uridines is located between the adenine tracks. This leader can form two different secondary structures that may have regulatory significance.

The isolation, characterization and sequence of two divergent β-tubulin genes from soybean (Glycine max L.)

Two divergent β-tubulin genes (designated Sβ-1 and Sβ-2) were isolated by screening a soybean genomic library with a Chlamydomonas reinhardtii β-tubulin cDNA probe. Restriction fragment analysis of the clones recovered, and of soybean genomic DNA, indicated that these represent two unique classes of structurally different β-tubulin genes in the soybean genome. However, it is possible that unidentified members of these classes or additional highly divergent classes of β-tubulin genes (thus far undetected) exist in the soybean genome. The Sβ-1 and Sβ-2 genomic clones were sequenced, revealing that both are potentially functional genes which would encode β-tubulins of 445 and 449 amino acids, respectively. A comparison of their derived amino acid sequences with β-tubulins from several organisms showed that they are most homologous to Chlamydomonas β-tubulin (85-87%), with lesser degrees of homology to β-tubulins of vertebrate species (79-83%), Trypanosoma brucei (80-81%) and Saccharomyces cerevisiae (66-68%). The amino acid sequences of Sβ-1 and Sβ-2 are as divergent from each other as they are from the Chlamydomonas β-tubulin. The amino acids at the diverged positions in Sβ-2 are nearly all conservative substitutions while in Sβ-1, 18 of the 69 substitutions were non-conservative. Both soybean β-tubulin genes contain two introns in exactly the same positions. The first soybean intron is located in the same position as the third intron of the Chlamydomonas β-tubulin genes. Codon usage in the two soybean β-tubulins is remarkably similar (D (2)=0.87), but differs from codon usage in other soybean genes.

Resistance of Rosa microtubule polymerization to colchicine results from a low-affinity interaction of colchicine and tubulin

The inhibition of the polymerization of tubulin from cultured cells of rose (Rosa. sp. cv. Paul's scarlet) by colchicine and the binding of colchicine to tubulin were examined in vitro and compared with data obtained in parallel experiments with bovine brain tubulin. Turbidimetric measurements of taxol-induced polymerization of rose microtubules were found to be sensitive and semiquantitative at low tubulin concentrations, and to conform to some of the characteristics of a nucleation and condensation-polymerization mechanism for assembly of filamentous helical polymers. Colchicine inhibited the rapid phase of polymerization at 24°C with an apparent inhibition constant (K i) of 1.4·10(-4) M for rose tubulin and an apparent K i=8.8·10(-7) M for brain tubulin. The binding of [(3)H]colchicine to rose tubulin to form tubulin-colchicine complex was mildly temperature-dependent and slow, taking 2-3 h to reach equilibrium at 24°C, and was not affected by vinblastine sulfate. The binding of [(3)H]colchicine to rose tubulin was saturable and Scatchard analysis indicated a single class of low-affinity binding sites having an apparent affinity constant (K) of 9.7·10(2) M(-1) and an estimated molar binding stoichiometry (r) of 0.47 at 24°C. The values for brain tubulin were K=2.46·10(6) M(-1) and r=0.45 at 37°C. The binding of [(3)H]colchicine to rose tubulin was inhibited by excess unlabeled colchicine, but not by podophyllotoxin or tropolone. The data demonstrate divergence of the colchicine-binding sites on plant and animal tubulins and indicate that the relative resistance of plant microtubule polymerization to colchicine results from a low-affinity interaction of colchicine and tubulin.

Aspergillus nidulans beta-tubulin genes are unusually divergent

Aspergillus nidulans has two beta-tubulin genes: benA, which is involved in both vegetative growth and asexual sporulation, and tubC, which is involved mainly in asexual sporulation. Both genes have now been cloned and sequenced. benA encodes a polypeptide of 447 amino acids (aa) and tubC encodes one of 449 aa. The two polypeptides differ by 78 aa residues but the net charge for the two proteins remains the same. The divergence between the amino acid sequences of the Aspergillus beta-tubulins is greater than that for any other two beta-tubulins yet described in the same organism. The benA gene has eight introns and the tubC gene has five, all of which correspond in amino acid position to introns in benA. The positions of some of these introns are conserved in other beta-tubulin genes. The 5'-splice site, internal, and 3'-splice site consensus sequences are similar to those found in other fungal introns. The transcriptional start points for each gene have been determined using primer extension and/or S1 nuclease mapping. Neither the benA gene nor the tubC gene contains a TATA sequence in its 5'-flanking region. The tubC gene has two repeated upstream sequences which are not found in benA. The sites of polyadenylation have been determined for each gene using S1 nuclease mapping. Neither gene contains a polyadenylation signal, AATAAA, typical of other eukaryotic genes.

Amino acid sequence data of alpha-tubulin from myxamoebae of Physarum polycephalum

About 96% of the amino acid sequence of an alpha-tubulin from the slime mould Physarum polycephalum has been determined. Of 430 sequenced amino acids, 30 differ from the deduced amino acid sequence of a recently published alpha-tubulin complementary DNA from the plasmodial form of P. polycephalum. The myxamoebal alpha-tubulin differs from all other known alpha-tubulins in one of the last three C-terminal amino acids that are Gly-Glu-Tyr instead of the usual Glu-Glu-Tyr. These last three amino acids are preceded by 11 residues that appear to be particularly susceptible to mutation. No heterogeneity was found whilst sequencing the myxamoebal alpha-tubulin, indicating that only one type of alpha-tubulin is present in myxamoebae. This alpha-tubulin appears to be less conserved than the previously described plasmodial alpha-tubulin, supporting the hypothesis that the structural constraints on tubulin in axonemes have a significant effect on its rate of mutation.

Amino-acid sequence data of beta-tubulin from Physarum polycephalum myxamoebae

Starting with 7.7 mg of a beta-tubulin isolated from myxamoebae of the slime mould Physarum polycephalum, 90% of the sequence has been determined by the Edman degradation of peptides generated by cyanogen bromide, trypsin and Staphylococcus aureus protease. Differences to other beta-tubulins are mainly conservative and spread evenly throughout the chain except for a high concentration at the C-terminus. The Physarum beta-tubulin shows most homology to Chlamydomonas beta-tubulin (90.5%) and least homology to yeast beta-tubulin (S. cerevisiae, 73.4%). Two tryptic peptides were isolated in approximately equal quantities which were identical except in one position (S/ALTVPELTQRMFDA) showing that at least two beta-tubulins are present in myxamoebae. However, since this was the only heterogeneity found, these beta-tubulins are probably very similar.

Sequence, evolution and differential expression of the two genes encoding variant small subunits of ribulose bisphosphate carboxylase/oxygenase in Chlamydomonas reinhardtii

We have sequenced the two genes for the small subunit of ribulose bisphosphate carboxylase/oxygenase (Rubisco) in Chlamydomonas reinhardtii and analyzed their expression. The two genes encode variant small subunits that differ by four amino acid residues. Both genes are expressed and each is transcribed into an RNA of distinct size. The accumulation of the two RNAs changes depending on the growth conditions, so the small subunit composition of Rubisco may be expected to differ in response to the environment. The C. reinhardtii small subunit sequence is homologous to those of vascular plants or cyanobacteria, but is longer at the amino terminus and in internal positions. The number and location of the intervening sequences in the genes from C. reinhardtii and from other plants differ. In several cases, internal length differences in the polypeptide coincide with the positions of introns in the coding sequence. Thus, changes in the exon structure of the genes during evolution may have been accompanied by substantial changes in the encoded protein. The translation and splicing signals in C. reinhardtii are similar to those of other eukaryotes, but the transcription signals are less conserved and the highly biased codon usage is very unusual.

Chlamydomonas reinhardtii tubulin gene structure

DNA sequencing studies have provided a picture of the total information available at the gene level for tubulin production in C. reinhardtii. The data indicates that diversity at the gene level is very limited and that all the microtubules in the cell are composed of a very similar set of tubulins. These studies contrast with similar studies of S. pombe alpha-tubulin genes and chicken beta-tubulin genes that show much heterogeneity among members of the same gene family. Further studies will be needed to investigate whether the high degree of conservation of tubulin genes is unique or common among lower eukaryotes, and what mechanisms are used to maintain homogeneity in C. reinhardtii tubulin gene families. Our DNA sequence analysis, in addition to the work of Brunke et al., has provided information on the noncoding, and possibly regulatory, portions of the tubulin genes. For example, the promoter regions of the 4 tubulin genes share a consensus sequence of 16 nucleotides upstream of the TATA box. This sequence could be involved in regulating the coordinate expression of the genes. Although little homology exists generally in the noncoding region of the genes, striking homology between the third IVS in each beta-tubulin gene is observed. Small elements homologous to the beta-tubulin IVS 3 also exist in the second IVS of each alpha-tubulin gene. In addition, considerable homology in the 5' noncoding portion of the alpha-tubulin transcripts has been noted. These homologies may be the result of recent gene conversion events, and may not have functional significance. The possibility, however, must also be considered in future experiments that these elements may play a role in regulating the expression of the tubulin genes.

Tubulin evolution: ciliate-specific epitopes are conserved in the ciliary tubulin of Metazoa

In spite of their overall evolutionary conservation, the tubulins of ciliates display electrophoretic and structural particularities. We show here that antibodies raised against Paramecium and Tetrahymena ciliary tubulins fail to recognize the cytoplasmic tubulins of all the metazoans tested. Immunoblotting of peptide maps of ciliate tubulins reveals that these antibodies react with one or very few ciliate-specific epitopes, in contrast to polyclonal antibodies against vertebrate tubulins, which are equivalent to autoantibodies and recognize several epitopes in both ciliate and vertebrate tubulins. Furthermore, we show that the anti-ciliate antibodies recognize ciliary and flagellar tubulins of metazoans ranging from sea urchin to mammals (with the exception of humans). The results support the conclusion that although duplication and specialization of tubulin genes in metazoans may have led to distinct types of tubulins, the axonemal one has remained highly conserved.

Use of monoclonal antibodies to analyse the expression of a multi-tubulin family

We have used a panel of monoclonal antibodies in a study of the expression of multiple tubulins in Physarum polycephalum. Three anti-beta-tubulin monoclonal antibodies, DM1B, DM3B3 and KMX-1 all reacted with the beta 1-tubulin isotypes expressed in both myxamoebae and plasmodia. However, these antibodies showed a spectrum of reduced reactivity with the plasmodial beta 2-tubulin isotype - the competence of recognition of this isotype was graded DM1B greater than KMX-1 greater than DM3B3. The anti-alpha-tubulin monoclonal antibody, YOL 1/34 defined the full complement of Physarum alpha-tubulin isotypes, whilst the anti-alpha-tubulin monoclonal antibody, KMP-1 showed a remarkably high degree of isotype specificity. KMP-1 recognises all of the myxamoebal alpha 1-tubulin isotypes but only recognises 3 out of the 4 alpha 1-tubulin isotypes expressed in the plasmodium (which normally focus in the same 2D gel spot). KMP-1 does not recognise the plasmodial specific alpha 2-tubulin isotype. This monoclonal antibody reveals a new level of complexity amongst the tubulin isotypes expressed in Physarum and suggests that monoclonal antibodies are valuable probes for individual members of multi-tubulin families.

Tubulin genes of the African trypanosome Trypanosoma brucei rhodesiense:nucleotide sequence of a 3.7-kb fragment containing genes for alpha and beta tubulins

Most tubulin genes of the African trypanosome Trypanosoma rhodesiense are contained in 3.7-kb tandemly repeating units. One member of the 3.7-kb repeat family has been isolated from a T. rhodesiense genomic library, cloned, and sequenced. The 3646-bp fragment contains a complete alpha-tubulin gene and portions of two beta-tubulin genes. No introns are present. The genes are separated by 634- and 333-bp intergenic regions, which lack typical eukaryotic promoter and poly(A) signal sequences. However, both intergenic regions exhibit some structural similarity with sequences proposed to be involved in transcription termination and poly(A) addition in yeast. The 634-bp intergenic region shows homology to the "mini-exon" sequence associated with variable surface glycoprotein (VSG) and other trypanosome mRNAs. A comparable sequence is not found in the 333-bp intergenic region. T. rhodesiense alpha and beta-tubulins exhibit about 84-85% amino acid (aa) sequence homology with tubulins of mammals; the genes show about 74-75% nucleotide sequence homology. The alpha-tubulin contains 451 aa and the beta tubulin 442 aa; both have tyrosine as the C-terminal aa.

An evaluation of tubulin as a molecular clock

The available sequence data for tubulin indicates that it cannot be used as a molecular clock. Apparent alpha-tubulin mutation rates, for example, vary from 0.16 to 3.8 PAMs per 100 million years depending on which two alpha-tubulins are compared. All animal alpha-tubulin mutation rates seem to be quite low, whereas those of non-animals are relatively high. A similar division is not present amongst the beta-tubulins; their apparent mutation rates, however, vary just as much. For any given tubulin, the largest number of amino acid sequence differences are obtained when comparing it to the tubulins of yeasts. Sequence comparisons with the tubulins of unicellular algae and chelates show far fewer differences. Cytochrome c data, however, show that the ciliates diverged from animals well before the yeasts. This means, therefore, that the average tubulin mutation rates in yeasts and ciliates since the time they shared a common ancestor must be quite different. The high mutation rate of yeast tubulins may possibly reflect the absence of cilia. Structural constraints imposed on tubulin by the large number of interactions with other components of the complex ciliary axoneme probably have a significant effect on its rate of mutation.