Alternative 5' exons either provide or deny an initiator methionine codon to the same alpha-tubulin coding region

ZFP91 zinc finger protein expression pattern in normal tissues and cancers

Zinc finger protein 91 (ZFP91) gene has been recently acknowledged to possess oncogenic properties. To date, its expression has been examined only in a handful of human organs and cancer types. The aim of the present study was to characterize, for the first time, the ZFP91 expression pattern in a range of human tissues and cancer types. ZFP91 mRNA expression was examined using Cancer Survey cDNA sets. Utilized cDNA samples represented 15 human organs and 17 cancer types. ZFP91 mRNA expression was the highest in the testes and lymph nodes. It was downregulated in testis cancer, lymphoma and thyroid cancer, and upregulated in prostate cancer. Among the analyzed cancer types, ZFP91 expression was markedly elevated in sarcomas and melanoma. On a protein level, a large-scale reverse phase protein array was employed providing samples from 11 organ types and from cancers derived from these organs. ZFP91 protein expression was revealed to be generally stable across the tested samples and was only moderately elevated in breast, ovarian and pancreatic cancers. To the best of our knowledge, this is the first study to thoroughly analyze the ZFP91 expression pattern in human tissues and cancers. The obtained results provide the foundation for further work aiming to reveal its full biological significance.

Tubulin superfamily genes in Tribolium castaneum and the use of a Tubulin promoter to drive transgene expression

The use of native promoters to drive transgene expression has facilitated overexpression studies in Drosophila and other insects. We identified 12 Tubulin family members from the genome sequence of the red flour beetle, Tribolium castaneum, and used the promoter from one of these to drive constitutive expression of a transgene. The activity of the T. castaneum alpha-Tubulin1 (TcalphaTub1) putative promoter was pre-tested in conjunction with an eye-color gene, T. castaneum vermilion (Tcv), by transient expression in Tcv-deficient embryos. Such embryos showed complete rescue of larval eyespot pigmentation. We also examined the TcalphaTub1 expression pattern in germline transformants using the enhanced green fluorescent protein (EGFP) reporter. Beetles transformed with this piggyBac-based reporter ubiquitously expressed EGFP at all stages.

Molecular modeling of the axial and circumferential elastic moduli of tubulin

Microtubules play a number of important mechanical roles in almost all cell types in nearly all major phylogenetic trees. We have used a molecular mechanics approach to perform tensile tests on individual tubulin monomers and determined values for the axial and circumferential moduli for all currently known complete sequences. The axial elastic moduli, in vacuo, were found to be 1.25 GPa and 1.34 GPa for alpha- and beta-bovine tubulin monomers. In the circumferential direction, these moduli were 378 MPa for alpha- and 460 MPa for beta-structures. Using bovine tubulin as a template, 269 homologous tubulin structures were also subjected to simulated tensile loads yielding an average axial elastic modulus of 1.10 +/- 0.14 GPa for alpha-tubulin structures and 1.39 +/- 0.68 GPa for beta-tubulin. Circumferentially the alpha- and beta-moduli were 936 +/- 216 MPa and 658 +/- 134 MPa, respectively. Our primary finding is that that the axial elastic modulus of tubulin diminishes as the length of the monomer increases. However, in the circumferential direction, no correlation exists. These predicted anisotropies and scale dependencies may assist in interpreting the macroscale behavior of microtubules during mitosis or cell growth. Additionally, an intergenomic approach to investigating the mechanical properties of proteins may provide a way to elucidate the evolutionary mechanical constraints imposed by nature upon individual subcellular components.

Protein expression of lymphocytes in HLA-DR transgenic pigs by a proteomic approach

Matching donor and recipient human leucocyte antigen (HLA-II) could conquer cell-mediated rejection following transplantation. Transgenic pigs carrying HLA genes that "humanize" porcine organs, tissues, and cells were successfully generated. This study further clarifies the effect of HLA-DR transgenes on lymphocyte protein expression, via a proteomic approach. Lymphocytes were isolated from two HLA-DR transgenic pigs and three nontransgenic littermates on 157 d after birth. Soluble protein of 1x10(7) cells was separated using 2-DE. In total, 301 colloidal CBB-stained protein spots detected on all five 2-D gels were quantified. Thirty-three proteins were differentially expressed by a factor of 1.5. These proteins were subsequently identified by MALDI-TOF MS and MALDI-TOF/TOF MS/MS. These proteins were sorted into the following categories: chaperones, T-lymphocyte function, DNA/RNA processing, cytoskeleton-associated proteins, signal transduction, enzymes, and unknown. Previous studies have suggested that some of the identified proteins are associated with lymphocyte activation/proliferation. The identities of the unidentified spots and the systematic effect of these up- and down-regulated proteins on T-cell function in HLA-DR transgenic pigs require further exploration.

Sexual selection, genetic conflict, selfish genes, and the atypical patterns of gene expression in spermatogenic cells

This review proposes that the peculiar patterns of gene expression in spermatogenic cells are the consequence of powerful evolutionary forces known as sexual selection. Sexual selection is generally characterized by intense competition of males for females, an enormous variety of the strategies to maximize male reproductive success, exaggerated male traits at all levels of biological organization, co-evolution of sexual traits in males and females, and conflict between the sexual advantage of the male trait and the reproductive fitness of females and the individual fitness of both sexes. In addition, spermatogenesis is afflicted by selfish genes that promote their transmission to progeny while causing deleterious effects. Sexual selection, selfish genes, and genetic conflict provide compelling explanations for many atypical features of gene expression in spermatogenic cells including the gross overexpression of certain mRNAs, transcripts encoding truncated proteins that cannot carry out basic functions of the proteins encoded by the same genes in somatic cells, the large number of gene families containing paralogous genes encoding spermatogenic cell-specific isoforms, the large number of testis-cancer-associated genes that are expressed only in spermatogenic cells and malignant cells, and the overbearing role of Sertoli cells in regulating the number and quality of spermatozoa.

A possible meiotic function of the peculiar patterns of gene expression in mammalian spermatogenic cells

This review focuses on the striking differences in the patterns of transcription and translation in somatic and spermatogenic cells in mammals. In early haploid cells, mRNA translation evidently functions to restrict the synthesis of certain proteins, notably protamines, to transcriptionally inert late haploid cells. However, this does not explain why a substantial proportion of virtually all mRNA species are sequestered in translationally inactive free-messenger ribonucleoprotein particles (free-mRNPs) in meiotic cells, since most mRNAs undergo little or no increase in translational activity in transcriptionally active early haploid cells. In addition, most mRNAs in meiotic cells appear to be overexpressed because they are never fully loaded on polysomes and the levels of the corresponding protein are often much lower than the mRNA and are sometimes undetectable. A large number of genes are expressed at grossly higher levels in meiotic and/or early haploid spermatogenic cells than in somatic cells, yet they too are translated inefficiently. Many genes utilize alternative promoters in somatic and spermatogenic cells. Some of the resulting spermatogenic cell-altered transcripts (SCATs) encode proteins with novel functions, while others contain features in their 5'-UTRs, secondary structure or upstream reading frames, that are predicted to inhibit translation. This review proposes that the transcriptional machinery is modified to provide access to specific DNA sequences during meiosis, which leads to mRNA overexpression and creates a need for translational fine-tuning to prevent deleterious consequences of overproducing proteins.

Modulation of drug resistance by alpha-tubulin in paclitaxel-resistant human lung cancer cell lines

Beta(beta)-tubulin isotype variation has recently been implicated in the modulation of resistance to paclitaxel in human lung cancer cells and in primary human ovarian tumour samples. Whether alpha-tubulin is involved in drug resistance has not been reported. We have generated a paclitaxel-resistant cell line (H460/T800) from the sensitive human lung carcinoma parental cell line NCI-H460. The resistant cells are more than 1000-fold resistant to taxol and overexpress P-glycoprotein. Interestingly, H460/T800 cells also overexpress alpha- and beta-tubulin as detected by Western blot analysis. From Northern blot analysis, the mechanism of tubulin overexpression appears to be post-transcriptional. To understand whether alpha-tubulin plays a role in drug resistance, we transfected antisense human kalpha1 cDNA construct into the H460/T800 paclitaxel-resistant cells. The antisense clones displayed a reduced alpha-tubulin expression, and the cells were 45-51% more sensitive to paclitaxel and other known antimitotic drugs, compared with vector transfected controls. Complementary experiments of transfecting the sense kalpha1 cDNA into H460 cells conferred a 1.8- to 3.3-fold increase in the IC(50) of several antimitotic agents. Our study suggests that alpha-tubulin is one of the factors that contributes to drug resistance.

TUBA8: A new tissue-specific isoform of alpha-tubulin that is highly conserved in human and mouse

We have cloned and sequenced a cDNA from a human adult skeletal muscle cDNA library, encoding for a novel isoform of alpha-tubulin (tuba8) that is preferentially expressed in heart, skeletal muscle, and testis. A genomic DNA sequence from the chromosomal region 22q11 allowed us to determine the complete structure of the TUBA8 gene that mirrors the canonical exon/intron organization of the vertebrate alpha-tubulin genes. We also cloned and sequenced the cDNA of its murine homologue (MMU-TUBA8). The latter encodes for a protein that differs from its human counterpart in only three amino acids, revealing an extreme rate of conservation that is even extended to both the 3' and 5' UTRs of the mRNAs. Sequence comparison of these novel isoforms with other known alpha tubulins shows that tuba8 is the most divergent member of the mammalian alpha-tubulin family. The sequence peculiarity of the human and murine tuba8 strongly suggests that they might have functional significance and, according to the multi-tubulin hypothesis, that they might play specific functional roles in the cell cytoskeleton.

Tex27, a gene containing a zinc-finger domain, is up-regulated during the haploid stages of spermatogenesis

Tex27 is a gene encoding a protein containing a zinc-finger domain in the carboxy terminal region and a transactivation domain in the amino terminal region. The Tex27 cDNA was isolated from a subtractive library that was enriched for genes preferentially expressed during the development of the seminiferous epithelium. Northern and in situ hybridization analyses demonstrated that Tex27 is differentially expressed in the testis, showing an increased expression in the germ cells corresponding to postmeiotic stages of spermatogenesis. This expression pattern in testis has been described for other C2H2-type zinc-finger proteins in mouse and human, like CTfin51, Zpf29, Sp1, and Zpf37. RFLP-Southern assays revealed that Tex27 is conserved in mammals. The polypeptide analysis and expression pattern suggest that Tex27 is a potential transcription factor preferentially expressed in postmeiotic cells during mouse spermatogenesis.

Mechanisms of action of and resistance to antitubulin agents: microtubule dynamics, drug transport, and cell death

PURPOSE

To analyze the available data concerning mechanisms of action of and mechanisms of resistance to the antitubulin agents, vinca alkaloids and taxanes, and more recently described compounds.

DESIGN

We conducted a review of the literature on classic and recent antitubulin agents, focusing particularly on the relationships between antitubulin agents and their intracellular target, the soluble tubulin/microtubule complex.

RESULTS AND CONCLUSION

Although it is widely accepted that antitubulin agents block cell division by inhibition of the mitotic spindle, the mechanism of action of antitubulin agents on microtubules remains to be determined. The classic approach is that vinca alkaloids depolymerize microtubules, thereby increasing the soluble tubulin pool, whereas taxanes stabilize microtubules and increase the microtubular mass. More recent data suggest that both classes of agents have a similar mechanism of action, involving the inhibition of microtubule dynamics. These data suggest that vinca alkaloids and taxanes may act synergistically as antitumor agents and may be administered as combination chemotherapy in the clinic. However, enhanced myeloid and neurologic toxicity, as well as a strong dependence on the sequence of administration, presently exclude these combinations outside the context of clinical trials. Although the multidrug resistance phenotype mediated by Pgp appears to be an important mechanism of resistance to these agents, alterations of microtubule structure resulting in altered microtubule dynamics and/or altered binding of antitubulin agents may constitute a significant mechanism of drug resistance.

Cloning, characterisation and expression of the alpha-tubulin genes of the leech, Hirudo medicinalis

We have isolated two alpha-tubulin cDNAs from the leech, Hirudo medicinalis. Both encode putative proteins of 451 amino-acids which differ from each other at only two positions. Southern blotting suggests that there are only two alpha-tubulin genes in the leech. The genes contain two introns and, because of the extremely high homology of the nucleotide sequence from the second intron to the end of the genes, we have inferred that a gene conversion event about 9.5 million years ago has homogenised the Hirudo alpha-tubulin sequences. Using in situ hybridisation to tissue sections, we have shown that the two genes are probably expressed in all neurons of the leech ganglia and that their spatial distribution remains unchanged during neuronal regeneration. The deduced amino-acid sequences of the leech alpha-tubulins show that they have greatest similarity to those from a platyhelminth, echiuran and mollusc with rather less to arthropod alpha-tubulins. The protein sequences of the leech alpha-tubulins have been compared with representatives of those from across all phyla to determine if any specific feature labels certain isotypes of tubulin for neuronal expression.

Sequence characterization of a newly identified human alpha-tubulin gene (TUBA2)

We report on the isolation and initial characterization of a human alpha-tubulin gene named TUBA2. This gene is located in the 13q11 region and has been considered a candidate gene for two nonsyndromic deafnesses, DFNB1 and DFNA3. The gene, with a minimum size of 6.5 kb, contains five exons and four introns starting at codon positions 1, 76, 125, and 352, one of which is inserted between the initiation methionine codon and the codon specifying the second amino acid, arginine 2. Neither rearrangement nor point mutation was found in the coding region of the gene in DFNB1- and DFNA3-affected patients. The gene was therefore unlikely to be responsible for either of these deafnesses. During the characterization of TUBA2, the gene encoding connexin 26 was proven to be responsible for both DFNB1 and DFNA3 (D. P. Kelsell et al., 1997, Nature 387: 80-83). However, the present data offer the possibility of testing the involvement of the TUBA2 gene in the Clouston hidrotic ectodermal dysplasia and the Kabuki syndrome, two genetic diseases that have recently been mapped to the 13q11 region.

Characterization of a domain of the genome of BmNPV containing a functional gene for a small capsid protein and harboring deletions eliminating three open reading frames that are present in AcNPV

The nucleotide sequence of a 1.5-kb fragment of the genome of Bombyx mori nuclear polyhedrosis virus (BmNPV) has been determined. An open reading frame (ORF) has been identified, which encodes a protein of a predicted molecular mass of 15 kDa (p15). Analysis of the p15 sequence revealed that it shares significant similarities with a number of previously characterized viral capsid proteins. Two mRNAs, 0.7- and 1.3-kb, are transcribed from the p15 gene. The 0.7-kb transcript appears before BmNPV DNA replication, while the 1.3-kb transcript is transcribed only after viral DNA replication. The transcription start sites for the 0.7- or 1.3-kb transcripts have been localized into two areas mapping 114 and 557/559 bp upstream of the p15 translation initiation codon, respectively, and the two transcripts appear to share a common poly(A) addition site located 114 bp downstream of the translation termination codon. Comparisons of the nucleotide sequence of the 1.5-kb BmNPV fragment with that of another isolate of BmNPV and with Autographa californica NPV (AcNPV) genomic DNA reveal that the corresponding region of AcNPV encompasses 4.1 kb of DNA and three additional ORFs that are absent from the BmNPV genome. These findings raise questions about the origin and functional relevance of the putative polypeptides encoded by the three ORFs of AcNPV.

Differential expression of tubulin isotypes during the cell cycle

Microtubules play an essential role in cell division. Little is known about possible variations of total tubulin and tubulin isotype expression during the cell cycle. We analyzed the total tubulin content, tubulin polymerization status and tubulin isotype content in resting and dividing human K562 leukemic cells and human MES-SA sarcoma cells. Although the total cellular tubulin content increases as the cells progress toward mitosis, the total tubulin/total protein ratio is stable during the cell cycle. Reverse transcriptase-polymerase chain reaction was applied to analyze the levels of expression of alpha, beta, and gamma-tubulin isotypes. Whereas alpha-tubulin isotype and gamma-tubulin transcripts were found to be expressed at constant levels throughout the cell cycle, some of the beta-tubulin isotype transcripts were found to be more highly expressed in dividing then in resting cells. Both of the class IV beta-tubulin isotype transcripts (human 5 beta and beta 2, Class IVa and IVb, respectively) were expressed in dividing K562 and MES-SA cells at twice the levels found in resting cells. Increased expression of the class IV isotype proteins in dividing cells was confirmed by immunoblotting, both in K562 and in MES-SA cells. A larger fraction of total cell tubulin was found to be polymerized in dividing cells (36-40%) than in resting cells (27-30%). The degree of polymerization of class IV tubulin in dividing and resting cells was similar to that of total tubulin. These results show that total tubulin is expressed as constant levels throughout the cell cycle but that the degree of polymerization is increased as cells are committed to division. The relative overexpression of the two class IV beta-tubulin isotypes in dividing cells suggests functional specificity for these isotypes and a regulatory role of these isotypes on the microtubule network during mitosis.

Production and utilization of detyrosinated tubulin in developing Artemia larvae: evidence for a tubulin-reactive carboxypeptidase

The reversible, enzymatically driven removal and readdition of its carboxy-terminal tyrosine are major posttranslational modifications of alpha-tubulin. To study these processes isoform-specific antibodies were produced and subsequently used to characterize tyrosinated and detyrosinated tubulin in the brine shrimp, Artemia. Tyrosinated tubulin existed in relatively constant amounts on western blots of cell-free protein extracts from Artemia at all developmental stages examined, whereas detyrosinated tubulin was present after 20-24 h of postgastrula growth. In agreement with the blots, the detyrosinated isoform was observed in immunofluorescently stained larvae after 24 h of incubation, appearing first in structures of a transient nature, namely spindles and midbodies. The elongated muscle cells encircling the gut and the epithelium bordering the gut lumen were stained extensively with antibody to detyrosinated tubulin. Detyrosination was accompanied by the appearance of a tubulin-reactive carboxypeptidase, which used both nonpolymerized and polymerized tubulin as substrate. The enzyme bound to microtubules very poorly, if at all, under conditions used in this work. Several inhibitors of carboxypeptidase A had no effect on the carboxypeptidase from Artemia and revealed similarities between this enzyme and others thought to be tubulin specific. The use of inhibitors also indicated that the carboxypeptidase from Artemia recognized aspects of tubulin structure in addition to the carboxy-terminal tyrosine. Our results support the idea that detyrosinated tubulin appears in microtubules of varying stability, and they demonstrate that Artemia possess a carboxypeptidase with the potential to detyrosinate tubulin during growth of larvae.

A widely expressed novel C2H2 zinc-finger protein with multiple consensus phosphorylation sites is conserved in mouse and man

We have cloned a murine cDNA whose deduced sequence encodes a 455-amino-acid (aa) zinc-finger protein (Zfp), PZf (penta Zf protein). Sequence analysis shows that PZf has multiple phosphorylation consensus sites for casein kinase II and protein kinase C in its N-terminal portion. This region (aa 1 to 197), which does not share significant homology to known aa sequences, has a number of charged (39 Glu, 15 Asp, 23 Lys, 22 Arg) and hydroxyl (20 Ser, 12 Thr) aa. This potentially phosphorylatable region is followed by five C2H2 Zf in the middle of the protein. The Pzf gene is transcribed as a 5-kb mRNA in all murine tissues examined. The human genome also seems to contain one or more Pzf-related genes.

A novel carbonic anhydrase II mRNA isolated from mature chicken testis displays a TATA box and other promoter sequences in a leader 5' untranslated region not present in somatic tissues

The primary structure of a novel carbonic anhydrase II-encoding cDNA clone (CAII) isolated from a chicken testis cDNA library is presented. The size of the CAII mRNA obtained from meiotic and haploid chicken testis cells is larger than the corresponding mRNA from immature testis and somatic tissues. The nucleotide sequence of the chicken testis CAII clone revealed a protein-coding region identical to the published sequence of CAII mRNA from erythroid cells. However, the 5' untranslated region (UTR) of the testis CAII mRNA is larger than the corresponding somatic sequence. The 5' UTR contains a leader sequence not present in the CAII mRNA isolated from erythroid cells or chick retina. The additional 5' UTR of the mRNA displays a TATA box, located 23-30 bp upstream from the cap site of the CAII mRNA transcribed in erythroid cells, and several G+C-rich boxes. Our results suggest that the use of a testis-specific promoter would result in the incorporation of somatic promoter sequences into the 5' UTR of the testis message.

The carboxy-terminal peptide of detyrosinated alpha tubulin provides a minimal system to study the substrate specificity of tubulin-tyrosine ligase

The ATP-dependent tubulin-tyrosine ligase (TTL) restores the carboxy-terminal tyrosine of alpha tubulin in alpha beta tubulin that has been previously detyrosinated. Here we show that the carboxy-terminal tetradecapeptide of detyrosinated alpha tubulin is used by TTL as a substrate, albeit at 50-fold lower efficiency than alpha beta tubulin. The minimal system provided by the TTL/peptide combination mirrors the TTL/tubulin system in all aspects tested, and shows a pronounced substrate inhibition. Synthetic peptides varying in length and/or containing single amino acid replacements were used to analyze the TTL specificity for the carboxy-terminal sequence of detyrosinated alpha tubulin. Peptides ending like alpha tubulin with the sequence Gly-Glu-Glu are optimally tyrosinated once a peptide length of 12 residues is reached. Position -1 of this recognition sequence, to which the tyrosine is added, must be glutamic acid. Position -2 accepts only an acidic amino acid but glutamic acid is by far preferred over aspartic acid. These results explain why a subpopulation of brain alpha tubulin, which ends with the sequence Gly-Glu, is not tyrosinated by TTL. The carboxy-terminal dodecapeptide of brain alpha tubulin with its polyglutamyl side-chain on position -6 shows the same substrate activity as the corresponding synthetic peptide lacking the side-chain. We discuss the substrate specificity of TTL for different alpha tubulins and speculate why tubulin is a better substrate than the optimal peptide covering the carboxy-terminal of detyrosinated alpha tubulin.

Intron and intronless transcription of the chicken polyubiquitin gene UbII

We have previously reported that the chicken polyubiquitin gene UbII is preferentially expressed during spermatogenesis and we show here that UbII is the predominant polyubiquitin gene expressed in early embryogenesis. Two main initiation sites were detected. Transcription from the initiation site used in early embryos results in the presence of an intron in the 5'-untranslated region of the transcripts as has been reported for other polyubiquitin messages. In mature testis, however, the use of a different initiation site, located within the intron, produces intronless transcripts. Distinct promoter sequences, present in each initiation site, may regulate the differential expression observed in this gene.

High level expression of nonacetylatable alpha-tubulin in Chlamydomonas reinhardtii

Following the discovery of acetylated alpha-tubulin in the flagella of Chlamydomonas, many studies have documented the presence of acetylated alpha-tubulin in a variety of evolutionarily divergent organisms. While this posttranslational modification may define an isoform with a unique function, the primary effect of alpha-tubulin acetylation remains unknown. To study the function of alpha-tubulin acetylation, we have transformed Chlamydomonas, an organism in which almost all of the flagellar tubulin and a subset of the cytoplasmic microtubules are acetylated, with an alpha 1-tubulin gene whose product cannot be acetylated. Specifically, the codon for lysine 40, the lysine that is acetylated, has been replaced with the codon of nonacetylatable amino acids. To distinguish mutagenized alpha-tubulin from that produced by the two endogenous alpha-tubulin genes, mutant alpha-tubulin was tagged with an epitope from influenza virus hemagglutinin. Utilizing the constitutive Chlamydomonas rubisco small subunit S2 promoter, we have obtained in selected clones high levels of nonacetylatable alpha-tubulin expression approximating 50-70% of the total flagellar alpha-tubulin. Immunofluorescence and immunoblot analysis of transformed cells indicated that nonacetylatable alpha-tubulin could assemble, along with endogenous alpha-tubulin, into both cytoplasmic and flagellar microtubules. However, no gross phenotypic effects were observed, suggesting that the effect of alpha-tubulin acetylation is subtle.

Sequence of the gene encoding the mitochondrial capsule selenoprotein of mouse sperm: identification of three in-phase TGA selenocysteine codons

The mitochondrial selenoprotein is a major structural protein of the keratinous mitochondrial capsule in mammalian sperm, a structure that functions in shaping mitochondria into the helical sheath surrounding the flagellum. A cDNA clone (Kleene et al., 1990) was isolated previously encoding a protein whose predicted size and amino acid content of > 20% cysteine and proline closely resembled a selenoprotein in the bull mitochondrial capsule. The sequences of additional cDNAs and genomic DNA reported here reveal that the mouse mitochondrial capsule selenoprotein reading frame begins 54 codons further upstream than previously reported. Significantly, these 54 codons contain three in-phase UGA codons, which normally signify stop but encode selenocysteine in bacterial and mammalian selenoproteins. The coding region of the mitochondrial capsule selenoprotein gene is interrupted by a single intron. S1 mapping and primer extension demonstrate that the vast majority of MCS mRNAs are spliced using consensus 5' and 3' slice junctions in mammalian cells. However, two cDNAs have been identified that apparently represent rare mRNA variants produced by use of cryptic splice sites.

Alternative 3' processing of Xenopus alpha-tubulin mRNAs; efficient use of a CAUAAA polyadenylation signal

The Xenopus laevis alpha-tubulin gene X alpha T14 produces two mRNAs of 1.7 and 2.15 kb and we have shown that this is due to the use, at approximately equal frequency, of alternative 3' processing sites. Unusually, the hexanucleotide polyadenylation signal responsible for use of the downstream site, pA2, is CAUAAA in contrast to the consensus AAUAAA used at the upstream site, pA1. Since such a variant hexanucleotide would normally be expected to reduce drastically the efficiency of 3' processing, we have examined the 3' flanking sequences involved in pA2 usage in injected oocytes. In deletion mutants with 40 bp or 440 bp of 3' flanking DNA use of pA2 was almost totally abolished whereas when 770 bp of the natural flank was present pA2 was used normally. This polyadenylation signal therefore requires an unexpectedly large amount of flanking DNA and we have identified in the required region a member of a novel family of 450 bp interspersed repeats that we have termed Pir elements. We speculate that because of the variant hexanucleotide efficient use of pA2 has to be potentiated by the Pir element, perhaps through an effect on transcriptional pausing or termination.

Tris-tricine and Tris-borate buffer systems provide better estimates of human mesothelial cell intermediate filament protein molecular weights than the standard Tris-glycine system

Human mesothelial cells contain a number of well defined intermediate filament proteins (IFs) that have been completely sequenced including vimentin and the cytokeratins (K7, K8, K18, and K19). The electrophoretic migration of these IFs was monitored as a function of second dimension gel buffer composition using various systems including Tris-glycine (pH 8.3 or 9.2), Tris-glycine with 20% methanol, Tris-borate, Tris-tricine, and sodium phosphate. All of the second dimension buffer chemistries yielded patterns of sufficient resolution to identify the major cytoskeletal proteins but differed in the relative mobilities of the IFs. Using gene sequence calculated molecular weight data, the major cytoskeletal polypeptides of human mesothelial cells were ranked from highest molecular weight to lowest molecular weight. This rank order of sequence calculated molecular weights was then compared to the rank order determined form the actual migration of the polypeptides in the different gel systems. With the Tris-tricine and the Tris-borate gel systems as well as gene sequence data, KS = vimentin greater than beta-tubulin = K7 greater than K18 greater than K19 greater than actin. With the pH 8.3 and 9.2 Tris-glycine systems, as well as the sodium phosphate gel system, the rank order of the polypeptides did not correspond to gene sequence data. Adding 20% methanol to the Tris-glycine system resulted in IF migration that more closely corresponded to the gene sequence derived data. Migration position of the IFs depended upon the temperature of the second dimension separation as well. In mesothelial cells, the migration of a total of 15-25% of the polypeptides was influenced by differing buffer systems.(ABSTRACT TRUNCATED AT 250 WORDS)

Identification of members of the protein phosphatase 1 gene family in the rat and enhanced expression of protein phosphatase 1 alpha gene in rat hepatocellular carcinomas

We isolated four kings of cDNA clones of isotypes of catalytic subunits of protein phosphatase 1 (PP-1) from rat liver and testis cDNA libraries. For the cloning, cDNA fragments of dis2ml and dis2m2, which encode mouse PP-1 catalytic subunit, were used as probes. Two of the four isotypes were thought to be derived from the same gene and produced by alternative splicing. Based on the comparative study of their nucleotide and deduced amino acid sequences with those reported, these cDNA clones were named rat PP-1 alpha, PP-1 gamma 1, PP-1 gamma 2 and PP-1 delta. The deduced amino acid sequences of these four cDNA clones showed about 90% identity. Their amino-terminal regions were highly conserved, and their differences were mainly in the carboxy-terminal regions. Furthermore, several amino acids located in the middle regions of the peptides were conserved in all the isotypes of the catalytic subunits of PP-1, PP-2A, PP-2B and PP-2C. These conserved regions are suggested to be the functional domains of the catalytic subunits of protein phosphatases. Rat hepatocellular carcinomas induced by a food mutagen, 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline showed increased expression of PP-1 alpha, but no increased expression of PP-1 gamma 1, PP-1 gamma 2 or PP-1 delta. Involvement of PP-1 alpha in hepatocarcinogenesis or in hepatic cell proliferation was suspected.

Protein phosphatases possibly involved in rat spermatogenesis

The expression of mRNAs for catalytic subunits of serine/threonine protein phosphatases 1 (PP-1) and 2A (PP-2A) in various rat tissues were examined. Four kinds of probes were used to detect mRNAs for two isotypes of PP-1 (dis2m1 and dis2m2), and two isotypes of PP-2A (PP-2A alpha and PP-2A beta). mRNAs for all of these four catalytic subunits were expressed in almost all tissues at substantial levels. They were expressed in two different sizes in most tissues. Remarkable evidence is that the smaller sized mRNAs of dis2m1 and PP-2A beta, 1.8 kb and 1.4 kb in length, respectively, were specifically highly expressed in testis. Both these smaller sized mRNAs began to be expressed at the age when meiosis started and were detected in testicular germ cells at the pachytene stage of meiotic prophase. Protein phosphatases which have peptides encoded by dis2m1 and PP-2A beta as catalytic subunits may play important roles in spermatogenesis.

Transcription of testicular angiotensin-converting enzyme (ACE) is initiated within the 12th intron of the somatic ACE gene

Angiotensin-converting enzyme (ACE) is a zinc-containing dipeptidyl carboxypeptidase that catalyzes the conversion of angiotensin I to the potent vasoconstrictor angiotensin II. By analyzing cDNA and genomic DNA, we have constructed a consensus sequence encoding the testis isozyme of mouse ACE. Testis ACE cDNA contains 2,435 base pairs and encodes a protein of 732 amino acids. The N-terminal 66 amino acids are unique to the testis isozyme, while the remaining 666 are identical to the carboxyl half of mouse somatic ACE. The overall conservation of amino acid sequence between the testis isozymes of the mouse, rabbit, and human is 78 to 84%. The conservation of amino acids for the N-terminal domain uniquely expressed within the testis is 63 to 67% between these species. Primer extension and RNase protection experiments show that RNA transcription of the testis ACE isozyme begins 16 or 17 bases upstream from the translation start site. A sequence element resembling a TATA box is found 25 bases 5' of the transcription start site. To create its unique isozyme of ACE, the testis begins mRNA transcription in the middle of the exonic-intronic structure of somatic ACE, within a sequence treated as an intron by somatic tissues. Testis ACE is not the result of alternative RNA splicing but seems due to the start of transcription at a unique site within the ACE gene.

Transcription of testicular angiotensin-converting enzyme (ACE) is initiated within the 12th intron of the somatic ACE gene

Angiotensin-converting enzyme (ACE) is a zinc-containing dipeptidyl carboxypeptidase that catalyzes the conversion of angiotensin I to the potent vasoconstrictor angiotensin II. By analyzing cDNA and genomic DNA, we have constructed a consensus sequence encoding the testis isozyme of mouse ACE. Testis ACE cDNA contains 2,435 base pairs and encodes a protein of 732 amino acids. The N-terminal 66 amino acids are unique to the testis isozyme, while the remaining 666 are identical to the carboxyl half of mouse somatic ACE. The overall conservation of amino acid sequence between the testis isozymes of the mouse, rabbit, and human is 78 to 84%. The conservation of amino acids for the N-terminal domain uniquely expressed within the testis is 63 to 67% between these species. Primer extension and RNase protection experiments show that RNA transcription of the testis ACE isozyme begins 16 or 17 bases upstream from the translation start site. A sequence element resembling a TATA box is found 25 bases 5' of the transcription start site. To create its unique isozyme of ACE, the testis begins mRNA transcription in the middle of the exonic-intronic structure of somatic ACE, within a sequence treated as an intron by somatic tissues. Testis ACE is not the result of alternative RNA splicing but seems due to the start of transcription at a unique site within the ACE gene.

Transcription of the rat and mouse proenkephalin genes is initiated at distinct sites in spermatogenic and somatic cells

During spermatogenesis, several genes are expressed in a germ cell-specific manner. Previous studies have demonstrated that rat and mouse spermatogenic cells produce a 1,700-nucleotide proenkephalin RNA, while somatic cells that express the proenkephalin gene contain a 1,450-nucleotide transcript. Using cDNA cloning, RNA protection, and primer extension analyses, we showed that transcription of the rat and mouse spermatogenic-cell RNAs is initiated downstream from the proenkephalin somatic promoter in the first somatic intron (intron As). In both species, the germ cell cap site region consists of multiple start sites distributed over a length of approximately 30 base pairs. Within rat and mouse intron As, the region upstream of the germ cell cap sites is GC rich and lacks TATA sequences. A consensus binding site for the transcription factor SP1 was identified in intron As downstream of the proenkephalin germ cell cap site region. These features are characteristic of several previously described promoters that lack TATA sequences. Homologies were also identified between the proenkephalin and rat cytochrome c spermatogenic-cell promoters, including the absence of a TATA box, a multiple start site region, and several common sequences. This promoter motif thus may be shared with other genes expressed in male germ cells.

Transcription of the rat and mouse proenkephalin genes is initiated at distinct sites in spermatogenic and somatic cells

During spermatogenesis, several genes are expressed in a germ cell-specific manner. Previous studies have demonstrated that rat and mouse spermatogenic cells produce a 1,700-nucleotide proenkephalin RNA, while somatic cells that express the proenkephalin gene contain a 1,450-nucleotide transcript. Using cDNA cloning, RNA protection, and primer extension analyses, we showed that transcription of the rat and mouse spermatogenic-cell RNAs is initiated downstream from the proenkephalin somatic promoter in the first somatic intron (intron As). In both species, the germ cell cap site region consists of multiple start sites distributed over a length of approximately 30 base pairs. Within rat and mouse intron As, the region upstream of the germ cell cap sites is GC rich and lacks TATA sequences. A consensus binding site for the transcription factor SP1 was identified in intron As downstream of the proenkephalin germ cell cap site region. These features are characteristic of several previously described promoters that lack TATA sequences. Homologies were also identified between the proenkephalin and rat cytochrome c spermatogenic-cell promoters, including the absence of a TATA box, a multiple start site region, and several common sequences. This promoter motif thus may be shared with other genes expressed in male germ cells.

Testis-specific transcription initiation sites of rat farnesyl pyrophosphate synthetase mRNA

A variety of rat tissues were screened at low stringency with a rat farnesyl pyrophosphate (FPP) synthetase cDNA. In testis, an FPP synthetase-related RNA was detected that was larger than the liver FPP synthetase mRNA and was present at very high levels comparable with liver FPP synthetase RNA levels obtained from rats fed diets supplemented with cholestyramine and mevinolin. Sequence analysis of testis cDNA clones, together with primer extension and S1 nuclease experiments, indicated that testis FPP synthetase transcripts contain an extended 5' untranslated region. The 5' extension contained one or two out-of-frame upstream ATGs, depending on the site of transcription initiation. Protein in vitro translation studies indicated that the extended 5' untranslated region may play a role in regulating the translation of the FPP synthetase polypeptide in rat testis. Southern blot analysis with a probe containing both testis and liver 5' untranslated sequences provided evidence that both liver and testis transcripts derive from the same gene. The data suggest that an upstream testis-specific promoter results in the abundant production of FPP synthetase transcripts that are translated at low efficiency; another promoter functions in liver and other somatic tissues and directs the regulated synthesis of shorter discrete transcripts.

Testis-specific transcription initiation sites of rat farnesyl pyrophosphate synthetase mRNA

A variety of rat tissues were screened at low stringency with a rat farnesyl pyrophosphate (FPP) synthetase cDNA. In testis, an FPP synthetase-related RNA was detected that was larger than the liver FPP synthetase mRNA and was present at very high levels comparable with liver FPP synthetase RNA levels obtained from rats fed diets supplemented with cholestyramine and mevinolin. Sequence analysis of testis cDNA clones, together with primer extension and S1 nuclease experiments, indicated that testis FPP synthetase transcripts contain an extended 5' untranslated region. The 5' extension contained one or two out-of-frame upstream ATGs, depending on the site of transcription initiation. Protein in vitro translation studies indicated that the extended 5' untranslated region may play a role in regulating the translation of the FPP synthetase polypeptide in rat testis. Southern blot analysis with a probe containing both testis and liver 5' untranslated sequences provided evidence that both liver and testis transcripts derive from the same gene. The data suggest that an upstream testis-specific promoter results in the abundant production of FPP synthetase transcripts that are translated at low efficiency; another promoter functions in liver and other somatic tissues and directs the regulated synthesis of shorter discrete transcripts.

Murine beta 1,4-galactosyltransferase: both the amounts and structure of the mRNA are regulated during spermatogenesis

Previously we have shown that the gene encoding murine beta 1,4-galactosyltransferase (beta 1,4-GT; UDPgalactose:N-acetyl-D-glucosaminyl-glycopeptide 4-beta-D-galactosyltransferase, EC 2.4.1.38) is unusual in that it specifies two sets of mRNAs of about 3.9 and 4.1 kilobases (kb). Translation of the 3.9- and 4.1-kb mRNAs results in the predicted synthesis of two related membrane-bound forms of the protein of 386 amino acids (short form) and 399 amino acids (long form), respectively. In this study we have examined the expression of beta 1,4-GT during murine spermatogenesis. Spermatogonia contain a 4.1-kb transcript that is comparable in size to the beta 1,4-GT mRNA identified in somatic cells. During differentiation from spermatogonia (2n) to pachytene spermatocytes (4n), the amount of beta 1,4-GT mRNA is reduced to barely detectable levels. Continued differentiation to round spermatids (n) is coincident with a renewed production of beta 1,4-GT mRNA to levels comparable with those detected in spermatogonia. However, the characteristic 4.1-kb mRNA detected in spermatogonia is replaced by two truncated transcripts of 2.9 and 3.1 kb. By S1 nuclease analysis, the 2.9- and 3.1-kb transcripts were shown to encode the same open reading frame as the 4.1-kb transcript found in somatic cells. The shorter round spermatid transcripts arise as a consequence of the use of alternative poly(A) signals. Lastly, we show that, in direct contrast to all somatic tissues and cell lines examined to date, male germ cells synthesize only the long form of the beta 1,4-GT polypeptide.

The 5' splice site: phylogenetic evolution and variable geometry of association with U1RNA

The 5' splice site sequences of 3294 introns from various organisms (1-672) were analyzed in order to determine the rules governing evolution of this sequence, which may shed light on the mechanism of cleavage at the exon-intron junction. The data indicate that, currently, in all organisms, a common sequence 1GUAAG6U and its derivatives are used as well as an additional sequence and its derivatives, which differ in metazoa (G/1GUgAG6U), lower eucaryotes (1GUAxG6U) and higher plants (AG/1GU3A). They all partly resemble the prototype sequence AG/1GUAAG6U whose 8 contigous nucleotides are complementary to the nucleotides 4-11 of U1RNA, which are perfectly conserved in the course of phylogenetic evolution. Detailed examination of the data shows that U1RNA can recognize different parts of 5' splice sites. As a rule, either prototype nucleotides at position -2 and -1 or at positions 4, 5 or 6 or at positions 3-4 are dispensable provided that the stability of the U1RNA-5' splice site hybrid is conserved. On the basis of frequency of sequences, the optimal size of the hybridizable region is 5-7 nucleotides. Thus, the cleavage at the exon-intron junction seems to imply, first, that the 5' splice site is recognized by U1RNA according to a "variable geometry" program; second, that the precise cleavage site is determined by the conserved sequence of U1RNA since it occurs exactly opposite to the junction between nucleotides C9 and C10 of U1RNA. The variable geometry of the U1RNA-5' splice site association provides flexibility to the system and allows diversification in the course of phylogenetic evolution.

Sequence of one alpha- and two beta-tubulin genes of Tetrahymena pyriformis. Structural and functional relationships with other eukaryotic tubulin genes

Macronuclear DNA of the ciliate Tetrahymena pyriformis contains only one size class of fragments coding for alpha-tubulin, alpha TT. We have isolated alpha TT from a partial plasmid library, using Chlamydomonas reinhardtii alpha-tubulin gene as a probe. This gene as well as the two beta-tubulin genes, beta TT1 and beta TT2, have been sequenced. None of these genes contains introns and all use TGA as the stop codon. In the coding region of the two beta-tubulin genes, there are several TAA and TAG stop codons that probably code for glutamine. The codon usage is very biased. Regions flanking the tubulin coding sequences are A + T-rich (75%) and quite different among themselves. In these regions there are several putative transcription-regulatory sequences. Nuclear transcripts begin and terminate at multiple sites. The beta-tubulin proteins differ only in two amino acid residues. Primary structure of Tetrahymena tubulins as well as their hydropathy indexes show a high degree of homology with tubulins from other organisms. Two-dimensional electrophoretic analysis of the ciliary tubulins shows the presence of eight alpha-tubulins and four beta-tubulins. The alpha-tubulins migrate faster than the beta-tubulins, in contrast with what happens with brain tubulins. We suggest that there are several alpha- and beta-tubulin isoforms and the migratory inversion observed may be due to post-translational modifications.

A survey of the alpha-tubulin gene family in chicken: unexpected sequence heterogeneity in the polypeptides encoded by five expressed genes

To characterize the alpha-tubulin gene family in chicken, we have isolated five chicken alpha-tubulin genes and determined the majority of the sequences of the encoded polypeptides. Three of these (c alpha 3, c alpha 5/6 and c alpha 8) encode novel, expressed alpha-tubulins that have not previously been analyzed, whereas one gene segment is a pseudogene and another appears capable of encoding a functional subunit (although we were unable to document its expression in a survey of chicken tissues). Together with two additional expressed, functional alpha-tubulins reported earlier, we conclude that the chicken alpha-tubulin family is comprised of at least five functional genes whose polypeptide products are substantially more heterogeneous than found in preceding analyses of vertebrate alpha-tubulins. Comparison of the amino acid sequences reveals that the five polypeptides are between 96 and 83% identical, with the extreme carboxy-terminal residues representing a highly heterogeneous variable domain. Since some alpha-tubulins undergo cyclic post-translational removal and readdition of a carboxy-terminal tyrosine, the notable sequence divergence in this domain suggests that individual tubulins probably participate to different extents in this modification cycle.

Comparative analysis of tubulin sequences

1. Information on the structure and evolution of tubulin has been obtained by comparing the available sequence data on 31 alpha-tubulins and 31 beta-tubulins. 2. Similar numbers of conserved amino acids are found amongst both alpha- and beta-tubulins (alpha: 48%, plus conservative substitutions: 72%; beta: 48%, plus conservative substitutions: 70%). About half of them are common to both subunits (23%, plus conservative substitutions: 45%). Four cysteines in the alpha-tubulins and 2 cysteines in the beta-tubulins are conserved. Only one cysteine (position 129) is conserved in all alpha- and beta-tubulins. 3. The longest unbroken stretch of identical amino acids between all the alpha- and beta-tubulins is found in positions 180-186 (Val-Val-Glu-Pro-Tyr-Asn), a region that appears to be important for binding the ribose moiety of GTP. Two other groups of amino acids implicated in GTP binding, one near position 70 and a glycine cluster at position 144 are also quite conserved. 4. Extra length differences between tubulin subunits, presumably present as extensions on the dimer surface, have been observed at position 50 and near position 360 in alpha-tubulins and in one case at position 57 in a beta-tubulin. 5. The introns of tubulin genes, many of them clustered in the first quarter of the tubulin coding region, do not appear to correspond to any particular structural or functional regions. 6. Mutation rates of tubulins vary considerably. The lowest alpha-tubulin homology (62.3%) is between a very divergent Drosophila alpha-tubulin and an alpha-tubulin from the yeast S. cerevisiae. The lowest beta-tubulin homology (63.3%) is between a yeast (S. cerevisiae) beta-tubulin and a mouse beta-tubulin expressed in hematopoietic tissue. In contrast, some mammalian and bird tubulins are almost identical. 7. Tubulin's heterogeneous C-termini are useful for identifying corresponding tubulins of different vertebrate species, many of which are remarkably conserved. Exceptions are the divergent beta-tubulins of erythrocyte and thrombocyte marginal bands. 8. We have proposed a model for tubulin evolution in metazoan organisms in which the release of structural constraints after gene duplication is a major cause of relatively rapid change.

Nucleotide sequence and expression of two beta-tubulin genes in Stylonychia lemnae

The gene-sized macronuclear DNA of the hypotrichous ciliate Stylonychia lemnae contains one size class of DNA molecules of 1.85 kb (1 kb = 10(3) base-pairs) coding for beta-tubulin. These DNA molecules consist of two different beta-tubulin genes, beta 1 and beta 2, which are amplified to about 150,000 (beta 1) and 30,000 (beta 2) copies per macronucleus. Both genes were cloned and sequenced entirely. The coding sequences of the two molecules (1329 base-pairs including TGA) predict identical amino acid sequences for the proteins and show a nucleotide homology of 97.2%. The nucleotide as well as the encoded amino acid sequences are highly conserved, when compared to beta-tubulin genes from vertebrates. The ciliate-specific codon TAA specifying glutamine is present only in the beta 2-tubulin gene, whereas glutamine is encoded soley by CAA in the beta 1-tubulin gene. The 5' and 3'-non-coding regions of both beta-tubulin genes are similar in length, but differ extremely in nucleotide sequence. Both beta-tubulin genes are transcriptionally active in S. lemnae, although not all putative transcription-regulatory sequences known from higher eukaryotes can be detected within the non-coding regions. The two transcription products localized by S1-mapping experiments show a similar length of about 1.40 kb and transcription seems to be regulated differently for beta 1 and beta 2.

Tissue-specific expression of insulin-like growth factor II mRNAs with distinct 5' untranslated regions

We have used RNA from human hypothalamus as template for the production of cDNAs encoding insulin-like growth factor II (IGF-II). The prohormone coding sequence of brain IGF-II RNA is identical to that found in liver; however, the 5' untranslated sequence of the brain cDNA has no homology to the 5' untranslated sequence of the previously reported liver cDNAs. By using hybridization to specific probes as well as a method based on the properties of RNase H, we found that the human IGF-II gene has at least three exons that encode alternative 5' untranslated regions and that are expressed in a tissue-specific manner. A probe specific to the brain cDNA 5' untranslated region hybridizes to a 6.0-kilobase transcript present in placenta, hypothalamus, adrenal gland, kidney, Wilms tumor, and a pheochromocytoma. The 5' untranslated sequence of the brain cDNA does not hybridize to a 5.3-kilobase transcript found in liver or to a 5.0-kb transcript found in pheochromocytoma. By using RNase H to specifically fragment the IGF-II transcripts into 3' and 5' fragments, we found that the RNAs vary in size due to differences in the 5' end but not the 3' end.

Identification of an acetylation site of Chlamydomonas alpha-tubulin

An acetylation site of Chlamydomonas axonemal alpha-tubulins was identified near, or within, the binding site of 6-11B-1, a monoclonal antibody specific for posttranslationally acetylated alpha-tubulins. In a first approach, axonemal proteins were hydrolyzed by formic acid, cyanogen bromide, or chymotrypsin and analyzed with immunoblots. The smallest alpha-tubulin peptide retained on nitrocellulose and containing antibody-binding site(s) was found to span amino acids 37-138 (alpha 37-138). A smaller antibody-binding peptide, identified as alpha 25-50, was obtained by complete digestion of alpha-tubulin with chymotrypsin. This fragment was purified by reversed-phase HPLC and assayed by its ability to bind 6-11B-1 in solution. Determination of the amino acid sequences of alpha 37-138 and alpha 25-50 showed that residue 40 in axonemal alpha-tubulin is epsilon N-acetyllysine. A sequence very similar to Chlamydomonas alpha 25-50 is found in the majority of alpha-tubulins analyzed so far. However, the corresponding region is markedly divergent in some alpha-tubulin isoforms from chicken, Drosophila, and yeast.