Structure and expression of the Chinese hamster thymidine kinase gene

Sp1 and NF-Y are necessary and sufficient for growth-dependent regulation of the hamster thymidine kinase promoter

Thymidine kinase (TK) genes from different species are growth- and cell cycle-regulated in a very similar manner; still, the promoter regions of these genes show little homology to each other. It was previously shown that the murine TK gene is growth-regulated by Sp1 and E2F. Here we have characterized cis-regulatory elements in the hamster promoter that are essential and sufficient to confer efficient and serum-responsive expression. The TK promoter was isolated from baby hamster kidney cells. DNase I protection experiments revealed a protected region from positions -24 to -99 relative to the transcription start site. Within this region, binding sites for the transcription factor Sp1 and a CCAAT box, which interacts with the transcription factor NF-Y, were identified. An E2F-like sequence was found not to bind protein, and its removal did not affect promoter activity. This was supported by the observation that cotransfection of a hamster TK reporter gene construct with E2F-1 does not lead to transactivation of the promoter. A 122-base pair region that contains a single Sp1 site, a CCAAT box, and a TATA element was found to be sufficient for serum-responsive expression of a reporter gene. Mutations that inactivate any one of these three elements caused a strong reduction or a loss of promoter activity.

Salvage pathway of pyrimidine synthesis: divergence of substrate specificity in two related species of teleostean fish

For nucleotide synthesis, cells use purine and pyrimidine nucleosides generated either through de novo synthesis or through utilization of salvage pathways. In the pyrimidine salvage pathway, thymidine is taken up by transport proteins and phosphorylated by the enzyme thymidine kinase to thymidine monophosphate. So far, all vertebrates analyzed are able to use radioactively labeled thymidine for the biosynthesis of nucleotides in brain tissue. However, when standard autoradiographic, immunohistochemical and biochemical procedures were applied for the detection of the incorporation of tritiated thymidine and the thymidine analogue 5-bromo-2'-deoxyuridine into DNA to two species of gymnotiform fish, a divergence in substrate specificity has been revealed. Although brain cells of the two species, Apteronotus leptorhynchus and Eigenmannia sp., can utilize 5-bromo-2'-deoxyuridine for pyrimidine synthesis, only Eigenmannia sp. is able to incorporate tritiated thymidine into DNA during the S phase of the cell cycle. We hypothesize that this inability to use thymidine for nucleotide synthesis is caused either by a defect in the transport system mediating the uptake of thymidine or by a deficiency in the thymidine kinase of A. leptorhynchus.

Protein that binds to the distal, but not to the proximal, CCAAT of the human thymidine kinase gene promoter

Mobility shift assays were used to examine protein binding to the human TK gene CCAAT boxes. Similar protein binding patterns were observed with probes containing either the proximal or distal CCAAT. However, probes containing both CCAAT boxes in which one of the CCAAT boxes was inactivated by mutation did not demonstrate identical binding patterns. One of the complexes formed with the longer probes was only observed when the distal CCAAT was intact. This species was not formed with probes that only contained an intact proximal CCAAT, and its formation could only be competed by oligonucleotides containing the distal CCAAT motif. This observation reveals the existence of a protein that can bind to the distal, but not to the proximal, CCAAT of the human TK promoter. This protein may account for the previous observation that the two CCAAT motifs are not functionally equivalent. The protein that binds to the distal, but not to the proximal, CCAAT (DTK-CBP) was also present in two human cell lines. Significantly more DTK-CBP was present in nuclear extracts of HepG2 and WI38 cells than in TK-ts13 cells. However, this protein was not observed in three different murine cell lines and one primary culture. Its abundance in some human cell lines suggests it might modulate the expression of human TK mRNA in cells that express this protein.

Production of vampire bat plasminogen activator DSPA alpha 1 in CHO and insect cells

Salivary plasminogen activator from the vampire bat Desmodus rotundus (DSPA alpha 1) is a promising new thrombolytic agent. Continuous growth of a stably transfected, methotrexate amplified, dhfr- CHO cell line yields up to 60 mg l-1 of DSPA alpha 1. Utilizing an engineered baculovirus 10 mg l-1 were produced in batches of Sf9 insect cells. Recombinant DSPA alpha 1 is purified from both sources using a one-step purification protocol. Although differences in glycosylation were detected, enzymatic activity and fibrin cofactor dependency are unaffected when DSPA alpha 1 derived from the two expression systems is compared.

Characterization of the murine thymidine kinase-encoding gene and analysis of transcription start point heterogeneity

We have determined the molecular organization and transcription start points (tsp) for the murine gene (TK) encoding thymidine kinase. The exon/intron structure and sequences present at the splice junctions of the mammalian TK genes have been highly conserved; however, the promoter sequences of these genes have diverged widely. Both the human and Chinese hamster TK promoter regions contain CCAAT and TATA consensus motifs, whereas the mouse promoter has neither element. This difference between species is reflected in that, unlike the hamster and human TK genes, transcription initiates from numerous specific tsp within a 100-bp region in the mouse TK gene. The complex pattern of tsp seen in the endogenous gene was not maintained in transfected cell lines containing TK promoter::beta-globin (HBB) fusions. Transcription from the murine TK:HBB fusion genes initiated from a small number of tsp that were clustered downstream from the ATG in hybrids containing TK coding sequences, and in the HBB 5' UTR in hybrids that did not. Few or no specific tsp were detected from the upstream sites used in the endogenous mouse TK gene.

Thymidine kinase-deficient mutants of Aedes albopictus mosquito cells

Aedes albopictus mosquito cells resistant to the thymidine analog 5-bromodeoxyuridine (BrdU) were obtained using a single-step selection procedure. The resistant cells were characterized with respect to growth in the presence of BrdU, incorporation of [3H]uridine and [3H]thymidine, and thymidine kinase activity in crude extracts. The LC50 for TK-6 cells was 95 micrograms BrdU/ml, and for TK-8 cells was 45 micrograms/ml. Both clones incorporated [3H]uridine at levels corresponding to those in wild-type cells. TK-6 and TK-8 cells did not incorporate [3H]thymidine into acid-precipitable material, nor did they contain measurable thymidine kinase activity. Thymidine kinase activity in crude extracts from wild-type cells had a Km of 2 microM and a Vmax of 10 pmol.min-1.mg-1 protein.

Transcription initiation and temporal expression of thymidine kinase mRNA in Chinese hamster cells

The induction of thymidine kinase mRNA has proved to be a valuable model for understanding regulatory events at the G1/S boundary of the cell cycle (1, 2, 3). As an initial step toward characterizing the regulation of this gene in Chinese hamster cells, I have mapped the transcription start sites for TK mRNA in CHEF/18 cells. Two closely spaced sites of transcription initiation were detected downstream of a nonconsensus TATAA element in the promoter region. Using primer extension analyses, I demonstrated that the transcription initiation sites remained constant while the absolute levels of TK mRNA varied during the cell cycle in synchronized populations of Chinese hamster cells.

Protein binding sites within the human thymidine kinase promoter

DNase I footprint analysis, using total HeLa cell nuclear extract and purified transcription factor Sp1, was carried out to determine the various protein binding sites within the human thymidine kinase promoter. The promoter has two separate CCAAT elements and multiple Sp1-binding sites, as well as at least one undefined protein binding site. Detailed analysis of protein binding to the two CCAAT elements showed that changing the spacing between the two CCAAT elements altered both protein binding to the distal CCAAT element as well as promoter activity. Both CCAAT elements can act as functional transcription elements, but are not oriented for optimal promoter strength in the human tk promoter. Our studies show that a promoter fragment that has been previously shown to be the minimal region to maintain a serum responsive promoter regulation apparently contains only a single Sp1-binding domain and the more distal of the CCAAT elements.

Computer-aided active-site-directed modeling of the herpes simplex virus 1 and human thymidine kinase

Thymidine kinase (TK), which is induced by Herpes Simplex Virus 1 (HSV1), plays a key role in the antiviral activity of guanine derivatives such as aciclovir (ACV). In contrast, ACV shows only low affinity to the corresponding host cell enzyme. In order to define the differences in substrate binding of the two enzymes on molecular level, models for the three-dimensional (3-D) structures of the active sites of HSV1-TK and human TK were developed. The reconstruction of the active sites of HSV1-TK and human TK were developed. The reconstruction of the active sites started from primary and secondary structure analysis of various kinases. The results were validated to homologous enzymes with known 3-D structures. The models predict that both enzymes consist of a central core beta-sheet structure, connected by loops and alpha-helices very similar to the overall structure of other nucleotide binding enzymes. The phosphate binding site is made up of a highly conserved glycine-rich loop at the N-terminus of the proteins and a conserved region at the C-terminus. The thymidine recognition site was found about 100 amino acids downstream from the phosphate binding loop. The differing substrate specificity of human and HSV1-TK can be explained by amino-acid substitutions in the homologous regions. To achieve a better understanding of the structure of the active site and how the thymidine kinase proteins interact with their substrates, the corresponding complexes of thymidine and dihydroxypropoxyguanine (DHPG) with HSV1 and human TK were built. For the docking of the guanine derivative, the X-ray structure of Elongation Factor Tu (EF-Tu), co-crystallized with guanosine diphosphate, was taken as reference. Fitting of thymidine into the active sites was done with respect to similar interactions found in thymidylate kinase. To complement the analysis of the 3-D structures of the two kinases and the substrate enzyme interactions, site-directed mutagenesis of the thymidine recognition site of HSV1-TK has been undertaken, changing Asp162 in the thymidine recognition site into Asn. First investigations reveal that the enzymatic activity of the mutant protein is destroyed.

Purification and characterization of thymidine kinase from regenerating rat liver

Thymidine kinase (EC 2.7.1.21) from regenerating rat liver has been purified 70,000-fold to apparent homogeneity by affinity chromatography. Molecular weight of the native enzyme was found to be about 54,000, as determined by gel filtration. Electrophoresis in polyacrylamide gels containing sodium dodecyl sulfate yielded a single band with a molecular weight of 26,000, suggesting that thymidine kinase is a dimer of very similar or identical subunits. The Michaelis constant for thymidine is 2.2 microM. ATP acts as a sigmoidal substrate with a 'Km' of 0.2 mM. Reaction kinetics and product inhibition studies reveal the enzymatic mechanism to be sequential.

Nucleotide sequence of the Escherichia coli thymidine kinase gene provides evidence for conservation of functional domains and quaternary structure

Using lambda bacteriophage clones from the Kohara Escherichia coli library spanning minutes 25.5 to 28.5 on the E. coli chromosome (strain W3110), two overlapping DNA fragments were identified which were able to confer thymidine kinase (TK) enzyme activity to a TK- strain of E. coli (KY895). This genetic complementation assay was used in concert with subcloning procedures to identify the minimal region (a 900 bp EcoRI-SalI fragment) which contained the E. coli thymidine kinase gene (tdk). The nucleotide sequence of the EcoRI-SalI fragment and a small portion of the adjoining downstream fragment was determined. Computer analysis of the derived sequence indicated the presence of a rightward-reading open reading frame of 615 bp which was capable of encoding a 205-amino-acid polypeptide with a predicted Mr of 23458 daltons. The in vivo transcriptional activity of this locus was confirmed by Northern blot hybridization analysis of RNA isolated from E. coli JM101 or KY895 which detected a 650-nucleotide RNA transcribed from this region. This places the tdk gene at approximately minute 27.35 on the E. coli W3110 chromosome, about 15 kb downstream from the narG locus and approximately 25 kb upstream of the trp operon. Although the predicted Mr of the E. coli TK protein was 23.5 kDa, gel-filtration analyses suggested that, like eukaryotic thymidine kinases, the active form of this enzyme is a multimeric complex.(ABSTRACT TRUNCATED AT 250 WORDS)

Thymidine kinase from Tetrahymena thermophila. Purification and immunological analysis

Thymidine kinase is an enzyme involved in DNA precursor metabolism and DNA replication. The synthesis of this enzyme is highly regulated during the cell cycle and the activity of the enzyme is also regulated by feedback inhibition. Genes encoding thymidine kinase have been extremely useful as selectable markers for introducing DNA into a number of cells. In order to study cell cycle regulation of thymidine kinase, the gene which encodes this enzyme, as well as aspects of DNA replication in the ciliated protozoan Tetrahymena thermophila, we have purified thymidine kinase from Tetrahymena. Two forms of thymidine kinase with native molecular masses of 59 kDa and 80 kDa have been identified and purified 6800- and 4600-fold, respectively. The 59-kDa enzyme, a homodimer of 30-kDa subunits, has been purified to near homogeneity and polyclonal antibodies have been raised against the 30-kDa subunit. Serological studies indicate that the two enzymes are antigenically distinct. The antibody against the Tetrahymena protein cross-reacts with a polypeptide in Chinese hamster ovary (CHO) cell extracts of 26 kDa which corresponds to the reported size of Chinese hamster thymidine kinase protein.

Introns in the 3'-untranslated region can inhibit chimeric CAT and beta-galactosidase gene expression

The expression of a cyc::cat [cytochrome c/chloramphenicol acetyltransferase (CAT)] chimeric gene was stimulated 100-fold by the inclusion of a cyc intron in the 5'-untranslated region. In contrast, a single intron in the 3'-untranslated region was at best only slightly stimulatory, and surprisingly, inhibited expression of cat when an intron was also included in the 5'-untranslated region. This inhibition was independent of the identity of the downstream intron, occurring when either the simian virus 40 (SV40) small t intron or a cyc intron was located downstream from the cat coding region. Analysis of CAT mRNA levels, using a riboprobe spanning the 5' end of the CAT message, revealed that the stimulatory effect of a 5'-noncoding region intron were manifest at both the protein and RNA levels, whereas the inhibitory effects of 3'-noncoding region introns were detectable only at the protein level. The effects of intron position on chimeric gene expression were observed in both primate and rodent cell lines and also when the beta-galactosidase coding region was substituted for that of cat. Therefore, the common placement of an intron in the 3'-noncoding region is not the most beneficial to the expression of cyc chimeric genes. The position of introns within a transcriptional unit is a major factor to be considered when optimizing the efficiency of animal cell expression vectors.

Deletion and hypermethylation of thymidine kinase gene in V79 Chinese hamster cells resistant to bromodeoxyuridine

Previous studies on V79 Chinese hamster cells have shown that bromodeoxyuridine (BrdU) -resistant variants deficient in thymidine kinase (TK) activity arise by a multistep process which is initiated by a random event and progresses gradually during serial culture in the presence of the drug. In order to determine the molecular basis for the loss of TK activity in these cells, the TK gene was isolated from a lambda phage library of genomic V79 DNA, using a fragment of the human TK gene as a probe. One phage isolated contained the entire TK gene in a 15-kb insert, as demonstrated by the ability of the phage DNA to transform Ltk- mouse cells to the TK+ phenotype. Five fragments spanning the entire gene were then subcloned into the plasmid pUC12 for DNA methylation studies. With these probes it was shown by hybridization analysis that the copy number of the TK gene in V79 cells is about four times the copy number in CHO cells and Chinese hamster liver cells. Southern hybridization analysis of the DNA from first-stage variants partially resistant to BrdU indicated that partial resistance was accompanied by deletion of a number of copies of the TK gene in V79 cells. However, the subsequent gradual transition to full BrdU resistance and full loss of TK activity was correlated with a gradual hypermethylation of sites in the 5' region of the TK gene, with no further change in gene copy number.

Steady-state and nuclear run-on analyses of transcription in a temperature-sensitive Chinese hamster cell mutant with a defect in RNA metabolism

We have further characterized a temperature-sensitive mutant of Chinese hamster lung fibroblasts in tissue culture with a defect in RNA metabolism. The mutant phenotype is reflected in transcription in crude extracts or in isolated nuclei, when these are made from cells shifted to the nonpermissive temperature; however, differential heat inactivation between mutant and wild-type extracts cannot be demonstrated with cell-free systems. We tentatively conclude that the mutation may affect initiation of transcription which cannot be observed in our in vitro systems. Partially purified RNA polymerase I, II, and III fractions are indistinguishable from wild type. A temperature shift does not affect transcription by RNA polymerase III measured with intact cells or by nuclear run-on experiments. The nuclear run-on and other experiments suggest that RNA polymerase II-dependent transcription is inhibited before RNA polymerase I-dependent transcription. This conclusion is also supported by Northern analyses of selected mRNAs in nonsynchronized and synchronized cells after a shift to the nonpermissive temperature.

DNA methylation and genetic inactivation at thymidine kinase locus: two different mechanisms for silencing autosomal genes

Patterns of methylation of CpG dinucleotides in the promoter region of the thymidine kinase (TK) gene in wild-type and TK-deficient Chinese hamster cell lines were studied. Whereas wild-type cells were unmethylated, three conventionally derived TK-deficient cell lines were all almost completely methylated in the promoter region. Demethylation at a number of different CpG sites was observed upon selection for reexpression of the TK gene. Of thirteen HhaI (GCGC) or HpaII (CCGG) sites studied, the highest correlation between absence of methylation and at least partial TK activity was obtained at one HhaI site within 20 bp of the putative cap site. Silencing in the three conventionally derived mutants is therefore accompanied by hypermethylation of the promoter-associated CpG-rich island. We contrast this situation with another type of silencing event, in which TK was coordinately inactivated at a high frequency with at least one other linked allele. Methylation of the promoter region of TK was not associated with this event, but two lines of evidence suggested a role for methylation at sites other than in the promoter region of TK.

Enzymes of nucleotide metabolism: the significance of subunit size and polymer size for biological function and regulatory properties

The 72 enzymes in nucleotide metabolism, from all sources, have a distribution of subunit sizes similar to those from other surveys: an average subunit Mr of 47,900, and a median size of 33,300. The same enzyme, from whatever source, usually has the same subunit size (there are exceptions); enzymes having a similar activity (e.g., kinases, deaminases) usually have a similar subunit size. Most simple enzymes in all EC classes (except class 6, ligases/synthetases) have subunit sizes of less than 30,000. Since structural domains defined in proteins tend to be in the Mr range of 5,000 to 30,000, it may be that most simple enzymes are formed as single domains. Multifunctional proteins and ligases have subunits generally much larger than Mr 40,000. Analyses of several well-characterized ligases suggest that they also have two or more distinct catalytic sites, and that ligases therefore are also multifunctional proteins, containing two or more domains. Cooperative kinetics and evidence for allosteric regulation are much more frequently associated with larger enzymes: such complex functions are associated with only 19% of enzymes having a subunit Mr less than or equal to 29,000, and with 86% of all enzymes having a subunit Mr greater than 50,000. In general, larger enzymes have more functions. Only 20% of these enzymes appear to be monomers; the rest are homopolymers and rarely are they heteropolymers. Evidence for the reversible dissociation of homopolymers has been found for 15% of the enzymes. Such changes in quaternary structure are usually mediated by appropriate physiological effectors, and this may serve as a mechanism for their regulation between active and less active forms. There is considerable structural organization of the various pathways: 19 enzymes are found in various multifunctional proteins, and 13 enzymes are found in different types of multienzyme complexes.

42 bp element from LDL receptor gene confers end-product repression by sterols when inserted into viral TK promoter

The LDL receptor, which mediates the cellular uptake of cholesterol, is subject to classic end-product repression when cholesterol accumulates in the cell. We here show that the sensitivity to end-product repression depends upon a 42 bp element in the 5'-flanking region of the human LDL receptor gene. This sequence, designated sterol regulatory element 42 (SRE 42), contains two 16 bp direct repeats that exhibit positive and negative transcriptional activities. Cells transfected with a fusion gene containing SRE 42 inserted into the promoter of the herpes simplex viral TK gene produced abundant mRNA when grown without sterols. When sterols were present, the mRNA was reduced by 57%-95%, depending on the number of copies of SRE in the fusion gene. These transfection data plus DNAase I footprinting experiments suggest a model of end-product repression in which the end product (sterols) opposes the action of a positive transcription factor that binds to a discrete promoter element.

Identification and nucleotide sequence of the thymidine kinase gene of Shope fibroma virus

The thymidine kinase (TK) gene of Shope fibroma virus (SFV), a tumorigenic leporipoxvirus, was localized within the viral genome with degenerate oligonucleotide probes. These probes were constructed to two regions of high sequence conservation between the vaccinia virus TK gene and those of several known eucaryotic cellular TK genes, including human, mouse, hamster, and chicken TK genes. The oligonucleotide probes initially localized the SFV TK gene 50 kilobases (kb) from the right terminus of the 160-kb SFV genome within the 9.5-kb BamHI-HindIII fragment E. Fine-mapping analysis indicated that the TK gene was within a 1.2-kb AvaI-HaeIII fragment, and DNA sequencing of this region revealed an open reading frame capable of encoding a polypeptide of 176 amino acids possessing considerable homology to the TK genes of the vaccinia, variola, and monkeypox orthopoxviruses and also to a variety of cellular TK genes. Homology matrix analysis and homology scores suggest that the SFV TK gene has diverged significantly from its counterpart members in the orthopoxvirus genus. Nevertheless, the presence of conserved upstream open reading frames on the 5' side of all of the poxvirus TK genes indicates a similarity of functional organization between the orthopoxviruses and leporipoxviruses. These data suggest a common ancestral origin for at least some of the unique internal regions of the leporipoxviruses and orthopoxviruses as exemplified by SFV and vaccinia virus, respectively.