P53-responsive genes and the potential for cancer diagnostics and therapeutics development.

P53 protein regulates cell responses to DNA damage to keep genomic stability by transactivation and trans-repression of its downstream target genes. P53 protein also has activators, inactivators, or co-factors via interaction with other proteins. Both the p53-regulated genes and interacted proteins form a huge network. As tumors usually escape from proliferating controls by means of accumulation of genetic alterations, p53 is one of the most important tumor suppressor genes that can be targeted for diagnosis, prognosis, and therapeutic intervention. Reviewing the p53-network is of great importance. In this review, we are focusing on cancer-related p53 downstream-regulated genes. Various methods dealing with the discovery of p53-regulated genes by the detection of gene expression have been applied. Recently high throughput functional genomics methods, such as DNA microarray, serial analysis of gene expression (SAGE), differential display, and protein two-dimensional gel electrophoresis, have provided a wealth of information on the dynamics of cell context responses. Hundreds of genes have been discovered whose transcriptions are regulated by p53 protein. They were grouped, based on their functions, into sub-classes including cell-cycle regulation, DNA repair, angiogenesis, metastasis, and multidrug resistance. P53 plays a pivotal role in keeping genomic stability and tumor suppression. The deeper we investigate the cell responses as mediated by p53, the more complex p53-network becomes. However, understanding p53-network, offers great opportunities to develop more sensitive and accurate diagnostic/prognostic tools, as well as more efficient therapies for cancer.

Modulation of the Escherichia coli tryptophan repressor protein by engineered peptides.

We have used the E. coli tryptophan repressor (TrpR) as a model protein for modulation by engineered peptides both in vivo and in vitro. The tryptophan operator promoter-lacZ reporter system was used to investigate the in vivo ability of several synthetic peptides to modulate TrpR function. GMSA (gel mobility shift analysis) was used to study the in vitro ability of the peptides to modulate binding of the TrpR protein to the operator DNA. Peptides WRW, DRW, DW, RW enhanced TrpR binding to the operator in vivo at 100 microM concentrations. The same peptides enhanced TrpR binding to the operator in vitro at 1 mM concentrations. The peptide RRW reduced TrpR binding to the tryptophan operator both in vivo and in vitro. Thus the peptide RRW acted more as an inducer than corepressor. The peptide WR could neither enhance nor impede binding between TrpR and the operator in vivo or in vitro, suggesting that the presence of a carboxyl tryptophan residue may be necessary for binding to the TrpR protein. Thin layer chromatography was used to ensure that the peptides had not been subject to proteolysis during the in vitro gel mobility shift assays.

Isolation of cmr, a novel Escherichia coli chloramphenicol resistance gene encoding a putative efflux pump.

A novel gene designated cmr, which mapped to 18.8 min of the Escherichia coli K-12 genome, was shown to mediate resistance to chloramphenicol when it was expressed from a multicopy vector. The accumulation of chloramphenicol was significantly less in cells overexpressing cmr than in control cells harboring the vector without insert. After the addition of a proton motive force blocker, the level of accumulation of chloramphenicol in the resistant cells rapidly approached the levels found in sensitive cells carrying only the chromosomal cmr. Northern (RNA) blot analyses revealed that the cmr gene is expressed as a 1.3-kb transcript. This size corresponds very well with a predicted size of 1,293 nucleotides (nt) based on the mapping of the transcription initiation site to a G residue 24 nt upstream of the start codon and the presence of a putative rho-independent terminator sequence ending 36 nt downstream of the 1,233-nt open reading frame encoding the putative Cmr protein. The 411-residue-long derived amino acid sequence contains 12 putative transmembrane segments and displays significant sequence similarities to several known drug resistance protein sequences of the major facilitator family. We provide evidence strongly suggesting that the resistance mediated by Cmr involves active exclusion of chloramphenicol.

In vivo interaction between mutated tryptophan repressors of Escherichia coli.

By expressing a mutant trpR gene in an Escherichia coli strain that is trpR and has beta-galactosidase activity fused to the trp promoter/operator, thus putting the beta-galactosidase activity under the control of the Trp repressor, we can determine quantitatively the relative repression activity of such mutant(s). We used this technique to analyse the biological consequences of substituting certain amino acid residues in only one of the two corepressor binding pockets. By combining two compatible plasmids in this strain, one expressing the mutant T44M and the other expressing only one substitution at a time at position 85, we analysed the repression activity of the resulting interactions in vivo. This approach allowed us to engineer active dimer repressors made of two inactive or partially active monomers. Amino acid substitutions at position 85 with a positive or with an indole ring (W) appeared to complement T44M, which amino acids with a negative charge did not. Only L substitution at position 85 appeared to restore activity among the hydrophobic amino acids tested. Similar to the wild-type repressor activity, the successful mutant-mutant interactions were L-tryptophan dependent. In vivo regulation by three known L-tryptophan analogues demonstrated the same trend of regulation among the wild-type repressors and the active mutant-mutant combinations.

Biotechnology domain.

Biotechnology and the use of biologically based agents for the betterment of mankind is an active field which is founded on the interaction between many basic sciences. This is achieved in coordination with engineering and technology for scaling up purposes. The application of modern recombinant DNA technology gave momentum and new horizons to the field of biotechnology both in the academic setting and in industry. The applications of biotechnology are being used in many fields including agriculture, medicine, industry, marine science and the environment. The final products of biotechnological applications are diverse. In the medical applications of biotechnology, for example, the field has been evolving in such a way that the final product could be a small molecule (e.g. drug/antibiotic) that can be developed based on genetic information by drug design or drug screening using a cloned and expressed target protein.

Retrospective molecular detection of Transthyretin Met 111 mutation in a Danish kindred with familial amyloid cardiomyopathy, using DNA from formalin-fixed and paraffin-embedded tissues.

Severe familial amyloid cardiomyopathy (FAC) in a Danish kindred is associated with a specific mutation (Met for Leu 111) in the transthyretin (TTR) gene. The mutation causes the loss of a DdeI restriction site in the gene, allowing molecular diagnostic studies. We studied formalin-fixed, paraffin-embedded tissues, up to 39 years old, from 29 family members of this kindred. DNA was partially purified from deparaffinized tissue sections and a DNA sequence of the TTR gene flanking the mutation site was amplified by the polymerase chain reaction (PCR), followed by restriction enzyme analysis. Amplified DNA was obtained from tissues representing 23 of the 29 persons. Ten out of the 23 family members were found to carry the TTR Met 111 mutation, whereas 13 were not affected. The results were consistent with known clinical data and with corresponding serum TTR examinations. This retrospective study shows that archival tissues can be used to confirm the diagnosis and disease pattern in members of families affected by hereditary diseases.

Intragenic complementation between Escherichia coli trp repressors with different defects in the tryptophan-binding pocket.

Site-directed mutagenesis of the trpR gene (encoding the trp repressor, TrpR) was used to replace Gly85 with tryptophan (Trp or W), in order to place Trp near its normal location in the L-tryptophan(L-W)-binding pocket. The resulting mutant protein (G85W) exhibits weak, but significant repressor activity in vivo that is independent of the presence of L-W in the media. This mutant negatively complements the chromosomal wild type (wt), but does not negatively complement either the wt or the super-repressor, E49K, when any of these alleles is expressed on a multicopy plasmid. Activity of the mutant repressor, G85W, when produced in vivo together with T44M, approaches that of the wt repressor. This result presumably reflects complementation between the two mutant polypeptides. Similar results are obtained when G85R or G85K are combined with T44M in vivo, but not when G85W is replaced by G85E. The level of repression is dependent on the presence of L-W in the media. The TrpR with two mutations altering both Gly85 (G85W, G85R, G85E or G85K) and Thr44 (T44M) has no repressor activity. These results suggest a type of site-specific intragenic complementation where only certain alterations at Gly85 complement T44M. In this study, a positive charge or an indole ring appears to be required for the observed intragenic complementation.

Molecular diagnosis of the transthyretin (TTR) Met111 mutation in familial amyloid cardiomyopathy of Danish origin.

Familial amyloid cardiomyopathy in a Danish kindred is associated with a specific mutation (Met for Leu111) in the transthyretin (TTR) gene, causing the loss of a recognition site for the restriction enzyme DdeI in the gene. We describe a diagnostic test for the molecular detection of this mutation. A sequence of the TTR gene containing the mutation was amplified by the polymerase chain reaction from isolated genomic DNA of two affected patients and several controls. DdeI digestion of the amplified DNA from the patients revealed 3 bands by gel-electrophoresis, whereas amplified DNA of the controls showed only 2 bands, consistent with complete digestion. Thus, the assumed heterozygous TTR Met111 mutation was confirmed in the affected patients.

A genetic analysis of an alpha-amylase super-secretor in yeast; implications for the regulatory pathway.

Extracellular glucoamylase activity was increased by a gene, which is present in super-secretor, but absent in low-secretor, strains of the yeast Saccharomyces cerevisiae. Genetic data indicated that this super-secretor gene is linked to the STA3 structural gene for glucoamylase. This gene appears to act specifically since it increased the secretion of glucoamylase but not of other secreted enzymes like acid phosphatase and invertase.

Initiation of rrn transcription in chloroplasts of Euglena gracilis bacillaris.

The site of initiation of chloroplast rRNA synthesis was determined by S1-mapping and by sequencing primary rRNA transcripts specifically labeled at their 5'-end. Transcription initiates at a single site 53 nucleotides upstream of the 5'-end of the mature 16S rRNA under all growth conditions examined. The initiation site is within a DNA sequence that is highly homologous to and probably derived from a tRNA gene-region located elsewhere in the chloroplast genome. A nearly identical sequence (102 of 103 nucleotides) is present near the replication origin. The near identity of the two sequences suggests a common mode for control of transcription of the rRNA genes and initiation of chloroplast DNA replication. The related sequence in the tRNA gene-region does not appear to serve as a transcript initiation site.

A multisite-directed mutagenesis using T7 DNA polymerase: application for reconstructing a mammalian gene.

A method to introduce multiple mutations and to reconstruct genes, using a single oligodeoxyribonucleotide and DNA polymerase with high processivity, such as modified T7 DNA polymerase [Tabor and Richardson, Proc. Natl. Acad. Sci. USA 84 (1987a) 4767-4771], is described. A eukaryotic cDNA, coding for porcine growth hormone (pGH), was reconstructed in this study to delete 75 bp and to introduce a G----A transition. The deletion removes 75 bp and brings an ATG just upstream from the codon for the first amino acid in the mature protein. Moreover, the G----A substitution creates a new PvuII restriction site to facilitate further manipulation of the gene. Maximum mutation frequency with this multisite-directed mutagenesis is reached within 15 min with an efficiency approaching 50%, when using the modified T7 DNA polymerase. No multisite-directed mutants were obtained when T4 DNA polymerase or Klenow (large) fragment of DNA polymerase I were used. The described method is also applicable to simple single site-directed mutations as well as to more complex gene reconstruction strategies.

Influence of gonadotropin-releasing hormone pulse amplitude, frequency, and treatment duration on the regulation of luteinizing hormone (LH) subunit messenger ribonucleic acids and LH secretion.

The effects of GnRH pulse amplitude, frequency, and treatment duration on pituitary alpha and LH beta subunit mRNA concentrations were examined in castrate-testosterone replaced male rats. Experimental groups received iv GnRH pulses (5, 25, or 125 ng) at 7.5-, 30-, or 120-min intervals for 8, 24, or 48 h. Saline pulses were given to control rats. Acute LH secretion was measured in blood drawn before and 20 min after the last GnRH pulse. In saline controls, alpha and LH beta mRNAs (150 +/- 14, 23 +/- 2 pg cDNA bound/100 micrograms pituitary DNA) fell to 129 +/- 14 and 18 +/- 2, respectively, after 48 h. In animals receiving GnRH pulses (7.5-min intervals), the 125-ng dose stimulated a slight increase (P less than 0.01) in alpha mRNA levels after 8 and 24 h and both LH subunit mRNAs were increased by the 25- and 125-ng doses after 48 h. The 30-min pulse interval injections (25- and 125-ng doses) increased LH beta mRNA levels after 8 h, but alpha mRNAs were not elevated until after 24 h. Maximum (3-fold) increases in alpha and LH beta mRNAs were seen in rats receiving 25-ng pulses every 30 min for 48 h. Using 120-min pulses, LH subunit mRNAs were not increased by any GnRH dose through 48 h. Acute LH release was not seen in rats receiving 5 ng GnRH pulses at any pulse interval.(ABSTRACT TRUNCATED AT 250 WORDS)

LH subunit mRNA concentrations during LH surge in ovariectomized estradiol-replaced rats.

In cycling rats, pituitary concentrations of luteinizing hormone (LH) beta-subunit mRNA increase two- to threefold before the afternoon proestrus LH surge without a corresponding increase in alpha-subunit mRNA. Estradiol (E2) treatment is known to allow expression of daily LH surges in ovariectomized (OVX) rats, and the timing, magnitude, and duration of LH secretion is similar to the LH surge on proestrus. The present study was conducted to examine whether the regulation of LH subunit mRNAs during the LH surge in OVX-E2-treated rats is similar to that present on proestrus. Female Holtzman rats were OVX and Silastic implants containing E2 were inserted subcutaneously under ether anesthesia. Some animals received bromocriptine (0.6 mg sc, twice/day beginning 1 h before surgery). On the 2nd day after surgery, groups of animals (n = 4-10/group) were decapitated at intervals between 1000 and 2100. LH and prolactin (PRL) levels were measured in trunk blood. LH subunit mRNA concentrations in the pituitaries were measured by dot-blot hybridization assay. In OVX-E2 rats the LH surge occurred at 1830 and was accompanied by a selective twofold increase in alpha-subunit mRNA (from 266 +/- 18 to 459 +/- 61 pg cDNA bound/100 micrograms pituitary DNA) and maximum values were present at 1730. LH beta-subunit mRNA (m = 29 +/- 1 pg cDNA bound/100 micrograms pituitary DNA) was unchanged throughout the day. Bromocriptine treatment resulted in the suppression of serum PRL (m = 23 +/- 2 ng/ml) and the LH surge was delayed by 1-1.5 h and somewhat blunted.(ABSTRACT TRUNCATED AT 250 WORDS)

Eliminated sequences with different copy numbers clustered in the micronuclear genome of Tetrahymena thermophila.

As the ciliated protozoan Tetrahymena thermophila develops a new macronucleus (MAC) from products of its micronucleus (MIC), several repetitive sequences are eliminated from the MAC genome. Four MIC DNA clones containing repetitive sequences that are eliminated from the MAC were obtained. One clone contains a representative from each of three families of eliminated sequences. One, present in 200-300 copies in the MIC, is almost completely eliminated from the MAC. A second, present in approximately 50 copies in the MIC, is scattered throughout the genome, although up to half of the family members examined could be localized to chromosome 2. Approximately one tenth of the members of this less repetitive family persist in the MAC while the rest are eliminated. The third type of eliminated sequence has three to four members, all of which are eliminated from the MAC. Three of the members are located on three of the five MIC chromosomes, and one could not be mapped. This sequence is clustered with the other two families of sequences in at least three of the four sites. All three types of eliminated sequences are found in similar arrangements in the MIC of several different inbred strains of T. thermophila.

Sequence and evolution of the regions between thr rrn operons in the chloroplast genome of Euglena gracilis bacillaris.

The rRNA genes are arranged in three sequential operons preceded by a fourth partial operon. Part or all of a 1462 nucleotide sequence extending from within the 3'-end of the 23S rRNA gene, across the 5S rRNA gene and a presumptive transcription terminator, to within the first structural gene (for 16S rRNA) of the rrn operon was determined for each region between operons. Homologies of the 3'-end of the 23S rRNA gene with the 4.5S rRNA genes of higher plant chloroplasts, and of the 5S rRNA gene with other 5S rRNA genes were examined. The region preceding the 16S rRNA gene, which is expected to contain sites for initiation and regulation of rrn transcription, includes a 305 base-pair sequence with substantial homology with structural genes elsewhere in the chloroplast genome. The homologies suggest that this portion of the leader evolved from copies of parts of the structural genes which had been inserted before the 16S rRNA genes. Thus the chloroplast rrn leader may provide a unique opportunity to study how a regulatory sequence evolved from well-defined structural genes.