Production of Fab fragments and Fab-steroid complexes suitable for crystal growth.
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Antibodies, Monoclonal↗
Biomedical subjects
K R Madden
Publications and source records attributed to K R Madden.
Biochemical and biophysical analyses of recombinant forms of human topoisomerase I.
Amino acid sequence comparisons of human topoisomerase I (Topo I) with seven other cellular Topo I enzymes reveal that the enzyme can be divided into four major domains: the unconserved NH2-terminal domain (24 kDa), the conserved core domain (54 kDa), a poorly conserved linker region (5 kDa), and the highly conserved COOH-terminal domain (8 kDa), which contains the active site tyrosine. To investigate this predicted domain organization, recombinant baculoviruses were engineered to express the 91-kDa full-length enzyme, a 70-kDa NH2-terminally truncated enzyme that is missing the first 174 residues, and a 58-kDa NH2- and COOH-terminally truncated core fragment encompassing residues 175-659. The specific activity of the full-length and Topo70 enzymes are indistinguishable from the native human Topo I purified from HeLa cells. Each protein is inhibited by camptothecin, topotecan, and 9-aminocamptothecin, but not by ATP. Activity is stimulated by Mg2+, Ba2+, Ca2+, Mn2+, spermine, and spermidine. The magnitude of the stimulatory effect of Mg2+ is inversely proportional to the salt concentration. Furthermore, at KCl concentrations of 300 mM or greater, the addition of Mg2+ is inhibitory. The effects of Mg2+ and the polycations spermine and spermidine are partially additive, an indication that the stimulatory mechanisms of the two substances are different. Activity was strongly inhibited or abolished by Ni2+, Zn2+, Cu2+, Cd2+, and Co2+. An examination of the hydrodynamic properties of full-length Topo I, Topo70, and Topo58 demonstrates that the core, linker, and COOH-terminal domains fold into a globular structure, while the NH2-terminal domain is highly extended. A comparison of the circular dichroism spectra of full-length Topo I and Topo70 demonstrates that residues 1-174 (approximately 21 kDa) of Topo I are largely if not completely unfolded. This observation is consistent with the fact that the NH2-terminal domain is dispensable for activity.
Adenosine Triphosphate↗
Preferential binding of human topoisomerase I to superhelical DNA.
Eukaryotic type I DNA topoisomerase provides swivels for removing torsional strain from the DNA helix during transcription and DNA replication. Previously it has been shown that the enzyme is associated with actively transcribed genes and replicating DNA. Using an inactive mutant form of the protein containing phenylalanine instead of tyrosine at position 723, we have investigated the binding properties of the protein as a function of substrate topology. A series of filter binding assays indicated that the protein strongly prefers to bind superhelical over completely relaxed SV40 DNA. The ability of a supercoiled DNA to compete against a relaxed DNA for binding increases as the number of superhelical turns in the DNA increases. Since positively supercoiled DNA is bound with the same preference as negatively supercoiled DNA, we hypothesize that topoisomerase I binds preferentially at the nodes created by the crossing of two duplex helices. The preference for binding superhelical DNA is also exhibited by the conserved core domain (amino acids 175-659) which is missing the active site region located near the C-terminus. These results suggest that this core domain may target the enzyme in vivo to regions of torsionally strained superhelical DNA.
Binding Sites↗
DNA topoisomerase I is involved in both repression and activation of transcription.
Reconstituted transcription reactions containing the seven general transcription factors, in addition to RNA polymerase II, respond poorly to transcriptional activators. Two factors, Dr2 and ACF, necessary for high levels of transcription in response to an activator have been identified. ACF can enhance basal and activated transcription. Dr2 represses basal transcription, but this can be overcome by transcriptional activators or TFIIA. Dr2 is human DNA topoisomerase I. The DNA relaxation activity of topoisomerase I is dispensable for transcriptional repression. The effect of Dr2 is specific for TATA-box-containing promoters and is mediated by the TATA-binding protein.
Amino Acid Sequence↗
Overexpression of human topoisomerase I in baby hamster kidney cells: hypersensitivity of clonal isolates to camptothecin.
The 3645-base pair human topoisomerase I complementary DNA (cDNA) clone isolated by D'Arpa et al. (Proc. Natl. Acad. Sci. USA, 85:2543-2547, 1988) and a mutated version of the cDNA encoding a protein with phenylalanine instead of tyrosine at position 723 have been overexpressed 2- to 5-fold in stably transfected baby hamster kidney cells. The overexpressed proteins are the same size as the topoisomerase I present in Hela cells, indicating that the cDNA clone contains the complete topoisomerase I coding sequence. Some human colon carcinoma cells have increased levels of topoisomerase I and are hypersensitive to the drug camptothecin. The overexpressed wild-type topoisomerase I does not affect the cell growth or morphology of the baby hamster kidney cells, suggesting that elevated levels of topoisomerase I alone are not sufficient to cause cell transformation. However, the overexpressed wild-type protein is active, as shown by the hypersensitivity of clonal cell lines to camptothecin. The mutant form of topoisomerase I is enzymatically inactive by two criteria. First, extracts of Escherichia coli cells carrying the mutant cDNA contain no activity capable of relaxing superhelical DNA under conditions where activity is easily detectable in extracts from cells containing the wild-type cDNA. Second, baby hamster kidney cells stably transfected by the mutant cDNA are no more sensitive to camptothecin than control untransfected cells. These results indicate that tyrosine 723 is essential for enzyme activity and are consistent with predictions based on homology comparisons with the yeast enzymes, that this is the active-site tyrosine in the human topoisomerase I.
Animals↗
Use of site-specific recombination to regenerate selectable markers.
A method which allows the repeated use of a single selectable marker in DNA transformations was demonstrated. This marker regeneration method employed portions of the Saccharomyces cerevisiae 2 microns circle plasmid: the inverted repeat sequences (FRTs), and the FLP gene whose product, a site-specific recombinase, catalyzes recombination events between FRTs. When FRTs were oriented as direct repeats and integrated into the genome of the yeast Pichia pastoris, FLP-mediated recombination resulted in the efficient and precise deletion of DNA located between the repeats. In the example described, the S. cerevisiae ARG4 gene, placed between a set of FRTs and integrated into Pichia in a prior transformation, was deleted by FLP, thereby regenerating an arginine-requiring phenotype in the P. pastoris strain.
Blotting, Southern↗
Functional characterization of the two alcohol oxidase genes from the yeast Pichia pastoris.
In Pichia pastoris, alcohol oxidase (AOX) is the first enzyme in the methanol utilization pathway and is encoded by two genes, AOX1 and AOX2. The DNA and predicted amino acid sequences of the protein-coding portions of the genes are closely homologous, whereas flanking sequences share no homology. The functional roles of AOX1 and AOX2 in the metabolism of methanol were examined. Studies of strains with disrupted AOX genes revealed that AOX1 was the major source of methanol-oxidizing activity in methanol-grown P. pastoris. The results of two types of experiments each suggested that the difference in AOX activity contributed by the two genes was a consequence of sequences located 5' of the protein-coding portions of the genes. First, the coding portion of AOX2 was able to functionally substitute for that of AOX1 when placed under the control of AOX1 regulatory sequences. Second, when labeled oligonucleotide probes specific for the 5' nontranslated region of each gene were used, it was apparent that the steady-state level of AOX1 mRNA was much higher than that of AOX2. Except for the difference in the amount of mRNA present, the two genes appeared to be regulated in the same manner. A physiological reason for the existence of AOX2 was sought but was not apparent.
Alcohol Oxidoreductases↗
Pichia pastoris as a host system for transformations.
We developed a methylotrophic yeast, Pichia pastoris, as a host for DNA transformations. The system is based on an auxotrophic mutant host of P. pastoris which is defective in histidinol dehydrogenase. As a selectable marker, we isolated and characterized the P. pastoris HIS4 gene. Plasmid vectors which contained either the P. pastoris or the Saccharomyces cerevisiae HIS4 gene transformed the P. pastoris mutant host. DNA transfer was accomplished by a modified version of the spheroplast generation (CaCl2-polyethylene glycol)-fusion procedure developed for S. cerevisiae. In addition, we report the isolation and characterization of P. pastoris DNA fragments with autonomous replication sequence activity. Two fragments, PARS1 and PARS2, when present on plasmids increased transformation frequencies to 10(5)/micrograms and maintained the plasmids as autonomous elements in P. pastoris cells.
Alcohol Oxidoreductases↗