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E B Kmiec

Publications and source records attributed to E B Kmiec.

At least 37 records · Page 2Linked to original sources
PubMed1998

The human REC2/RAD51B gene acts as a DNA damage sensor by inducing G1 delay and hypersensitivity to ultraviolet irradiation.

HsRec2/Rad51B is a 350-amino acid protein with a molecular mass of 38,300 Da that appears to be involved in cell cycle regulation and UV-induced apoptosis. The mouse and human genes were isolated based on their homology to a recombinational repair gene from Ustilago maydis and contain functional domains to hRAD51 and hLIM 15 (M. C. Rice et al., Proc. Natl. Acad. Sci. USA, 94: 7417-7422, 1997). Here, we report the results of studies on the behavior of CHO cells containing a plasmid encoding a wild-type hsRec2/Rad51B, a full-length protein with a single mutation at residue 163, which lies in the putative src site, and a truncated version of hsRec2/Rad51B, containing only the first 100 amino acids at the NH2 terminus. Using fluorescence-activated cell sorting analysis to follow the progression of cells through the cell cycle, we find that stable transfectants constitutively overexpressing the wild-type human Rec2/Rad51B protein exhibit a G1 delay. In addition, when irradiated with UV at a dose of 15 J/m2, CHO cells transfected with the various hREC2/RAD51B vectors exhibited different responses. Cells expressing the wild-type human Rec2/Rad51B underwent apoptosis, with the greatest cell death occurring 24 h after irradiation. The control cells, which contained an empty vector, and the cells expressing truncated hsRec2/Rad51B or the full-length Rec2 with a mutation at residue 163 did not. In summary, these findings of cell cycle slowing and UV-induced apoptosis in CHO cells constitutively expressing the human Rec2/Rad51B protein suggest that hsRec2/Rad51B plays a role in a DNA damage surveillance pathway.

Animals↗
PubMed1998

Binding characteristics of Ustilago maydis topoisomerase I to DNA containing secondary structures.

The binding affinity of purified native Ustilago maydis topoisomerase I enzyme for radiolabeled DNA substrates with various secondary structures was determined by gel shift and equilibrium binding analysis. Topoisomerase I exhibited cooperativity in binding to DNA regardless of the substrate structure. Further analysis demonstrated that cruciform DNA has two populations of binding sites for topoisomerase I while the other substrates (single-stranded DNA, DNA molecules containing six or one mismatched base pairs, hairpin, and fully homologous duplex DNA) have a single population of binding sites. The affinity of topoisomerase I for cruciform was found to be an order of magnitude higher affinity than for any of the other substrates. The high affinity of topoisomerase I for cruciform and specificity of topoisomerase I-cruciform structure interaction were confirmed by competition experiments. These studies demonstrate the high affinity of topoisomerase I for cruciform structure.

Base Sequence↗
PubMed1998

RecA-mediated joint molecule formation between O-methylated RNA/DNA hairpins and single-stranded targets.

Chimeric oligonucleotides consisting of one DNA strand paired with an O-methylated RNA strand interrupted by six DNA residues have been used in gene targeting experiments. Here we demonstrate that these hairpins can form a heteroduplex (or joint molecule) with single-stranded DNA targets in a reaction mediated by the E. coli RecA protein. One end of the double hairpin may unwind to form a 14-base-RecA filament which initiates the reaction. Chimeric oligonucleotides containing only O-methylated RNA residues on one strand or truncated hairpins lacking this 14-base segment did not participate in RecA-driven heteroduplex formation under these reaction conditions. The results presented here represent a first step in studying one facet of a strategy which uses O-methylated RNA residues as participants in homologous pairing events.

Base Sequence↗
PubMed1998

Targeted gene correction: a new strategy for molecular medicine.

Advances, over the past 20 years, in the genetic manipulation of mammalian cells form the scientific basis of gene therapy. A number of strategies are presently being used to replace or augment a dysfunctional gene with a correct copy of itself. Now, a novel approach to correct the dysfunctional gene in the chromosome is being developed. Data obtained from biochemical, cell-based and animal studies suggest that the era of gene repair is dawning. It is now conceivable that inherited and non-inherited disorders might be treated with a small molecular tool designed to fix the mutation directly. Here, the conceptualization of the technique and its barriers to success are discussed.

Animals↗
PubMed1997

A novel link between REC2, a DNA recombinase, the retinoblastoma protein, and apoptosis.

The REC2 recombinase is essential for recombinational repair following DNA damage as well as for successful meiosis and gene targeting in the corn smut Ustilago maydis. Here we report that overexpression of REC2 induced apoptotic cell death in human HuH-7, Hep G2, and Hep 3B hepatoma cells. Apoptosis was related to recombinase activity and was significantly increased by inhibition of retinoblastoma (Rb) expression with transforming growth factor-beta1. REC2-induced apoptosis was associated with a significantly reduced percentage of cells in the G1 phase of the cell cycle and a significant reduction in G2/M only in the Rb(-/-) Hep 3B cells. Overexpression of REC2 resulted in increased abundance of the hyperphosphorylated form of Rb. However, by immunoprecipitation REC2 was associated primarily with hypophosphorylated Rb, suggesting that REC2 may be involved in modulating the phosphorylation state of Rb. The A and B pocket domains with the spacer amino acid sequence and the carboxyl-terminal region of Rb were required for maximal binding to REC2. Overexpression of Rb significantly inhibited REC2-induced apoptosis even in the presence of transforming growth factor-beta1. Taken together, these data suggest a novel interaction of Rb with the recombinase REC2 and a role for this complex in bridging DNA recombination and apoptosis.

Apoptosis↗
PubMed1997

Isolation of human and mouse genes based on homology to REC2, a recombinational repair gene from the fungus Ustilago maydis.

A human and a mouse gene have been isolated based on homology to a recombinational repair gene from the corn smut Ustilago maydis. The new human (h) gene, termed hREC2, bears striking resemblance to several others, including hRAD51 and hLIM15. hREC2 is located on human chromosome 14 at q23-24. The overall amino acid sequence reveals characteristic elements of a RECA-like gene yet harbors an src-like phosphorylation site curiously absent from hRAD51 and hLIM15. Unlike these two relatives, hREC2 is expressed in a wide range of tissues including lung, liver, placenta, pancreas, leukocytes, colon, small intestine, brain, and heart, as well as thymus, prostate, spleen, and uterus. Of greatest interest is that hREC2 is undetectable by reverse transcription-coupled PCR in tissue culture unless the cells are treated by ionizing radiation.

Amino Acid Sequence↗
PubMed1997

The cloning and overexpression of a cruciform binding protein from Ustilago maydis.

The structural gene HMP1 encoding a cruciform DNA binding protein from Ustilago maydis has been cloned. Gene isolation was enabled by a polymerase chain reaction procedure using primers designed from amino acid sequence obtained from the purified protein. DNA sequence determination has revealed that the gene encodes a protein containing 98 amino acids with a calculated molecular weight of 10151. Comparison of the cDNA and genomic sequences indicated the presence of a single intron in the 5' coding region of the gene. The gene was over-expressed as a translational fusion with a hexahistidine leader sequence enabling affinity purification of the protein on an immobilized metal matrix. Protein isolated after over-expression exhibited cruciform binding activity, conforming earlier purified native protein results. Sequence analysis indicated that no HMG box was present and very little homology to other known cruciform binding proteins was found. It is plausible that HMP1 represents a novel class of proteins that recognize such secondary structures.

Amino Acid Sequence↗
PubMed1997

Targeted nucleotide exchange in the alkaline phosphatase gene of HuH-7 cells mediated by a chimeric RNA/DNA oligonucleotide.

Although a variety of methods has been devised for modification of hepatic genes, none has been effective for long-term correction of genetic disorders. In this study, we employed a recently described novel experimental strategy for site-directed nucleotide exchange in genomic DNA of HuH-7 human hepatoma cells. A chimeric 2'-O-methylated-RNA/DNA oligonucleotide containing sequences complementary to 25 bases of the alkaline phosphatase gene was constructed as a duplex containing a G to A substitution at nucleotide 935. Cells were transfected with oligonucleotides for 48 hours, then harvested for DNA isolation and polymerase chain reaction (PCR) amplification of exon 6 of the alkaline phosphatase gene. Colony lifts were hybridized to 17 mer 32P-labeled oligonucleotide probes specific to the 935-G and 935-A sequences. Hybridizing colonies were grown, plasmid DNA isolated, and sequenced. Transfection efficiency was determined at 24 hours by nuclear uptake of fluorescein-12-dUTP-labeled chimeric oligonucleotides. Colonies hybridizing with the 935-A probe were identified only from cells transfected with the specific chimeric oligonucleotide; and there was no evidence of cross-hybridization. Conversion of G to A at nucleotide 935 occurred at an overall frequency of up to 11.9% and when corrected for transfection efficiency approached 43%. No other alterations were detected in the sequence of exon 6 with the targeted nucleotide exchange. These results show that a single base pair alteration in the alkaline phosphatase gene of HuH-7 cells can be introduced at a relatively high frequency following transfection with chimeric RNA/DNA oligonucleotides. This technique offers a novel and potentially powerful strategy for site-directed hepatic gene alteration without the use of viral-based vectors.

Alkaline Phosphatase↗
PubMed1997

Interaction between Ustilago maydis REC2 and RAD51 genes in DNA repair and mitotic recombination.

A gene encoding a Ustilago maydis Rad51 orthologue has been isolated, rad51-1, a mutant constructed by disrupting the gene, was as sensitive to killing by ultraviolet light and gamma radiation as the rec2-1 mutant and slightly more sensitive to killing by methyl methanesulfonate. There was no suppression of killing by ultraviolet light when a rec2-1 strain was transformed with a multicopy plasmid containing RAD51, nor was there suppression when rad51-1 was transformed with a multicopy plasmid containing REC2. Recombination proficiency as measured by a gap repair assay was diminished in both rec2-1 and rad51-1 strains. In rec2-1 the frequency of recombination was decreased, but the spectrum of events was similar to that observed in wild type, while in rad51-1 the frequency as well as the spectrum of recombination events were different. Studies with the rec2-1 rad51-1 double mutant indicated that there was epistasis in the action of REC2 and RAD51 in certain repair and recombination functions, but some measure of independent action in other functions.

Amino Acid Sequence↗
PubMed1996

Correction of the mutation responsible for sickle cell anemia by an RNA-DNA oligonucleotide.

A chimeric oligonucleotide composed of DNA and modified RNA residues was used to direct correction of the mutation in the hemoglobin betaS allele. After introduction of the chimeric molecule into lymphoblastoid cells homozygous for the betaS mutation, there was a detectable level of gene conversion of the mutant allele to the normal sequence. The efficient and specific conversion directed by chimeric molecules may hold promise as a therapeutic method for the treatment of genetic diseases.

Alleles↗
PubMed1996

RNA facilitates RecA-mediated DNA pairing and strand transfer between molecules bearing limited regions of homology.

The RecA protein of Escherichia coli catalyzes homologous pairing and strand exchange between a wide range of molecules showing nucleotide sequence complementarity, including a linear duplex and a single-stranded DNA molecule. We demonstrate that RecA can promote formation of joint molecules when the duplex contains an RNA/DNA hairpin and a single-stranded circle serves as the pairing partner. A chimeric RNA/DNA hairpin can be used to form stable joint molecules with as little as 15 bases of shared homology as long as the RNA stretch contains complementarity to the circle. The joint molecule bears some resemblance to a triple helical structure composed of RNA residues surrounded by two DNA strands which are in a parallel orientation. Evidence is presented that supports the notion that short stretches of RNA can be used in homologous pairing reactions at lengths below that required for DNA-DNA heteroduplex formation.

Bacteriophage M13↗
PubMed1996

Targeted gene correction of episomal DNA in mammalian cells mediated by a chimeric RNA.DNA oligonucleotide.

An experimental strategy to facilitate correction of single-base mutations of episomal targets in mammalian cells has been developed. The method utilizes a chimeric oligonucleotide composed of a contiguous stretch of RNA and DNA residues in a duplex conformation with double hairpin caps on the ends. The RNA/DNA sequence is designed to align with the sequence of the mutant locus and to contain the desired nucleotide change. Activity of the chimeric molecule in targeted correction was tested in a model system in which the aim was to correct a point mutation in the gene encoding the human liver/bone/kidney alkaline phosphatase. When the chimeric molecule was introduced into cells containing the mutant gene on an extrachromosomal plasmid, correction of the point mutation was accomplished with a frequency approaching 30%. These results extend the usefulness of the oligonucleotide-based gene targeting approaches by increasing specific targeting frequency. This strategy should enable the design of antiviral agents.

Alkaline Phosphatase↗
PubMed1996

Genomic targeting and genetic conversion in cancer therapy.

A number of cellular transformations are due, in large part, to a single base mutation that alters the function of the expressed protein. Similarly, alterations in the DNA sequence of a gene involved in cell proliferation can have a significant effect on the viability of particular cells, Thus, the capacity to modulate the base sequence of such a gene would be a useful tool for cancer therapeutics. We have developed an experimental strategy that centers around site-specific DNA base mutation or correction using a unique chimeric oligonucleotide. This chimeric molecule has demonstrated higher recombinogenic activities than identical oligonucleotides containing only DNA residues, both in vitro and in vivo. The chimeric molecule is designed to hybridize to a target site within the genome and induce a single base mismatch at the residue targeted for mutation. The DNA structure created at this site is recognized by the host cell's repair system which mediates the correction reaction. The bcr-abl fusion gene, the product of a translocation between human chromosomes 9 and 22, and the cause of chronic myelogenous leukemia (CML) can be targeted for gene correction. This fusion gene is a good choice because (1) it is a unique target in CML; (2) it is a single copy target; (3) the DNA sequence of the fusion gene is unique. The goal of such experiments is to knock-out the fusion gene by changing a glutamine or lysine codon into a stop codon through a chimeric directed DNA repair system.

Apoptosis↗
PubMed1995

Assembly of nucleosomal DNA in a cell-free extract from wild-type and top1- strains of Ustilago maydis.

An in vitro nucleosome assembly system has been established from cell-free extracts of the fungus Ustilago maydis. The extract catalyzed DNA supercoiling in the absence of exogenously added co-factors such as ATP and MgCl2 and was inhibited by moderate concentrations (200 mM) of KCl or NaCl. DNA supercoiling occurs via the formation of nucleosomes. Similar extracts, displaying the same activity, were prepared from Saccharomyces cerevisiae and Candida albicans, suggesting that the extract preparation protocol may be useful for many lower eukaryotic systems. An extract prepared from a strain of U. maydis lacking topoisomerase I failed to catalyze nucleosome assembly, clearly implicating this enzyme in this process. Addition of purified topoisomerase I, and, to a lesser extent, topoisomerase II, to the top1- extract regenerated the supercoiling activity. Our results provide a method for preparing assembly extracts from organisms, that are particularly amenable to genetic manipulation.

Candida albicans↗
PubMed1994

The topoisomerase I gene from Ustilago maydis: sequence, disruption and mutant phenotype.

The Ustilago maydis genomic TOP1 gene encoding DNA topoisomerase I was cloned by amplifying a gene fragment using the polymerase chain reaction, and using this fragment to search a genomic DNA library by hybridization. The predicted peptide sequence exhibited 30-40% identity to other eukaryotic TOP1 genes, yet differed in several features. First, an unusually long acidic region was identified near the amino terminus (28/29 residues are acidic), which resembles other nucleolar peptide motifs. Second, an atypical carboxy-terminal 'tail', absent in other TOP1 genes, followed the active site tyrosine residue. A top1 gene disruption mutant was constructed by replacing the genomic TOP1 gene, with a top1::HygR null allele. This mutant lost the abundant topoisomerase I activity evident in wild-type U.maydis, and displayed a subtle coloration phenotype evident during cell senescence.

Amino Acid Sequence↗
PubMed1994

Genetic recombination of nucleosomal templates is mediated by transcription.

An in vitro system has been developed to examine the influence of transcription on genetic rearrangement. Using a homologous pairing assay, the transfer of one strand of a nucleosomal template onto a recipient DNA molecule was monitored as a function of RNA polymerase activity. Transcriptionally inactive nucleosomal DNA was refractory to homologous pairing. Homologous pairing was catalyzed, however, by the eukaryotic recombinase, rec1, when the nucleosomal template was being transcribed. The reaction was found to be dependent on the presence of rec1, RNA polymerase, NTPs and RNA synthesis. Heteroduplex formation between a short DNA duplex fragment assembled into a nucleosome and a single-stranded circle relied also on the presence of sequence homology between the duplex and the circle. The results of this study lend support to the notion that transcriptionally active regions within a chromosome are more apt to serve as sites of genetic recombination.

Cell-Free System↗
PubMed1994

DNA cruciforms facilitate in vitro strand transfer on nucleosomal templates.

A single, phased nucleosome assembled on a 240 bp DNA duplex molecule blocked Escherichia coli RecA protein-promoted strand transfer of the complementary strand of the duplex onto a homologous single-stranded circle. However, when a four-armed cruciform structure was coupled to either end of the duplex the barrier to strand transfer was overcome and joint molecules were efficiently formed. Micrococcal nuclease digestion indicated that the nucleosome was dissociated by the juxtaposition of the cruciform. We interpret these results to mean that cruciform structures can act over a distance to destabilize adjacent nucleosomes and suggest that, as a consequence, the chromatin structure surrounding a crossed strand recombination intermediate might be disrupted, enabling other recombination events to initiate or the process of branch migration to proceed.

Base Sequence↗