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Biomedical subjects

J W Drake

Publications and source records attributed to J W Drake.

At least 19 recordsLinked to original sources
PubMed1992

Duplication-targeted DNA methylation and mutagenesis in the evolution of eukaryotic chromosomes.

Mammalian genomes are threatened with gene inactivation and chromosomal scrambling by recombination between repeated sequences such as mobile genetic elements and pseudogenes. We present and test a model for a defensive strategy based on the methylation and subsequent mutation of CpG dinucleotides in those DNA duplications that create uninterrupted homologous sequences longer than about 0.3 kilobases. The model helps to explain both the diversity of CpG frequencies in different genes and the persistence of gene fragmentation into exons and introns.

Animals↗
PubMed1992

Mutation rates.

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Biological Evolution↗
PubMed1991

A constant rate of spontaneous mutation in DNA-based microbes.

In terms of evolution and fitness, the most significant spontaneous mutation rate is likely to be that for the entire genome (or its nonfrivolous fraction). Information is now available to calculate this rate for several DNA-based haploid microbes, including bacteriophages with single- or double-stranded DNA, a bacterium, a yeast, and a filamentous fungus. Their genome sizes vary by approximately 6500-fold. Their average mutation rates per base pair vary by approximately 16,000-fold, whereas their mutation rates per genome vary by only approximately 2.5-fold, apparently randomly, around a mean value of 0.0033 per DNA replication. The average mutation rate per base pair is inversely proportional to genome size. Therefore, a nearly invariant microbial mutation rate appears to have evolved. Because this rate is uniform in such diverse organisms, it is likely to be determined by deep general forces, perhaps by a balance between the usually deleterious effects of mutation and the physiological costs of further reducing mutation rates.

Bacteriophage lambda↗
PubMed1991

Mutation: major evolutionary trends.

The chemistry of the mutation process reflects not only the chemistry of DNA damage but also its subsequent metabolic processing by the cell. It is these latter steps that are the most important. They have evolved in ways that are only now coming to be understood and which reveal the effects of powerful evolutionary pressures.

Biological Evolution↗
PubMed1990

Frameshift and double-amber mutations in the bacteriophage T4 uvsX gene: analysis of mutant UvsX proteins from infected cells.

The bacteriophage T4 uvsX gene encodes a 43 kDa, single-stranded DNA-dependent ATPase, double-stranded DNA-binding protein involved in DNA recombination, repair and mutagenesis. Mutants of uvsX have a DNA-arrest phenotype and reduced burst size. Western blot immunoassay of UvsX peptides made by a number of amber mutants revealed amber peptides ranging from 25-32 kDa. Wild-type UvsX protein was also detected in lysates of cells infected with uvsX amber mutants, suggesting that their mutations are suppressed by translational ambiguity. We investigated the effects of mutations near the 5' end of uvsX. A frameshift mutation was engineered at codon 33. Western immunoblots for UvsX protein demonstrated that the frameshift mutant expresses no detectable wild-type UvsX; instead, a 37 kDa reactive peptide was detected. In order to determine if this peptide represents truncated UvsX protein, the mutation was regenerated in the cloned uvsX gene and expressed in transformed Escherichia coli. Endopeptidase digestion of the 37 kDa protein from the cloned gene generated peptide fragments indistinguishable from those obtained from wild-type UvsX. A double-amber mutant of uvsX was also generated by oligonucleotide site-directed mutagenesis. No UvsX protein was detected in lysates of cells infected with the uvsXam64am67 double mutant. Plaque size and sensitivity to UV inactivation for both the double-amber and the frameshift mutants were indistinguishable from those of other uvsX mutants. Mutations in uvsY had no demonstrable effect on efficiency of plating or UV sensitivity of uvsX mutants. Thus, null mutants of uvsX are viable.

Adenosine Triphosphatases↗
PubMed1990

Isolation and genetic characterization of new uvsW alleles of bacteriophage T4.

The uvsW gene of bacteriophage T4 is required for wild-type levels of recombination, for normal survival and mutagenesis after UV irradiation, and for wild-type resistance to hydroxyurea. Additionally, uvsW mutations restore the arrested DNA synthesis caused by mutations in any of several genes that block secondary initiation (recombination-primed replication, the major mode of initiation at late times), but only partially restore the reduced burst size. A uvsW deletion mutation was constructed to establish the null-allele phenotype, which is similar but not identical to the phenotype of the canonical uvsW mutation, and to demonstrate convincingly that the uvsW gene is nonessential (although uvsW mutations severely compromise phage production). In an attempt to uncouple the diverse effects of uvsW mutations, temperature-sensitive uvsWts mutants were isolated. Recombination and replication effects were partially uncoupled in these mutants, suggesting distinct and separable roles for uvsW in the two processes. Furthermore, the restoration of DNA synthesis but not recombination in the double mutants uvsW uvsX and uvsW uvsY prompts the hypothesis that the restored DNA synthesis is not recombinationally initiated.

Alleles↗
PubMed1990

Heat mutagenesis in bacteriophage T4: another walk down the transversion pathway.

Extracellular nonreplicating bacteriophage T4 particles accumulate mutations as functions of temperature, time, pH, and ionic environment via two mechanisms: 5-hydroxymethylcytidine deamination produces G.C----A.T transitions while a guanosine modification produces transversions. Neither frameshift mutations nor mutations at A.T base pairs are appreciably induced. We now show that heat induces G.C----T.A transversions which we suggest may arise via a G*.A mispair, in which G* is a modified guanosine that has experienced a glycosylic bond migration. The rate of this reaction at 37 degrees C is sufficient to present a genetic hazard, particularly to large genomes; thus, the lesion is probably efficiently repaired in cellular genomes.

Base Composition↗
PubMed1990

Measurements of certain environmental tobacco smoke components on long-range flights.

In December 1987, 10 portable nicotine and respirable particle measuring instruments were employed on 4 Boeing 747 flights, placed in all passenger classes and zones, in randomly selected non-perimeter seats, to assess environmental tobacco smoke (ETS). Measurements integrated the nicotine particle concentrations over the duration of the 5-h Tokyo-Hong Kong-Tokyo flights and over each half of the 14-h New York City-Tokyo flights. Number of cigarettes smoked per minute in sample areas explained a significant proportion of variability in the observed nicotine and respirable particle levels. The all-daytime Tokyo-Hong Kong-Tokyo flights with a different seating configuration showed higher levels of ETS variables. The cause cannot be identified from the six flight segments studied. Levels of ETS observed in these 747-100 and -200 flights (with all air conditioning packs operating) were lower than those observed in narrow body 727/737 aircraft, on short flights, in prior related tests. The 747's five air conditioning zones are reasonably effective in keeping ETS within the respective zones, and discharging it with relatively little entry into non-smoking areas.

Aircraft↗
PubMed1989

Mechanisms of mutagenesis.

Our understanding of mechanisms of mutation, which has expanded greatly in the past few decades, served as the original impetus to the formation of the Environmental Mutagen Society. The advances in genetics and chemistry that have conditioned our present degree of knowledge are here catalogued and the future is predicted.

Carcinogens, Environmental↗
PubMed1988

Clone size distributions of mutations induced by ethyl methanesulfonate in bacteriophage T4.

Size distributions of mutant clones can reveal important aspects of the mutation process. Previously published data on mutant clones induced by ethyl methanesulfonate (EMS) in bacteriophage T4 generated a distribution that was essentially flat, implying a mutagenic mechanism involving only rare mispairing by reacted bases. Here, methods for estimating the spontaneous component of such a distribution are used to generate a corrected distribution. The corrected distribution is strongly peaked, implying frequent (but not obligatory) mispairing. Frequent mispairing is in accord with current views of the fates of DNA lesions believed to mediate EMS-induced mutagenesis.

Clone Cells↗
PubMed1988

Bacteriophage T4 DNA polymerase determines the amount and specificity of ultraviolet mutagenesis.

Ultraviolet mutagenesis in bacteriophage T4 proceeds via error-prone repair (EPR) and requires the functional integrity of the uvsWXY system which mediates genetic recombination, recombinational repair, and mutability by diverse DNA damaging agents. Current opinion holds that mutagens acting through EPR generate DNA damage which blocks the progress of the replication complex and that EPR consists of the facilitated bypass of such inaccurate, damaged templates. This notion predicts that the T4 DNA polymerase (encoded by gene 43) mediates EPR in UV irradiated phage T4. This prediction is verified by the discovery that gene 43 mutations often enhance or reduce UV mutagenesis (which is scored by the induction of r mutants) and sometimes change its specificity.

Alleles↗
PubMed1977

Mutator mutations in bacteriophage T4 gene 42 (dHMC hydroxymethylase).

Temperature-sensitive mutations of bacteriophage T4 gene 42 produce diverse effects upon spontaneous mutation rate. G:C vector A:T transition rates are increased, often strongly; frameshift mutation rates are weakly increased; A:T vector G:C transition rates (and perhaps also A:T vector Py:Pu transversion rates) are decreased; and one G:C vector Py:Pu transversion rate is also decreased. These results, together with certain interactions between gene-42 mutator effects and both base analogue mutagenesis and the viral error-prone repair system, suggest that the dHMC hydroxymethylase coded by gene 42 affects mutation rates in a more complex manner than by the simple regulation of the concentration of the DNA precursor dHMCTP.

Base Sequence↗
PubMed1976

Heat mutagenesis in bacteriophage T4: the transversion pathway.

Heat induces transversions (as well as transitions) at G-C base pairs in bacteriophage T4. The target base for transversions is guanine,which is converted to a product which is sometimes replicated and transcribed as a pyrimidine.A model for this process is proposed in which the deoxyguanosine glycosidic bond migrates from N9 to N2: the resulting deoxyneoguanosine may pair with normal guanine to produce G-C leads to C-G transversions.

Base Sequence↗
PubMed1976

Heat mutagenesis in bacteriophage T4: the transition pathway.

G-C leads to A-T transitions are induced by heat, and arise from the deamination of cytosine (5-hydroxymethylcytosine in the case of bacteriophage T4) generating uracil. The reaction is proton-catalyzed, and is also characteristic of acid mutagenesis. Mutation rates and activation energies of mutation are site-specific, and are presumably influenced by neighboring bases. Rates of heat-induced mutation in bacteriophage T4 under conditions of temperature, pH, and ionic strength similar to those prevailing in higher eukaryotic cells suggest that heat mutagenesis may present a serious challenge to organisms with large genomes, and may comprise an important determinant of the rates of spontaneous mutation.

Chemical Phenomena↗
PubMed1976

Gamma-ray mutagenesis in bacteriophage T4.

137Cs-gamma irradiation of bacteriophage T4 induces large deletions plus a variety of types of point mutations. All mutations arise with single-hit kinetics, and all by a misrepair process. The estimated point mutation rate is 1.5 X 10(-9) per locus per rad.

Chromosome Aberrations↗