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R Bowater

Publications and source records attributed to R Bowater.

10 recordsLinked to original sources
PubMed2001

Bacterial DNA ligases.

DNA ligases join breaks in the phosphodiester backbone of DNA molecules and are used in many essential reactions within the cell. All DNA ligases follow the same reaction mechanism, but they may use either ATP or NAD+ as a cofactor. All Bacteria (eubacteria) contain NAD+-dependent DNA ligases, and the uniqueness of these enzymes to Bacteria makes them an attractive target for novel antibiotics. In addition to their NAD+-dependent enzymes, some Bacteria contain genes for putative ATP-dependent DNA ligases. The requirement for these different isozymes in Bacteria is unknown, but may be related to their utilization in different aspects of DNA metabolism. The putative ATP-dependent DNA ligases found in Bacteria are most closely related to proteins from Archaea and viruses. Phylogenetic analysis suggests that all NAD+-dependent DNA ligases are closely related, but the ATP-dependent enzymes have been acquired by Bacterial genomes on a number of separate occasions.

Adenosine Triphosphate↗
PubMed1994

Topological promoter coupling in Escherichia coli: delta topA-dependent activation of the leu-500 promoter on a plasmid.

The leu-500 promoter of Salmonella typhimurium is activated in topA mutants. We have previously shown that this promoter can be activated on circular plasmids in a manner that depends on transcription and translation of the tetracycline resistance gene tetA and insertion of its product into the cell membrane. We have suggested that in the absence of enzymatic relaxation by topoisomerase I, the local domain of transcription-induced DNA supercoiling reaches a steady-state level that leads to the activation of the leu-500 promoter. In the present paper, we have shown that the leu-500 promoter may also be activated in Escherichia coli. Comparison of the closely related pair of E. coli strains DM800 (delta topA) and SD108 (topA+) shows that the activation is dependent on the presence of a null mutation in topA. We have also shown that activation of the plasmid-borne leu-500 promoter depends, as in S. typhimurium, on the function of an adjacent tetA gene, suggesting that membrane anchorage of the TetA peptide prevents dissipation of transcription-induced supercoiling by superhelical diffusion. The activity of the leu-500 promoter is boosted by placing a divergent tac promoter on the side opposite to tetA. The topoisomer distributions of these plasmids extracted from the cell have been analyzed. We find that when the parent plasmid pLEU500Tc, containing the leu-500 promoter upstream of the complete tetA gene, is extracted from E. coli DM800 (delta topA), the distribution of linking numbers is bimodal. There is a fraction with a lower level of supercoiling (mean linking difference approximately -0.05) that is constant for all plasmids extracted from either delta topA or topA+ cells. In addition, we observe a second fraction with highly negatively supercoiled DNA (mean linking difference approximately -0.09) only in DNA extracted from delta topA cells. The proportion of the oversupercoiled fraction correlates with the activity of the leu-500 promoter: it is strongly reduced when the tetA promoter is deleted or when translation of TetA is prematurely terminated, while it is increased when the strong tac promoter is present in cis. We suggest that this oversupercoiled fraction represents the proportion of plasmid molecules active in tetA transcription and that it is this supercoiling that activates the leu-500 promoter.

Antiporters↗
PubMed1993

Characterization of the zinc-induced structural transition to *H-DNA at a d(GA.CT)22 sequence.

Zinc induces transition of a d(GA.CT)22 sequence to a novel DNA conformation, called *H-DNA. In this paper, the structural characteristics of this altered DNA conformation are determined. Formation of *H-DNA is induced at zinc concentrations higher than 70 microM (Zn/P = 2) and it is favoured by negative supercoiling and low ionic strength. Two different structural conformations of the d(GA.CT)22 sequence are observed upon increasing the zinc concentration. At low zinc concentration (Zn/P < 15), half of the purine strand falls back upon itself giving rise to the formation of an RRY intramolecular triplex (H*-triplex). At higher zinc concentration, the complete pyrimidine strand is single-stranded and an RR hairpin is formed (*H-hairpin). Protection towards dimethylsulphate modification suggests that zinc binds to the N-7 group of guanine residues in the *H-hairpin with a higher affinity than in B-DNA. The dissociation constant of the *H-zinc complex is estimated to be in the range of 10(-3) M to 10(-4) M.

Base Sequence↗
PubMed1992

Activity of a plasmid-borne leu-500 promoter depends on the transcription and translation of an adjacent gene.

leu-500 is a chromosomal promoter mutation in Salmonella typhimurium that normally causes the promoter to be inactive in the initiation of RNA synthesis. But in a strain that has mutations in topA, the gene encoding DNA topoisomerase I, the mutant promoter becomes active. We show that the leu-500 promoter can function on a plasmid when it is adjacent to the tetracycline-resistance gene tetA. Activation of the leu-500 promoter requires that the tetA gene is transcribed and translated and that the host cell is topA. We propose that the A----G mutation in the -10 region of the leu-500 promoter is compensated by local negative supercoiling arising from transcription of the tetA gene, which may reach elevated levels in a topA background, provided that diffusional dissipation is reduced due to anchoring of the TetA peptide in the membrane. This is a clear example of the modulation of the activity of a promoter by the activity of another promoter in cis, when they can be coupled through the topology of the template.

DNA Topoisomerases, Type I↗
PubMed1991

Large-scale stable opening of supercoiled DNA in response to temperature and supercoiling in (A + T)-rich regions that promote low-salt cruciform extrusion.

We have studied the properties of (A + T)-rich sequences derived from ColE1 that promote cruciform extrusion at low ionic strength in supercoiled plasmids. We compared the chemical reactivity of the sequences in negatively supercoiled DNA (using osmium tetroxide and bromoacetaldehyde) with the results of two-dimensional gel electrophoresis performed under the same conditions. Taken together, the results indicate the occurrence of cooperative helix-coil transitions in the (A + T)-rich DNA at low ionic strength, to form stable, denatured regions. The extent of the open region is a function of temperature and superhelix density, with an additional local destabilization brought about by the presence of cruciform structures. We present a simple statistical mechanical model of the helix-coil transition in the (A + T)-rich DNA, from which we have obtained estimates of the free energy for average base-pair opening of 0.31 kcal mol-1 and that for the formation of a helix-coil junction of 4.9 kcal mol-1, in 45 mM Tris-borate, pH 8.3, 0.5 mM EDTA. The results offer a model for the C-type mechanism of cruciform extrusion. Inverted repeats that are incorporated into the melted region undergo hairpin loop formation below 50 degrees C, and upon closure of the melted region, by reduction of temperature or increased ionic strength, they remain as a fully extruded cruciform structure.

Acetaldehyde↗
PubMed1990

Kinetics of ATP and inorganic phosphate release during hydrolysis of ATP by rabbit skeletal actomyosin subfragment 1. Oxygen exchange between water and ATP or phosphate.

We have used the technique of phosphate: water oxygen exchange to measure the rate of ATP and Pi release and Pi binding to myosin subfragment 1 and actomyosin subfragment 1 from rabbit skeletal muscle. The oxygen exchange distributions for ATP and Pi release fit a simple kinetic model with a single set of rate constants for each step. For actomyosin subfragment 1 (20 degrees C, pH 7.0, I = 50 mM), the rate constant governing ATP release is approximately 8 s-1, Pi release is at approximately 60 s-1 and Pi rebinds to an ADP state at greater than 120 M-1 s-1. These rate constants are similar to those that may occur for undistorted cross-bridges within glycerinated rabbit psoas fibers (Bowater, R., Webb, M. R., and Ferenczi, M. A. (1989) J. Biol. Chem. 264, 7193-7201.

Actins↗
PubMed1989

Measurement of the reversibility of ATP binding to myosin in calcium-activated skinned fibers from rabbit skeletal muscle. Oxygen exchange between water and ATP released to the solution.

We have measured the rate constant for ATP release from myosin heads of Ca2+-activated, demembranated muscle fibers using the technique of phosphate-water oxygen exchange. Single rabbit psoas fibers were held in an activating solution in [18O]water ([MgATP] = 8 mM, ionic strength = 0.2 M, pH = 7.0, 24 degrees C). After about 20% hydrolysis of ATP, product Pi and remaining ATP were isolated, and the distribution of 18O in both molecules was analyzed using a mass spectrometer. The exchange in Pi was similar to that previously reported (Hibberd, M. G., Webb, M. R., Goldman, Y. E., and Trentham, D. R. (1985) J. Biol. Chem. 260, 3496-3501). The amount of 18O in ATP gave a rate constant of about 4 s-1 for ATP release, if it is assumed that each rate constant in the pathway of ATP hydrolysis has the same value for all myosin ATPase sites. However, the distribution of 18O in both released Pi and ATP is not well explained by a single pathway for ATP hydrolysis. We present a model that indicates how such distributions could arise from a range of values for the rate constants for Pi and ATP release from actomyosin, and this range is determined by differences in the amounts of strain in attached crossbridges. The kinetic information obtained from these isotope exchange experiments is compared to show that they give a compatible set of rate constants for actomyosin in fibers.

Actomyosin↗
PubMed1988

Demembranated muscle fibers catalyze a more rapid exchange between phosphate and adenosine triphosphate than actomyosin subfragment 1.

The rate of ATP in equilibrium with Pi exchange, that is, the incorporation of medium Pi into ATP during the net hydrolysis of ATP, has been measured for rabbit psoas muscle fibers, myofibrils, and actomyosin subfragment 1 (acto-S1). The maximum exchange rate in fibers at saturating [Pi] is 0.04 s-1 per myosin head at 8 degrees C, pH 7, and an ionic strength of 0.2 M. The dependence of the rate on Pi concentration can be approximated by a hyperbola with an apparent dissociation constant (Km) of 3 mM. Myofibrils catalyze ATP in equilibrium with Pi exchange with a similar Km but at a slightly lower rate. In contrast, the soluble acto-S1 system, in which ATP hydrolysis is not coupled to tension generation, catalyzes exchange at a rate 500 times lower than that of fibers at low Pi concentration, and the Km for Pi is greater than 50 mM. The difference between the ATP in equilibrium with Pi exchange of fibers and of acto-S1 is discussed in terms of a model in which Pi binds to a force-generating state AM'-ADP and, due to mechanical constraint, the average free energy of this state is higher in the fiber than in acto-S1.

Adenosine Triphosphate↗