An ATP-dependent deoxyribonuclease from diplococcus pneumoniae. I. Partial purification and some biochemical properties

ATP-dependent exonuclease V from Micrococcus luteus. The enzyme-DNA complex, the processive mechanism, and the role of ATP

Some kinetic predictions of the proposed processive mechanism for the hydrolysis of DNA by the ATP-dependent enzyme exonuclease V have been checked. The method is to trap enzyme molecules not attached to radioactive DNA substrate with an excess of nonradioactive DNA, so that enzyme molecules attached to the radioactive substrate contribute to the liberation of radioactive products only until they dissociate from it. The experiments show that enzyme molecules remain attached to a T7 double-stranded DNA molecule, while hydrolysing it, for about 2 min under our conditions, in agreement with the predictions of the processive mechanism. However, the mechanism of degradation of single-stranded DNA is not processive. Formation of an enzyme-DNA complex is largely dependent on the presence of ATP. This formation does not appear to be synchronous. ATP analogs do not stimulate formation of, nor stabilize, the enzyme-DNA complex. EDTA causes dissociation of enzyme molecules from the DNA complex.

Purification and properties of two deoxyribonucleases of Pseudomonas aeruginosa

A survey of the major deoxyribonucleases in Pseudomonas aeruginosa strain PAO was undertaken. Two activities predominated in Brij-58 lysates of this organism. These have been purified from contaminating nuclease activities, and some of their properties have been elucidated. The first was a nuclease that degraded heat-denatured deoxyribonucleic acid (DNA) to mono- and dinucleotides. The activity of this enzyme was confined to single-stranded DNA, and 100% of the substrate was hydrolyzed to acid-soluble material. The Mg2+ optimum is low (1 to 3mM), and the molecular weight is 6 X 10(4). The second predominant activity was an adenosine 5'-triphosphate (ATP)-dependent deoxyribonuclease. This enzyme had an absolute dependence on the presence of ATP Mg2+ concentrations of approximately 10 mM. Five moles of ATP was consumed for each mole of phosphodiester bonds cleaved. The acid-soluble products of the reaction consisted of short oligonucleotides from one to six bases in length. Only 50% of the double-stranded DNA was rendered acid soluble in a limit digest. The molecular weight of this enzyme is 3 X 10(5). The observation of these enzymes in P. aeruginosa is consistent with the possibility that recombinational pathways similar to those of Escherichia coli are operating in this organism.

Membrane location of a deoxyribonuclease implicated in the genetic transformation of Diplococcus pneumoniae

The cellular localization of enzymes in Diplococcus pneumoniae was examined by fractionation of spheroplasts. A deoxyribonuclease implicated in the entry of deoxyribonucleic acid (DNA) into the cell during genetic transformation was located in the cell membrane. This enzyme, the major endonuclease of the cell (endonuclease I), which is necessary for the conversion of donor DNA to single strands inside the cell and oligonucleotides outside, thus could act at the cell surface. Another enzyme, the cell wall lysin (autolysin), was also found in the membrane fraction. Other enzymes, including amylomaltase, two exonucleases, and adenosine triphosphate-dependent deoxyribonuclease, and a restriction type endonuclease, were located in the cytosol within the cell. None of the enzymes examined were predominantly periplasmic in location. Spheroplasts were obtained spontaneously on incubation of pneumococcal cells in concentrated sugar solutions. The autolytic enzyme appears to be involved in this process. Cells that were physiologically competent to take up DNA formed osmotically sensitive spheroplasts two to three times faster than cells that were not in the competent state. Although some genetically incompetent mutants also formed spheroplasts more slowly, other such mutants formed them at the faster rate.

Studies on deoxyribonucleases from Haemophilus influenzae on DNA agarose affinity chromatography. Two-step purification of ATP-dependent deoxyribonuclease

In a first part of this report, purification and characterization of several nucleased from lysates of Haemophilus influenzae are described. The enzymes bind to DNA with agarose columns and are removed by elution with phosphate buffer. Among the considered enzymes, the exonucleases 1 and 3, and endonuclease, a DNA polymerase and a restriction enzyme were recovered mixed by raising the phosphate concentration from 0.1 to 0.3 M, while the ATP-dependent DNAase recovered well purified, by raising the phosphate concentration to 0.45 M. After a rechromatography, on a second DNA with agarose column, of the peak of the ATP-dependent DNAase, the specific activity tested with 3H-labeled DNA was 125 units/mg of protein, representing a 300-fold purification of the original crude extract. In a second part, we have investigated the inactivation, at various pH, of transforming DNA of Haemophilus influenzae wild strain Rd with the different eluted fractions of the column, in order to determine the importance of contamination with other enzymatic activities, and also in order to confirm the nature of theisolated enzymes with a biological method. Finally, with enzymatic extracts of mutant strain Rd com minus 56, a strain which integrates shorter than normal pieces of DNA and which is suspected to possess and "activated specific endonuclease" able to recognize even small conformational modifications in paired structures, we tried to detect this activity on artificially constructed heteroduplex regions in DNA.

Competence for deoxyribonucleic acid uptake and deoxyribonuclease action external to cells in the genetic transformation of Diplococcus pneumoniae

A mutant of Diplococcus pneumoniae that apparently does not require activator can become competent for uptake of deoxyribonucleic acid (DNA) when grown in dilute cultures or in the presence of trypsin. Development of competence in both mutant and wild strains is temperature dependent, being 10-fold greater at 30 C than at 37 C. Induction of competence on a shift from 37 to 30 C requires protein synthesis and the presence of Mg(2+) and Ca(2+); uptake of DNA does not require protein synthesis. Competence decays exponentially at higher temperatures. As well as taking up DNA, competent cells release oligonucleotide fragments of donor DNA in the medium external to the cells. Normal strains release fragments comparable in amount to the DNA taken up; but, in a mutant selected for inability to degrade DNA in agar, the amount of fragments formed external to the cells is only 40% of DNA uptake. Requirements for external deoxyribonuclease action are identical to those for DNA uptake: prior development of competence and the presence during treatment with DNA of Mg(2+) ions and a source of energy.

Adenosine triphosphate-dependent deoxyribonuclease from Diplococcus pneumoniae: fate of transforming deoxyribonucleic acid in a strain deficient in the enzymatic activity

The adenosine triphosphate-dependent deoxyribonuclease is required for wild-type levels of deoxyribonucleic acid (DNA) repair and genetic recombination. In an attempt to determine the physiological function of this enzyme in pneumococcal transformation, the fate of transforming DNA was followed in a wild-type strain and in a strain lacking the enzymatic activity. The qualitative and quantitative findings were closely comparable in the two strains through the step of physical association of a single strand of donor DNA with the recipient chromosome. These results are interpreted to mean that the enzyme may be involved in the subsequent hypothetical removal of excess polynucleotide sequences during conversion of the presumed hydrogen-bonded intermediate into a covalently linked recombinant structure.

Uncoupling of the recBC ATPase from DNase by DNA crosslinked with psoralen

Exonucleolytic cleavage of DNA by the recBC DNase is accompained by a DNA-dependent ATP hydrolysis that ceases when the DNA that has been digested to a limit. On the other hand, DNA that has been crosslinked by 4,5',8-trimethylpsoralen in the presence of 360-nm light remains an effective cofactor in the ATPase reaction, but is resistant to digestion by the enzyme. Psoralentreated DNA is degraded by pancreatic DNase, micrococcal nuclease, and Escherichia coli B restriction enzyme, but not by Neurospora crassa nuclease, suggesting that crosslinking did not grossly distort the duplex structure of the DNA. The psoralen-DNA is not a potent inhibitor, but competes with single-stranded DNA from bacteriophage fd for the recBC DNase to roughly the same extent as does normal duplex DNA. DNA treated with psoralen in the dark, exposed to 360-nm light in the absence of psoralen, or treated with the intercalating agents ethidium bromide, 9-aminoacridine, ICR-191, or actinomycin D, responds to the enzyme no differently from untreated DNA. However, DNA crosslinked with mitomycin C or nitrogen mustard behaves similarly to psoralen-treated DNA. The relationship of these findings to models for the function and control of the recBC ATPase and nuclease, and the advantages of psoralen as a DNA crosslinking agent, are discussed.

Deoxyribonucleic acid-dependent nucleotide phosphohydrolase activity in purified vaccinia virus

A nucleotide phosphohydrolase (adenosine triphosphatase), which is associated with vaccinia virus cores, has been solubilized and shown to be deoxyribonucleic acid dependent.