Studies on ATP-dependent deoxyribonuclease of Haemophilus influenzae: involvement of the enzyme in the transformation process

An ATP-dependent deoxyribonuclease deficient mutant of Haemophilus influenzae has been isolated on the basis of sensitivity to methyl methane sulfonate (mms). Furthermore, the involvement of the ATP-dependent deoxyribonuclease in the process of transformation in H. influenzae has been demonstrated. Among the 75 mms-sensitive mutants, two mutants lacking ATP-dependent deoxyribonuclease were isolated. One mutant $\text{Rd}\text{mms-s}$ 21 has no measurable ATP-dependent deoxyribonuclease activity, is almost transformation deficient and has normal DNA uptake after being submitted to competence protocole. The second ATP-dependent deoxyribonuclease deficient mutant which has abnormal DNA uptake is still under investigation. Furthermore, the enzyme deficient mutant mms-s 21 transformed back to mms-resistance, recovers the ATP-dependent deoxyribonuclease as well as the transforming ability. The involvement of the ATP-dependent deoxyribonuclease in the process of transformation in H. influenzae is therefore positively established.     

One of the classes of revertants of a rec H Bacillus subtilis mutant]

A class of revertants of Bacillus subtilis mutant rec H, which completely restored the ability to transformation but without restoring the activity of ATP-dependent deoxyribonuclease, is isolated and studied. Reversions are located in the same chromosome region as the original mutation. The detection of such revertants points out the existence of more than one recombination pathway for Bac. subtilis transformation.     

Structural Genes of ATP-dependent Deoxyribonuclease of <Emphasis Type="Italic">Escherichia coli</Emphasis>

RECOMBINATION-deficient (Rec^?) mutants of E. coli express pleiotropic alterations of various phenotypes such as increased ultraviolet light sensitivity, altered patterns of DNA degradation after irradiation, inability to support growth of certain λ phage mutants and many others in addition to reduced recipient ability in mating with Hfr bacteria¹. Yet the primary function of any one of the genes responsible for these alterations has not been elucidated. In this paper, the characteristics of recB and recC mutants having temperature-sensitive functions are described. Particular attention is paid to the properties of the ATP-dependent deoxyribonuclease which is known to be missing in recB and recC mutants^2–5.     

Inactivation of ATP-dependent deoxyribonuclease of Micrococcus luteus by 2,3-butanedione

ATP-dependent deoxyribonuclease from Micrococcus luteus was purified to near homogeneity by a procedure involving gentle cell lysis, ammonium sulfate fractionation, TEAE-cellulose chromatography, Sephadex G-150 gel filtration and DNA-cellulose chromatography. Treatment of the enzyme with 2,3-butanedione, which binds specifically to arginyl residues, caused rapid loss of enzyme activities and the effect was enhanced by borate ion. The reaction obeyed first order kinetics with respect to the butanedione concentration, indicating that at least one functional arginyl residue is involved in the inactivation reaction. The enzyme was protected from inactivation by the presence of a low concentration of ATP, but not of ADP, AMP or adenosine. These results indicate that ATP-dependent deoxyribonuclease of Micrococcus luteus has functional arginyl residue(s) at an ATP-binding site.     

Increased ATP-dependent proteolytic activity in lon-deficient Escherichia coli strains lacking the DnaK protein.

Extracts made from Escherichia coli null dnaK strains contained elevated levels of ATP-dependent proteolytic activity compared with levels in extracts made from dnaK+ strains. This ATP-dependent proteolytic activity was not due to Lon, Clp, or Alp-associated protease. Comparison of the levels of ATP-dependent proteolytic activity present in lon rpoH dnaK mutants and in lon rpoH dnaK+ mutants showed that the level of ATP-dependent proteolytic activity was elevated in the lon rpoH dnaK mutant strain. These findings suggest that DnaK negatively regulates a new ATP-dependent proteolytic activity, independently of sigma 32. Other results indicate that an ATP-dependent proteolytic activity was increased in a lon alp strain after heat shock. It is not yet known whether the same protease is associated with the increased ATP-dependent proteolytic activity in the dnaK mutants and in the heat-shocked lon alph strain.     

Isolation and characterization of mutants of Haemophilus influenzae deficient in an adenosine 5''-triphosphate-dependent deoxyribonuclease activity.

By a direct assay approach, mutants of Haemophilus influenzae Rd that are deficient in adenosine 5'-triphosphate-dependent deoxyribonuclease activity (add-) were isolated and characterized. A large proportion (50 to 90%) of the cells in cultures of these mutants failed to produce visible colonies when plated. An extensive analysis of the recombination proficiency of these strains revealed that the transformation frequency (transformants per competent cell) in the mutants was similar to that found in the wild type, but that the transformation efficiency (transformants per microgram of irreversibly bound deoxyribonucleic acid [DNA]) was reduced approximately fourfold. Sensitivities of the mutants to gamma rays, ultraviolet radiation, and methyl methane sulfonate were only slightly greater than wild-type levels. The rate of degradation of host DNA after ultraviolet irradiation was significantly reduced in the mutants. It is suggested that the adenosine 5'-triphosphate-dependent deoxyribonuclease in H. influenzae plays a nonessential role in DNA recombination and repair.     

An endo-exonuclease activity of yeast that requires a functional RAD52 gene

Summary Extracts of Rad⁺ and radiation-sensitive (rad) mutants of the yeast Saccharomyces cerevisiae were examined for total Mg²⁺-dependent alkaline deoxyribonuclease activity and the presence of a nuclease that crossreacts immunologically with an antiserum raised against an endoexonuclease from Neurospora crassa, an enzyme exhibiting both deoxyribo- and ribonuclease activities. No significant differences were observed in total deoxyribonuclease activity between Rad⁺ and rad mutants. The antibody precipitable activity, however, was found to be 30%–40% of the total alkaline deoxyribonuclease activity in logarithmically growing Rad⁺ cells. Extracts of stationary phase cells were lacking in antibody precipitable activity. Using immunoblot methods, a 72 kDa crossreacting protein was identified from logarithmically growing cells that was absent from stationary phase cells. In all radiation-sensitive mutants examined, except rad52, at least 20% of total activity was precipitable. Extracts from logarithmically growing rad52 mutants, including a rad52::LEU2 insertion mutant, exhibited less than 10% of the Rad⁺ precipitable activity; however, some crossreacting material was detected. Although, the level of endo-exonuclease activity is influenced by the RAD52 gene, it is not the product of this gene. The total deoxyribonuclease and the antibody precipitable endo-exonuclease activities were also followed during meiosis. Unlike the Rad⁺ strain which had previously been shown to have increased levels of total and immunoprecipitable endo-exonuclease as cells underwent meiosis, the rad52 mutant exhibited no increases in either category of nuclease activity. Given the importance of the RAD52 gene in repair, recombination and mutagenesis, the endo-exonuclease may be a significant component of these processes.     

Replacement of the lysine residue in the consensus ATP-binding sequence of the AddA subunit of AddAB drastically affects chromosomal recombination in transformation and transduction of Bacillus subtilis

The ATP-dependent deoxyribonuclease enzyme complex (AddAB) of Bacillus subtilis possesses two consensus ATP-binding sequences, located in the N-terminal region of both subunits. The highly conserved lysine residues in both consensus ATP-binding sequences were replaced by glycine, resulting in the mutant enzyme complexes AddAB-A-K36G (AddA*B) and AddAB-B-K14G (AddAB*). The mutation in subunit AddA reduced DNA repair and chromosomal transformation, and abolished bacteriophage PBS1-mediated transduction. This mutation also resulted in a complete loss of the ATP-dependent exonuclease and helicase activity. In contrast, the mutation in subunit AddB had only marginal effects. The recF and addAB genes are not required for transformation with plasmid DNA, but have overlapping activities in transformation with chromosomal DNA. By contrast to RecF, the AddAB enzyme is essential for PBS1-mediated transduction. However, recF has a more important function with respect to DNA repair than addAB .     

Two pH optima of adenosine 5'-triphosphate dependent deoxyribonuclease from Bacillus laterosporus

The various catalytic activities of the ATP-dependent deoxyribonuclease (DNase) of Bacillus laterosporus have pH optima at 6.3 and 8.3. Although the pH profile of ATP-dependent DNase activity on duplex DNA is bell shaped with a maximum at about pH 8.3, ATP-dependent DNAse activity on single-stranded DNA has optima at pH 6.3 and 8.3. ATPase activities dependent on double-stranded and single-stranded DNA have a high bell-shaped peak with a maximum at pH 6.3 with a low and broad shoulder at about pH 8.3. ATP-independent DNase activity also has optima at pH 6.3 and 8.3. The ratio of the amount of ATP hydrolyzed per number of cleaved phosphodiester bonds in DNA increases with decrease in the pH value of the reaction. The ratios obtained at pH 8.3 and 6.3 were respectively about 3 and 22 with duplex DNA as substrate and 5 and 17 with single-stranded DNA as substrate. Formation of a single-stranded region of 15000-20000 nucleotides, which is linked to duplex DNA and about half of which has 3'-hydroxyl termini, was observed at about pH 6.3, but not at above pH 7.5. Furthermore, the optimum concentrations of divalent cations for the activity producing the single-stranded region and the activity hydrolyzing ATP were identical (3 mM Mn2+ or 5 mM Mg2+). Thus the two activities are closely related. These results indicate that the enzyme has two different modes of action on duplex DNA which are modulated by the pH.     

The use of a novel plate assay in a search for yeast mutants defective in deoxyribonucleases

Summary Methods by which the intracellular enzymes deoxyribonuclease, ribonuclease and protease can be assayed in whole colonies of Saccharomyces cerevisiae on agar plates are described. A search for mutants deficient in deoxyribonuclease has been carried out. Two types of mutant are descried. One apparently fails to produce deoxyribonuclease, ribonuclease or protease on agar plates and the other apparently fails to produce deoxyribonuclease and ribonuclease.     

The use of a novel plate assay in a search for yeast mutants defective in deoxyribonucleases.

Methods by which the intracellular enzymes deoxyribonuclease, ribonuclease and protease can be assayed in whole colonies of Saccharomyces cerevisiae on agar plates are described. A search for mutants deficient in deoxyribonuclease has been carried out. Two types of mutant are described. One apparently fails to produce deoxyribonuclease, ribonuclease or protease on agar plates and the other apparently fails to produce deoxyribonuclease and ribonuclease.     

Identification of a region in the N-terminus of Escherichia coli Lon that affects ATPase, substrate translocation and proteolytic activity

Lon, also known as protease La, is an AAA+ protease machine that contains the ATPase and proteolytic domain within each enzyme subunit. Three truncated Escherichia coli Lon (ELon) mutants were generated based on a previous limited tryptic digestion result and hydrogen-deuterium exchange mass spectrometry analyses performed in this study. Using methods developed for characterizing wild-type (WT) Lon, we compared the ATPase, ATP-dependent protein degradation and ATP-dependent peptidase activities. With the exception of not degrading a putative structured substrate known as CcrM (cell-cycle-regulated DNA methyltransferase), the mutant lacking the first 239 residues behaved like WT ELon. Comparing the activity data of WT and ELon mutants reveals that the first 239 residues are not needed for minimal enzyme catalysis. The mutants lacking the first 252 residues or residues 232-252 displayed compromised ATPase, protein degradation and ATP-dependent peptide translocation abilities but retained WT-like steady-state peptidase activity. The binding affinities of WT and Lon mutants were evaluated by determining the concentration of λ N (K(λN)) needed to achieve 50% maximal ATPase stimulation. Comparing the K(λN) values reveals that the region encompassing 232-252 of ELon could contribute to λ N binding, but the effect is modest. Taken together, results generated from this study reveal that the region constituting residues 240-252 of ELon is important for ATPase activity, substrate translocation and protein degradation.     

Escherichia coli mutants defective in the uncH gene.

Plasmids carrying cloned segments of the unc operon of Escherichia coli have been used in genetic complementation analyses to identify three independent mutants defective in the uncH gene, which codes for the delta subunit of the ATP synthetase. Mutations in other unc genes have also been mapped by this technique. ATPase activity was present in extracts of the uncH mutants, but the enzyme was not as tightly bound to the membrane as it was in the parental strain. ATP-dependent membrane energization was absent in membranes isolated from the uncH mutants and could not be restored by adding normal F1 ATPase from the wild-type strain. F1 ATPase prepared from uncH mutants could not restore ATP-dependent membrane energization when added to wild-type membranes depleted of F1. Membranes of the uncH mutants were not rendered proton permeable as a result of washing with low-ionic-strength buffer.     

Bacteriophage-induced functions in Escherichia coli K (lambda) infected with rII mutants of bacteriophage T4

Rutberg, Blanka (Karolinska Institutet, Stockholm, Sweden), and Lars Rutberg. Bacteriophage-induced functions in Escherichia coli K(lambda) infected with rII mutants of bacteriophage T4. J. Bacteriol. 91:76-80. 1966.-When Escherichia coli K(lambda) was infected with rII mutants of phage T4, deoxycytidine triphosphatase, one of the phage-induced early enzymes, was produced at initially the same rate as in r(+)-infected cells. Deoxyribonuclease activity was one-third to one-half of that of r(+)-infected cells. This lower deoxyribonuclease activity was observed also in other hosts or when infection was made with rI or rIII mutants. Presence of chloramphenicol did not allow a continued synthesis of phage deoxyribonucleic acid in rII-infected K(lambda). No phage lysozyme was detected nor was any antiphage serum-blocking antigen found in rII-infected K(lambda). It is suggested that the rII gene is of significance for the expression of phage-induced late functions in the host K(lambda).     

Distribution of acid and alkaline deoxyribonucleases in white and grey matter regions of growing and aging chick brain

The activities of acid and alkaline deoxyribonucleases in the white and grey matter areas of growing and old chick cerebrum were measured. Two marker enzymes for glial cells, butyrylcholinesterase and carbonic anhydrase were also measured in these regions. Higher specific activities of both butyrylcholinesterase and carbonic anhydrase were found in the white matter region at all the stages studied. Acid and alkaline deoxyribonuclease activities were observed in both white and grey matter. The decrease in the specific activity of acid deoxyribonuclease with advancement of age was more pronounced as compared to the alkaline deoxyribonuclease Marked reduction in total acid deoxyribonuclease activity in white matter, beyond the age of 130 days, was observed. On the other hand, total alkaline deoxyribonuclease activity in both white and grey matter continued to increase with age Further, the activity per mg of DNA also increased in white matter of the old brain. These results indirectly suggest a continued role for alkaline deoxyribonuclease in glial cells formed at a later age.     

The use of several energy-coupling reactions in characterizing mutants of Escherichia coli K12 defective in oxidative phosphorylation.

Oxidative phosphorylation, ATP-32Pi exchange, ATP-dependent quenching of acridine-dye fluorescence, ATP-dependent transhydrogenase and ATP-dependent transport of thiomethyl beta-D-galactoside are shown to be experimentally equivalent tools to study the functional state of the ATPase complex in Escherichia coli wild-type and mutant strains defective in oxidative phosphorylation. According to these criteria ten mutants in the ATPase complex were classified having lesions in the unc A,B region of the chromosome. The first mutant type lacks ATPase activity, but the membrane-integrated part of the complex remains functional (class I). The second mutant type lacks a functional membrane-integrated part, but retains ATPase activity (class II). The third mutant type is shown to be defective in both parts of the ATPase complex (class III).     

Identification of two fructose transport and phosphorylation pathways in Xanthomonas campestris pv. campestris.

Summary Fructose was shown to be phosphorylated by a specific phosphoenolpyruvatc-dependent phosphotransferase system (PTS) in Xanthomonas campestris pv. campestris. Transposon mutagenesis of X. campestris was performed and two mutants affected in growth on fructose were isolated. Both mutants were deficient in PTS activity. Comparison of the rate of uptake and phosphorylation of fructose in the wild-type and in the mutant strains revealed the presence of a second fructose permeation and phosphorylation pathway in this bacterium: an unidentified permease coupled to an ATP-dependent fructokinase. One of the two mutants was also deficient in fructokinase activity. Chromosomal DNA fragments containing the regions flanking the transposon insertion site were cloned from both mutant strains. Their physical study revealed that the insertion sites were separated by 1.4 kb, allowing the reconstruction of a wild-type DNA fragment which complemented one of the two mutants. The region flanking the transposon insertion site was sequenced in one of the mutants, showing that the transposon had interrupted the gene encoding the fructose Ell. The mutant strains also failed to utilize mannose, sucrose and mannitol, suggesting the existence of a branch point between the metabolism of fructose and of these latter carbohydrates.     

Localization of a determinant mediating partial macrolide resistance in Staphylococcus aureus

Four out of more than 8,200 Staphylococcus aureus strains isolated in Japan between 1961 and 1980 were constitutively resistant to a variety of macrolide antibiotics except tylosin and rokitamycin, but susceptible to lincosamide and streptogramin type B antibiotics (PM). The data obtained by agarose gel electrophoresis, CsCl-ethidium bromide density gradient analysis, diagnosis with ATP-dependent deoxyribonuclease, and a test transducing into a rec- mutant with phage 80L2 propagated on PM-resistant S. aureus all suggested that the determinant for the PM-resistance is located in chromosome.     

Isolation and genetic analysis of nuclease halo (nuh) mutants of Neurospora crassa.

Summary Nuclease halo (nuh) mutants of the ascomycete Neurospora crassa have been isolated which are characterized reduced release of deoxyribonuclease (DNase) activities from colonies grown on sorbose-containing agar media. To identify nuh mutants, mutagenized isolates were transferred to commercial DNase test agar, or grown on minimal medium and then overlayed with agar that contained heat-denatured DNA. DNase activity was visualized by acid precipitation which produced clear rings of digestion (haloes) around the colonies.To identify the number of genes in which mutations lead to reduced release of nuclease activity, eleven nuh mutants were checked for close linkage and linked pairs were tested for complementation. These mutants were assigned to eight genes, and all except one were mapped in six small regions of the Neurospora linkage maps. In addition, among a large number of existing mutants which were tested for nuclease haloes, two mutants were found that showed the Nuh phenotype, namely uvs-3 and uvs-6. One of the isolated nuh mutants was also found to be sensitive to UV and was mapped close to uvs-3; it may represent a new allele of this gene.As a first step towards identification of genuine nuclease mutants, extensively backcrossed strains of mutants from different genes have been assayed for nuclease activity with denatured DNA in extracts. A pronounced reduction, compared to wild type at the same stage of growth, was found in uvs-3 and also in nuh-3, a mutant that is not UV-sensitive.     

Identification of a deoxyribonuclease implicated in genetic transformation of Diplococcus pneumoniae.

A mutation of Diplococcus pneumoniae, end-1, reduces the major deoxyribonuclease activity of the cell, an endonuclease, to 10% of its normal value without impairing transformation. Further mutations, called noz, abolish the residual endonuclease activity and block transformation. The residual endonuclease is similar to the wild-type enzyme in size, charge, divalent cation dependence, inhibition by ribonucleic acid, and formation of oligonucleotide products. However, the mutant endonuclease is more temperature sensitive, which suggests that the end-1 mutation occurred in a structural gene for the enzyme. Genetic analysis showed that the noz mutations occur at the same genetic locus. A number of new end mutants were analyzed. Those that retained more than 1.4% of the normal endonuclease activity were essentially normal in transformation; those with less than 1% were defective. The transformation-defective end mutants appear to be blocked in the entry of deoxyribonucleic acid (DNA) since they carry out the prior step of binding DNA to the outside of the cell. The major endonuclease of the cell may act as a DNA translocase by attacking and degrading one strand of DNA, thereby facilitating entry of the complementary strand into the cell.