Studies on invitro DNA synthesis: II. Isolation of a protein which stimulates deoxynucleotide incorporation catalyzed by DNA polymerases of E.coli

Purified RNA polymerase, DNA polymerase III and unwinding protein of $\text{Escherichia}\text{coli}$ catalyze limited rifampicin sensitive fd or ØX 174 DNA-dependent DNA synthesis. A protein has been partially purified from $\text{E.}\text{coli}$ which stimulates rifampicin sensitive dXMP incorporation in this system 20 to 30 fold. This protein also stimulates DNA synthesis catalyzed by DNA polymerases I and II; the stimulation occurs in reactions primed with natural and synthetic DNAs as well as RNA-DNA hybrids. The protein is not a product of the known dna genes. In contrast to the above system of purified enzymes, rifampicin sensitive dXMP incorporation in crude extracts of $\text{E.}\text{coli}$ is specifically dependent on fd but not ØX 174 DNA. An additional factor has been isolated from extracts of $\text{E.}\text{coli}$ which restores specificity to the purified rifampicin sensitive system by preventing ØX 174 DNA from serving as a template.     

Genetics and function of DNA ligase in Escherichia coli

The characterization of two classes of DNA ligase mutants in Escherichia coli is described. The first class consists of three mutations coding for a temperature-sensitive ligase and defines the structural gene for DNA ligase (lig). The second class of mutants (lop) overproduces an apparently wild-type enzyme; a genetic diploid analysis implies that these are promoter or operator mutations, lig and lop are cotransduced by phage P1 and map at 46 minutes on the E. coli map. Detailed studies of two lig mutants (lig4 and lig ts7) are reported, lig ts7 is a conditionally lethal mutation, proving the essential nature of the ligase gene product. Neither mutant has a major defect in recombination or ultraviolet-repair, but both show retarded sealing of 10 S pulse-labeled DNA (Okazaki fragments).     

Development of mutagenicity test using Escherichia coli K-12 as indicator organism

A derivative of Escherichia coli K-12 (strain $\text{343}\text{113}$) has been developed in which mutations in several genes can be detected simultaneously by plating parts of the bacterial population on different selective media. The mutation types include reversions from differently induced auxotrophies (nad^-, arg^-) aand (forward) mutations leading to resistance against 5-methytryptophan and to gal⁺ phenotype. It is assumed that many types of DNA alteration, including deletions and changes involving gross DNA regions, will lead to viable detectable mutants.The usefulness of strain E. coli$\text{343}\text{113}$ was tested in spot tests, in liquid tests, in tests with extracts of mammalian organs, and in mammalian-mediated tests. It is concluded that strain $\text{343}\text{113}$ is at least as useful in routine mutagenicity testing (especially in mammalian-mediated assays) as other present bacterial strains.     

The specific uptake of cloned Haemophilus DNA.

During the process of transformation $\text{Haemophilus}\text{influenzae}$ cells bind its own DNA but little or no foreign DNA. This specificity for recognition of DNA was studied by cloning Haemophilus DNA in $\text{E. coli}$. Haemophilus DNA fragments were cloned using plasmid pBR322 as a vector. The fragment cH7 cloned in pBR322 was found to be homologous to Haemophilus DNA and shown to bind irreversibly to competent Haemophilus cells. The fact that cH7 isolated from $\text{E. coli}$ lacks Haemophilus modification leads to the conclusion that modification does not play a role in the uptake mechanism. Uptake specificity is a function of recognition sequences that reside in DNA itself.     

The incision and strand rejoining step in the excision repair of 5,6-dihydroxy-dihydrothymine by crude E. coli extracts

Strand resealing in the $\text{in}$$\text{vitro}$ excision repair of 5,6-dihydroxy-dihydrothymine in osmium tetroxide oxidized polyd(A-T) by crude $\text{E.}$$\text{coli}$ extracts is accomplished by polynucleotide ligase. Osmium tetroxide oxidized polyd(A-T)_serves as a chemically well defined model substrate containing damage of the kind introduced into DNA by ionizing radiation. In the first incision step of excision repair approximately one endonucleolytic nick is introduced into the polymer by extracts of $\text{E.}$$\text{coli}$ endoI^? and $\text{E.}$$\text{coli}$ endoI^?$\text{uvr}$A6^? per ring damaged thymine residue removed.     

Localization of the structural gene for the ' subunit of RNA polymerase in Escherichia coli

A minicell-producing strain of $\text{E.}$$\text{coli}$ carrying an F′ factor, KLF10-1, forms minicells that contain plasmid but not chromosomal DNA. These minicells were found to synthesize two polypeptides corresponding precisely to the β and β′ subunits of RNA polymerase in SDS-polyacrylamide gel electrophoresis. In contrast, minicells obtained from an isogenic strain carrying F13-1 do not synthesize these proteins under similar conditions. These results indicate that the structural genes for the β′ as well as β subunits of the polymerase are located on the chromosomal segment (78 to 81 min on the standard genetic map of $\text{E.}$$\text{coli}$) carried by KLF10-1.     

Effects of depurination on the fidelity of DNA synthesis.

The effect of depurination of polynucleotide templates on the fidelity of DNA synthesis in vitro has been determined. The fidelity of DNA synthesis with Escherichia coli DNA polymerase I, avian myeloblastosis virus DNA polymerase and human placenta DNA polymerase-β is decreased as a result of depurination of the poly[d(A-T)], poly[d(G-C)]and poly[d(A)]templates. The error rate with poly[d(A-T)]increased from $\text{1}\text{17,500}$ to $\text{1}\text{2100}$ using E. coli Pol I, and from $\text{1}\text{4100}$ to $\text{1}\text{1500}$ using the myeloblastosis virus DNA polymerase. Depurination of poly[d(A)]increased the error rate from $\text{1}\text{21,000}$ to $\text{1}\text{6500}$ using E. coli Pol I, and from $\text{1}\text{19,300}$ to $\text{1}\text{6100}$ using the DNA polymerase-β from human placenta. Depurination of poly[d(G-C)]resulted in an increase in the error rate with E. coli Pol I from $\text{1}\text{9200}$ to $\text{1}\text{2200}$, and with the virus DNA polymerase from $\text{1}\text{2400}$ to $\text{1}\text{1300}$. This misincorporation is shown to be directly proportional to the extent of depurination. Deletion experiments and alkaline sucrose gradient analyses suggest that the incorporation of complementary and non-complementary nucleotides is dependent on polymerization, and occurs in the same newly synthesized product. Kinetic studies and nearest-neighbor analyses indicate that the incorporation of non-complementary nucleotides occurs randomly as single-base substitutions. The nearest-neighbor studies also suggest that any of the four deoxynucleotides can be incorporated opposite apurinic sites. The number of each nucleotide incorporated relative to the number of apurinic sites was determined to be $\text{1}\text{490}$ for dGTP, $\text{1}\text{115}$ for dCTP, $\text{1}\text{2·5}$ for dATP and $\text{1}\text{1·7}$ for dTTP with both the poly[d(A-T)] and poly[d(A)] templates. The frequencies of misincorporation relative to the number of apurinic sites with the poly[d(G-C)]template were $\text{1}\text{230}$ for dATP, $\text{1}\text{120}$ for dTTP, $\text{1}\text{2·4}$ for dGTP and $\text{1}\text{1·8}$ for dCTP. Hydrolysis at the apurinic sites by alkali treatment reversed the effects of depurination on fidelity. The error rates with the depurinated templates were reduced to within 2% of those obtained prior to depurination, providing additional evidence that the misincorporation after depurination results from apurinic sites on the template. These results suggest a possible relationship between depurination of DNA and errors in DNA replication and/or repair.     

DNA synthesis during the division cycle of three substrains of Escherichia coliBr

The relationship between chromosome replication and the bacterial division cycle has been examined in three substrains of Escherichia coli$\text{B}\text{r}$ obtained from different sources and designated $\text{B}\text{r}$ A, $\text{B}\text{r}$ F and $\text{B}\text{r}$ K. At growth rates greater than 1.0 doubling per hour (μ > 1.0), the time for a round of chromosome replication (C) was 42 minutes in all three substrains, but the time between the end of a round and cell division (D) was 22 minutes in $\text{B}\text{r}$ A, 16 minutes in $\text{B}\text{r}$ F and 14 minutes in $\text{B}\text{r}$ K. At slower growth rates C and D increased, but to significantly different extents in the three substrains. When μ = 0.5, C and D were approximately 80 and 40 minutes in $\text{B}\text{r}$ A, 60 and 20 minutes in $\text{B}\text{r}$ F, and 70 and 20 minutes in $\text{B}\text{r}$ K.As a consequence of the lengths of the C and D periods in the three stocks of E. coli$\text{B}\text{r}$, the patterns of chromosome replication during the division cycle differed. The most obvious difference was that E. coli$\text{B}\text{r}$ F and E. coli$\text{B}\text{r}$ K possessed periods devoid of DNA synthesis at both the beginning and the end of the division cycle during slow growth, whereas E. coli$\text{B}\text{r}$ A contained only one period devoid of DNA synthesis at the end of the cycle.     

Excision repair of DNA base damage

Exposure of cells to exogenous physical and chemical agents can result in damage to the DNA bases. DNA damage can lead to mutation, malignant transformation and cell death and may possibly be involved in cellular aging. Structurally related base modifications are expected to have similar biological effects regardless of the agent responsible for their formation. The biological effects may be a consequence of the local distortion of the DNA conformation by the lesion rather than of the chemical properties of the modified base $\text{per se}$. It may be useful, therefore, to classify DNA base damage according to their effect on DNA conformation. The elucidation of the structures of the DNA lesions produced $\text{in situ}$ in the living cell represents a prerequisite for the correlation of specific lesions with the biological effects and for the study of the cellular repair processes.Excision repair represents an ubiquitous mechanism in cells for the removal of damaged residues from the DNA. The most specific first step in excision repair is the recognition of the damage by an endonuclease followed by incision of the damaged DNA strand in the proximity of the damage. Several “repair endonucleases” have been characterized from bacteria while the search for the corresponding mammalian enzymes is only beginning. The second, probably less specific step, is the exonucleolytic degradation of the damaged portion of the DNA leading to the removal of the damaged residue. In $\text{E. coli}$ the removal of both cyclobutane-type photodimers and γ-ray products of the 5,6-dihydroxy-dihydrothymine type is accomplished by the 5′→3′ exonuclease associated with polymerase I. All three $\text{E. coli}$ polymerases appear to participate in the rebuilding of the degraded portion of the DNA. Studies on the corresponding enzymes in mammalian cells have been initiated. The last step of exicison repair involves the sealing of a phosphodiester bond of the DNA backbone and is accomplished by the enzyme polynucleotide ligase in bacterial and mammalian cells.     

Synthesis of diphtheria toxin in E. coli cell-free lysate

An $\text{E. coli}$ cell-free lysate was used to translate $\text{C. diphtheriae}$ RNA from nontoxinogenic C₇(?), C₇ infected with β tox⁺ corynebacteriophage, and $\text{C. diphtheriae}$ strain PW8. De novo synthesis of toxin was detected by immune precipitation with antitoxin, ADP-ribosylation of mammalian elongation factor 2 and rabbit skin test. The results indicated that toxin is produced in the $\text{E. coli}$ protein synthesizing system primed with RNA from cells infected with tox⁺ bacteriophage and is absent in systems primed with RNA from C₇(?) cells.     

The effect of 5-azacytidine on E. coli DNA methylase.

5-Azacytidine, when added to growing $\text{E.}$$\text{coli}$ K12, causes a decrease in DNA methylation assayed $\text{in}$$\text{vitro}$. This decrease is greater when $\text{E.}$$\text{coli}$ DNA is used as substrate than when calf thymus DNA is used. The decrease in activity is not due to the inhibition of protein synthesis caused by this drug, since neither chloramphenicol nor rifampin causes a decrease in enzyme activity. The effect is specific for the DNA(cytosine-5)methylase; the methylation of adenine is not affected. The concentration of drug that inhibits the DNA methylase by 50% is the same concentration that inhibits cell growth by 50%.     

1,10-Phenanthroline-cuprous ion complex, a potent inhibitor of DNA and RNA polymerases.

The inhibition by 1,10-phenanthroline of $\text{E. coli}$ DNA polymerase I has recently been attributed to the formation in the assay mixtures of a unique and effective inhibitor, the 2:1 1,10-phenanthroline-cuprous ion complex (1). We have now found that this coordination complex is also an effective inhibitor of $\text{E. coli}$ DNA dependent RNA polymerase, Micrococcus luteus DNA dependent DNA polymerase, and T-4 DNA dependent DNA polymerase. This conclusion is based either on the requirement of a thiol for 1,10-phenanthroline inhibition or on the reversal of 1,10-phenanthroline inhibition by the non-inhibitory cuprous ion specific chelating agent 2,9-dimethyl-1,10-phenanthroline. 2,2′,2″-Terpyridine is also very effective at relieving 1,10-phenanthroline inhibition. The reversal of 1,10-phenanthroline inhibition should be attempted before it is claimed that 1,10-phenanthroline inhibits any polymerases by coordinating a zinc ion at the active site.     

Inhibition of exonuclease V after infection of E. coli by bacteriophage T7

Exonuclease V ($\text{recBC}$ DNase) is inactivated in $\text{E. coli}$ between 4 and 7 min after infection by T7. This process requires protein sythesis. The inactivation does not occur when T7 is deficient for its RNA polymerase and thus does not express the genes involved in DNA replication and phage maturation. Some implications of this new function of T7 are discussed with respect to the processes of infection and DNA replication.     

Biochimica et Biophysica Acta: Vol. 307 (1973)

The present study evaluates the unsaturated fatty acid requirement in Escherichia coli. A derivative of a double mutant defective both in unsaturated fatty acid biosynthesis and in fatty acid degradation has been selected which grows equally well on anteisopentadecanoate ($\text{12-Me-14:0}$) or $\text{cis-Δ}{}^9\text{-}\text{octadecenoate}$ ($\text{cis-δ}{}^9\text{-18:1}$). When this strain is grown for many generations on $\text{12-Me-14:0}$, there is extensive incorporation of this analogue into the membrane phospholipid and essentially no detectable unsaturated fatty acids residues in any lipid-containing structures of the cell envelope. Secondly, as the maximal growth temperature of E. coli is approached, the minimum content of unsaturated fatty acid required by this strain for growth decreases to a few percent and is associated with the appearance of substantial amounts of $\text{12:0}$ (8%) and $\text{14:0}$ (50%) in the phospholipid. These experiments demonstrate that the cis unsaturated fatty acids of E. coli phospholipids can be replaced by residues which possess no special electronic configuration. Hence, the unsaturated fatty acids do not participate in specific interactions with other membrane components but serve a general role of controlling the packing of paraffin chains in the membrane bilayer.     

Occurrence in mammalian liver of a protein which replaces the B protein of E. coli quinolinate synthetase.

$\text{Escherichia coli}$ contains two proteins (A and B) which together convert dihydroxyacetone phosphate and aspartate to quinolinic acid, a precursor of NAD. Although mammalian liver homogenate does not catalyze this reaction it contains a protein which will replace the B protein of the $\text{E. coli}$ system. The behavior of the liver protein on Sephadex G-75 suggests it is much smaller than the $\text{E. coli}$ B protein. Liver B protein also appears to contain tightly bound FAD while FAD is easily removed from the $\text{E. coli}$ B protein. The pH optimum for the hybrid system $\text{E. coli}$ A protein-liver B protein is 9.0 while in the pure $\text{E. coli}$ system the optimum is pH 8.0. The hybrid system is inhibited by NAD to the same extent as the pure $\text{E. coli}$ system.     

Transposon (Tn5)-mediated suppressive integration of ColE1 derivatives into the chromosome of Escherichia coli K12 (dnaA)

While integration of ColE1 had not been observed previously by ordinary suppressive integration, a $\text{dnaA}$ (Ts) $\text{E. coli}$ strain with Tn$\text{5}$ at various sites of the chromosome and ColE1 or its mini-derivative, pAO3, but not pSC101, inserted by the same transposon produced integratively suppressed strains depending on the RecA function. In contrast to Hfr strains made with a stringently controlled plasmid, they contained the plasmid not only in an integrated but in an autonomous state at an amount comparable to the strain containing the plasmid only autonomously. Introduction of a RecA-deficient mutation to the strain with an integrated ColE1 derivative through conjugation failed. This is likely to be due to lethality of such a strain without RecA-dependent excision of the integrated high copy number plasmid or to quantitative deficiency of DNA polymerase I in addition to the $\text{recA}$ mutation.     

Glutamate transport driven by an electrochemical gradient of sodium ion in membrane vesicles of Escherichia coli B.

Membrane vesicles prepared from $\text{E. coli}$ B strain 29–78 require Na⁺ for the accumulation of glutamate. Respiratory-driven transport of glutamate but not lysine is sensitive to the ionophore monensin. An artificially-imposed sodium gradient and/or membrane potential drives glutamate uptake. These results suggest that glutamate is accumulated via a Na⁺/glutamate symport.     

Differential effect of neomycin on DNA dependent -DNA and RNA synthesis in vitro

Neomycin inhibits $\text{in vitro}$ DNA dependent DNA and RNA synthesis catalyzed by DNA polymerase I and RNA polymerase from $\text{E. coli}$. The effect of the antibiotic is more pronounced towards DNA synthesis. The inhibition of DNA synthesis is competitive with template DNA, does not reverse with excess deoxynucleoside triphosphate, Mg²⁺ or enzyme $\text{E. coli}$ DNA polymerase I. Neomycin does not reduce the number of potential 3′ -OH end or primer. It seems to shorten the size of the newly formed polynucleotide.     

Nature of the repair process associated with the recovery of Escherichia coli after exposure to Cd2+.

When different strains of $\text{Escherichia coli}$ are exposed to Cd²⁺, the cells accommodate after a long lag and proliferate. The time required for this response depends on the nature of the strain and the supplements in the growth medium. Immediately after exposure to Cd²⁺, considerable single strand breaks in the DNA are observed but the DNA is repaired prior to the initiation of cell proliferation. The finding that accommodation occurs in DNA polymerase I-deficient mutant cells suggests that DNA polymerase I may not be required for repair of damaged DNA in Cd²⁺-exposed cells. The recovery of Cd²⁺-exposed cells in a temperature-sensitive DNA ligase mutant cells at the permissive temperature (30° C) and failure to recover at the non-permissive temperature (42° C) indicates, however, that DNA ligase is involved in the repair of the single strand breaks associated with Cd²⁺-induced damage.     

Further characterization of a ribonucleotide-polymerizing enzyme from Histoplasma capsulatum. II. Possible role in cellular metabolism

An enzyme, ribonucleotide polymerase, isolated from the yeast phase of a fungus, $\text{Histoplasma capsulatum}$ has been found to stimulate the incorporation of dTMP in the reaction catalysed by DNA polymerase from $\text{H. capsulatum}$ and $\text{E. coli}$. The stimulation is dependent on the amount of ribonucleotide polymerase added. The data indicate that protein-protein interaction is responsible for the increase in DNA synthesis. It is suggested that ribonucleotide polymerase may be involved in supplying short RNA primers for DNA polymerase.