The folded genome of Escherichia coli isolated in a protein-DNA-RNA complex

Preferential ribosomal RNA synthesis in the lysate of Escherichia coli

The RNA synthesis in non-viscous lysates containing the intact folded chromosome and cytoplasm fractions prepared from Escherichia coli has been examined in vitro. The RNA synthesis not only by chain extension but also by new chain initiation occurs in this system. While the RNA synthesis by chain extension takes place on the chromosome fraction alone (Pettijohn et al., 1970), an addition of the cytoplasm fraction is necessary for the synthesis by new chain initiations (de novo synthesis). Analyses of the in vitro synthesized RNA by hybridization-competition and by sucrose gradient centrifugation show that 16S and 23S ribosomal RNAs account for about 40% of the total RNA products. The cytoplasm fraction is required for the de novo synthesis of ribosomal RNA at high relative rate. Guanosine tetraphosphate (ppGpp) does not specifically inhibit ribosomal RNA synthesis in this system.

Gamma-ray-induced thymine damage in the DNA in coliphage phi chi 174 and in E. coli

The radiation chemical reactivity of thymine residues has been compared for single-stranded phi chi 174 DNA free in solution and in the intact bacteriophage, as well as for native E. coli DNA in solution and inside the cell. The gamma-ray-induced release of [3H]H2O from thymine-methyl[3H] was measured to assess the reactivity of the thymine methyl group. Formation of ring-saturated products of the 5,6-dihydroxy-dihydrothymine type (see article) was determined by an alkali-acid degradation assay. It was observed that the formation of that the formation of [3H]H2O was suppressed by a factor of 9 in intact phi chi 174 bacteriophage compared to phi chi 174 DNA, whereas the formation of (see article) was only slightly suppressed in the phage. For E. coli cells the formation of [3H]H29 was reduced 790-fold compared with free E. coli DNA, and (see article) formation was reduced 140-fold. The extents of survival after gamma-irradiation of phi chi 174 phage plaque-forming ability and E. coli colony-forming ability were also determined. Under the conditions used in these experiments, a linear relationship was observed between the loss of biological activity and the formation of thymine damage for both phi chi 174 phage and E. coli cells.

Unfolding of the chromosome of Escherichia coli after treatment with rifampicin

Until recently it has been assumed that the factors being responsible for the condensation of the DNA in the nucleoid of Escherichia coli are destroyed by rifampicin because it has been impossible to obtain folded chromosomes from cells treated with this inhibitor. In this paper it is shown by viscosity and sedimentation measurements that unfolding of the DNA does not take place during the process of the cell lysis as it should be predicted from this assumption, but is occurring distinctly afterwards. Since the observed unfolding process is too slow to be caused simply by molecular movements it is concluded that it is brought about by the action of salts or detergents of the lysis medium. The structure of the nucleoid is still intact in vivo despite inhibition of RNA synthesis by rifampicin.

Detection of nonintegrated plasmid deoxyribonucleic acid in the folded chromosome of Escherichia coli: physiochemical approach to studying the unit of segregation

Physiocochemical evidence presented indicates plasmid deoxyribonucleic acid (DNA) can associate with host chromosome without linear insertion of the former into the latter. This conclusion is based on the observation that covalently closed circular (CCC) plasmid DNA can cosediment with undegraded host chromosome in a neutral sucrose gradient. When F plus bacteria are lysed under conditions that preserve chromosome, approximately 90% of CCC F sex factor plasmid (about 1% of the total DNA) is found in folded chromosomes sedimenting at rates between 1,500 and 4,000s. The remaining 10% of the CCC F DNA sediments at the rate (80S) indicative of the free CCC plasmid form. Reconstruction experiments in which 80S, CCC F DNA is added to F plus or F minus bacteria before cell lysis show that exogenous F DNA does not associate with folded chromosomes. In F plus bacteria, F plasmid is harbored at a level of one or two copies per chromosomal equivalent. In bacteria producing colicin E1, the genetic determinant of this colicin, the Col E1 plasmid, is harbored at levels of 10 to 13 copies per chromosomal equivalent; yet, greater than 90% of these plasmids do not cosediment with the 1,800S species of folded chromosome. However, preliminary evidence suggests one or two Col E1 plasmids may associate with the 1,800S folded chromosome. Based on evidence presented in this and other papers, we postulate F plasmid can link to folded chromosome because the physicochemical structure of the plasmid resembles a supercoiled region of the chromosome and, therefore, is able to interact with the ribonucleic acid that stabilizes the folded chromosome structure. Implications of this model for F plasmid replication and segregation are discussed.

A mild method for the isolation of folded chromosomes from Escherichia coli

Until now it has not been possible to obtain nuclear bodies from Escherichia coli after treatment with rifampicin. It was generally assumed that the cross-connections between the DNA double strands which are sensitive towards ribonuclease are destroyed under the influence of inhibitors of RNA synthesis like rifampicin. In this paper a new lysis procedure is described for preparing nuclear bodies from E. coli. These particles differ in some respects, especially in salt sensitivity from those prepared by earlier methods. Using the new lysis method it is also possible to obtain folded chromosomes from cells after treatment with rifampicin. These nuclear bodies can be destroyed by ribonuclease. Therefore, it has to be postulated that a fraction of RNA being sufficient to hold the chromosome in the folded shape is not susceptible to the action of rifampicin.

Isolation of membrane-associated folded chromosomes from Escherichia coli: effect of protein synthesis inhibition

The sedimentation properties of membrane-associated folded chromosomes prepared from Escherichia coli TAU-bar at 0 to 4 C were studied. Utilizing a modification of the procedure of Stonington and Pettijohn (1971), quantitative yields of membrane-associated folded chromosomes may be obtained. Folded chromosomes remained associated with the cell envelope during their replication and after completion of residual synthesis in the absence of required amino acids, as demonstrated by sedimentation velocities and the presence of high levels of cosedimenting protein. Membrane-associated folded chromosomes isolated from amino acid-starved cells sedimented more rapidly than membrane-associated folded chromosomes isolated from exponentially growing cells.

Membrane attachment of the chromosome in Bacillus subtilis mutants temperature-sensitive in DNA replication

We have examined three mutants of Bacillussubtilis temperature sensitive in DNA initiation and one temperature sensitive in DNA elongation, in order to investigate whether these lesions can cause or can result in a detachment of the membrane-bound chromosomal region. Our results argue against any effect of the mutations examined on the association between the chromosome and the membrane.

New method for large-scale preparation of covalently closed lambda DNA molecules

A combination of mutations in bacteriophage lambda and its host Escherichia coli K-12 provides a convenient system for the isolation of large quantities of covalently closed circular DNA molecules. We describe two procedures for the large scale preparation of lambda DNA in the duplex circular form.

The rep mutation. III. Altered structure of the replicating Escherichia coli chromosome

The rep gene function of Escherichia coli is essential for the replication of P2 and phiX174 double-stranded deoxyribonucleic acid (DNA). Compared with isogenic rep(+) strains, rep mutants show the following characteristics: larger cell size, more DNA per cell, and a slightly lower DNA/mass ratio. The replicating rep chromosomes show a steeper gradient of marker frequencies and contain more replicating forks per chromosome. The nucleoid body of rep mutants sediments faster and contains more DNA. We deduce that the rep function is required for the "normal" replication of the E. coli chromosome and that in its absence the E. coli chromosome replicates in an altered manner, perhaps involving slower-moving replicating forks.

Size of the chromosome of Pseudomonas aeruginosa PAO

Electron microscope examination and velocity sedimentation analysis of the deoxyribonucleic acid released from Pseudomonas aeruginosa spheroplasts indicate that this organism carries the bulk of its genetic determinants in a single duplex deoxyribonucleic acid molecule having a molecular mass of 2.1 x 10(9) daltons.

Replication of the Escherichia coli chromosome with a soluble enzyme system

Semi-conservative DNA synthesis is observed when the isolated, folded E. coli chromosome is supplemented with a DNA-free, soluble enzyme fraction, the four deoxynucleoside 5'-triphosphates, ATP, and Mg(++). The DNA synthesized in vitro remains associated with the folded chromosome during sedimentation through neutral sucrose, but is released as small DNA fragments in alkali. Sealing of these replicative intermediates to the chromosome requires the presence of both E. coli DNA polymerase I (EC 2.7.7.7) and DNA ligase (EC 6.5.1.2).

Coiled rings of DNA released from cells infected with bacteriophages T7 or T4 or from uninfected Escherichia coli

The replicating intracellular DNA of phage T7 was labeled at high specific activity with tritiated thymidine. The DNA of uninfected Escherichia coli was similarly labeled. Portions of cells which contained replicating phage T7 or E. coli DNA were lysed by a lysozyme, freeze-thaw, sodium lauryl sulfate procedure, and the DNA was spread on Millipore membranes for visualization by autoradiography. The DNA of phage T7 appeared to be highly concatenated reaching lengths of up to 721 mum. Much of the DNA of phage T7 and E. coli was retained in compact globular structures. In addition, orderly coiled rings of varying diameter up to about 43 mum were regularly observed. Similar coiled ring structures were also observed in autoradiographs of replicating phage T4 DNA which had been prepared in previous experiments. Worcel and Burgi (27) have presented evidence that E. coli chromosomes, when gently extracted from cells, are in a multilooped and superhelically twisted configuration. The coiled rings which we have observed may correspond to the relaxed, multilooped configurations which they find when the superhelical twists have been relieved by one or more nicks in each loop.

Unfolding of the host genome after infection of Escherichia coli with bacteriophage T4

The folded genome of Escherichia coli is converted to a slower-sedimenting form within 5 min after infection with bacteriophage T4 or T4nd28(den A)-amN82(44). Chloramphenicol sensitivity and response to UV-irradiation of the phage suggest participation of viral-induced functions.

Mode of Pisatin Induction: Increased Template Activity and Dye-binding Capacity of Chromatin Isolated from Polypeptide-treated Pea Pods

Increases in phenylalanine ammonia lyase activity and pisatin synthesis were induced in excised pea pods (a) by basic polypeptides such as protamine, histone, lysozyme, cytochrome c, and ribonuclease; (b) by the polyamines spermine, spermidine, cadaverine, and putrescine, and (c) by the synthetic oligopeptides poly-l-lysine, poly-dl-ornithine, and poly-l-arginine.Poly-l-lysine (1 milligram per milliliter, molecular weight 7,200) was utilized as a model inducer of pisatin and phenylalanine ammonia lyase. The poly-l-lysine-induced responses could be inhibited by adding the RNA synthesis inhibitors cordycepin or alpha-amanitin to the pods prior to or at the time of inducer application. Cordycepin added 1.5 hours after inducer no longer completely inhibited induction. The application of poly-l-lysine was shown to characteristically change the rate of RNA synthesis within 30 minutes. Ultrastructural changes in pea nuclei were detected within 3 hours, and gross changes in nuclear morphology were apparent at 14 hours after inducer application. The physical appearance of uranyl acetate-stained chromatin isolated from poly-l-lysine 2 hours after inducer application differed from that of water-treated tissues. The template properties of chromatin extracted from pods 3 hours after inducer application were consistently superior to control chromatin when assayed with Escherichia coli RNA polymerase (without sigma factor). Chromatin from poly-l-lysine-induced tissue also bound 49% more actinomycin D-(3)H.The DNA-complexing properties of inducer compounds and the induced changes in the template and dye-binding properties of pea chromatin formed the basis for a proposed mode of action for phytoalexin induction.

Effect of rifampin on the structure and membrane attachment of the nucleoid of Escherichia coli

Deoxyribonucleic acid (DNA) of Escherichia coli was found to be attached to the cell membrane at about 20 points. This was determined by fractionation of X-irradiated cells with the M band (magnesium-Sarkosyl crystals) technique. The number of attachment points was computed from the relationship between the amount of DNA in M bands and the number of double-strand breaks introduced by the X-ray treatment. The number of attachment points was decreased fourfold by treatment of cells with rifampin. This effect was apparently due to the action of the drug on ribonucleic acid (RNA) polymerase since the drug did not affect a mutant whose RNA polymerase is resistant to rifampin. This suggests that there may be two classes of attachment points of DNA on the membrane, some of which are removed by rifampin treatment and some which are not. Rifampin treatment also resulted in the uncondensing of isolated nucleoids and in an axial appearance of the nucleoids in ultrathin sections. The results suggest that RNA polymerase plays a role, direct or indirect, in maintaining the structure of the bacterial nucleoid and in some of its attachment to the membrane.

Molecular nature of mammalian cell DNA in alkaline sucrose gradients

Mammalian cell DNA that exhibited anomalous sedimentation in alkaline sucrose gradients was examined directly by electron microscopy. Its appearance was that of duplex DNA. In addition, some duplex DNA was observed under conditions in which the sedimentation anomaly was no longer apparent. Persistence of double-stranded DNA under denaturing conditions suggests caution in the interpretation of changes in the molecular weight or conformation of DNA based solely on analysis of sedimentation profiles.

Initiation of deoxyribonucleic acid replication in a temperature-sensitive mutant of B. subtilis: evidence for a transcriptional step

A mutant of Bacillus subtilis unable to initiate a new round of replication at 45 C has been described. Here we show that inhibition of DNA synthesis in this mutant is reversible and that DNA synthesis is resumed at low temperature, even in the presence of chloramphenicol. Initiation of a new replication cycle thus can occur in the absence of protein synthesis. A thermolabile component required for initiation therefore appears to be synthesized at 45 C in an inactive form and can be activated at 30 C in the presence of an inhibitor of protein synthesis. Although resistant to chloramphenicol, the reinitiation of replication occurring after lowering the temperature is sensitive to rifampin and streptolydigin.

Nucleoid condensation and cell division in Escherichia coli MX74T2 ts52 after inhibition of protein synthesis

The reorganization of the bacterial nucleoid of an Escherichia coli mutant, MX74T2 ts52, was studied by electron microscopy after protein synthesis inhibition by using whole mounts of cell ghosts, ultrathin-sectioning, and freeze-etching. The bacterial nucleoid showed two morphological changes after chloramphenicol addition: deoxyribonucleic acid (DNA) localization and DNA condensation. DNA localization was observed 10 min after chloramphenicol addition; the DNA appeared as a compact, solid mass. DNA condensation was observed at 25 min; the nucleoid appeared as a cytoplasm-filled sphere, often opened at one end. Ribosomes were observed in the center. Giant nucleoids present in some mutant filaments showed fused, spherical nucleoids arranged linearly, suggesting that the tertiary structure of the nucleoid reflects the number of replicated genomes. Inhibitors which directly or indirectly blocked protein synthesis and caused DNA condensation were chloramphenicol, puromycin, amino acid starvation, rifampicin, or carbonyl cyanide m-chlorophenyl hydrazone. All inhibitors that caused cell division in the mutant also caused condensation, although some inhibitors caused condensation without cell division. Nucleoid condensation appears to be related to chromosome structure rather than to DNA segregation upon cell division.

Reconstitution of colicin E2-induced deoxyribonucleic acid degradation in spheroplast preparations

Spheroplasts are insensitive to colicin E(2) and do not show deoxyribonucleic acid (DNA) degradation even in the presence of massive amounts of E(2). However, when both endonuclease I and E(2) were present, spheroplast DNA was degraded by an endonucleolytic activity which gave rise primarily to double-strand DNA cleavages, producing fragments having an average molecular weight of 9 x 10(6). Pancreatic ribonuclease could substitute for colicin E(2) in the reconstitution system, but pancreatic deoxyribonuclease could not replace endonuclease I. However, colicin E(2) could not activate transfer ribonucleic acid-inhibited endonuclease I in an in vitro system where pancreatic ribonuclease caused full stimulation.

DNA replication of induced prophage in Haemophilus influenzae

DNA synthesis during transition from the lysogenic state to the lytic cycle and throughout the latter has been studied in Haemophilus influenzae BC200 (HP1c1). Following exposure to ultraviolet light, there is a 30-min delay in DNA synthesis after which there is a rapidly increasing rate of phage DNA synthesis. The phage genome is replicated without extensive utilization of segments or of breakdown products of the bacterial chromosome. The mode of phage DNA replication was investigated by zonal sedimentation of labeled DNA in 5 to 20% neutral and alkaline sucrose gradients. Tritiated thymidine, incorporated during a 2-min pulse given at 38 min, chases rapidly into DNA, sedimenting like linear DNA of approximately 2 x 10(8) daltons, and then, at the expense of label in this peak, chases into slower-sedimenting phage DNA (2 x 10(7) daltons). The fast-sedimenting, rapidly labeled DNA satisfies certain criteria for being a concatenated replicative intermediate. Observations in the electron microscope revealed linear concatemers in the faster-sedimenting material and circular phage-sized DNA in the slower-sedimenting DNA. When induced cells are gently lysed with lysozyme and Brij 58 to maintain DNA-membrane associations and sedimented in neutral sucrose over a cesium chloride shelf, the concatemer is found with the cell-membrane-wall complex. Membrane-associated label chases to membrane-free material sedimenting like deproteinized HP1c1 DNA. When membrane-associated DNA from the cesium chloride shelf is deproteinized and resedimented in neutral sucrose, the sedimentation profile reveals that sedimentation rates of labeled DNA from this complex are indicative of sizes ranging from 2 x 10(8) daltons down to phage-sized pieces of 2 to 3 x 10(7) daltons. A model is presented which places HP1c1-DNA replication on the cell membrane where a concatemer of phage DNA is synthesized and subsequently degraded to phage-equivalent DNA. Phage-equivalent DNA is then either released from the membrane for packaging or is packaged while still membrane associated. Thus, the cell membrane is not only the site of DNA replication during which phage DNA is synthesized in multiple phage-equivalent concatemers but it is also the site at which these concatemers are selectively reduced to phage-sized pieces.

Effect of inhibition of macromolecule synthesis on the association of bacteriophage T4 DNA with membrane

The "Mg(2+)-Sarkosyl crystals" (M band) technique distinguishes between membrane-bound and free intracellular DNA. This procedure was employed to investigate the nature of the reactions necessary to convert input T4 DNA to a rapidly sedimenting form. Energy poisoning inhibits this attachment reaction. Neither protein nor DNA synthesis appears to be required, but experiments with rifampin and extensively irradiated T4 suggest that RNA synthesis is involved. These results were confirmed by a second procedure for the determination of rapidly sedimenting DNA.

Physiology and cytological chemistry blue-green algae

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State of adenovirus 2 deoxyribonucleic acid in the nucleus and its mode of transcription: studies with isolated viral deoxyribonucleic acid-protein complexes and isolated nuclei

Newly replicated adenovirus 2 deoxyribonucleic acid (DNA) can be isolated from the nucleus of HeLa cells by a gentle lysis procedure as a fairly homogeneous complex with a sedimentation of 73S. The viral DNA complex can be prepared completely free from host cell DNA. The viral complex is slightly active in ribonucleic acid (RNA) synthesis in vitro. Treatment of the complex with Pronase and sodium dodecyl sulfate converts the DNA to a form which sediments at 43S. Nuclei isolated from adeno-infected cells synthesize high-molecular-weight virus-specific RNA in vitro. Optimal RNA synthesis requires a divalent cation, preferentially manganese, and relatively high salt concentrations. The synthesis of virus-specific RNA by the isolated nuclei is strongly inhibited by low doses of alpha-amanitine. The latter experimental result is discussed in terms of the polymerase used to transcribe the adenovirus DNA in vivo.

Morphokinetic reaction of Streptococcus faecalis (ATCC 9790) cells to the specific inhibition of macromolecular synthesis: nucleoid condensation on the inhibition of protein synthesis

In glutaraldehyde-prefixed exponential-phase cells of Streptococcus faecalis the nucleoid is "frozen" in a dispersed configuration. Exposure of exponential-phase cells to threonine starvation or to antibiotics inhibiting protein synthesis resulted in progressive condensation of nucleoid fibrils producing an expanding central nucleoid zone or pool. The condensation of the nucleoid was observed to occur at a rate directly proportional to the rate of inhibition of protein synthesis. However, the extent of nucleoid condensation depended on continuing deoxyribonucleic acid synthesis. Significantly less nucleoid condensation occurred when cells were inhibited in deoxyribonucleic acid and protein synthesis than when cells were inhibited in protein synthesis alone. These results suggest a model in which, during nucleoid replication, the chromosome fibrils are normally maintained in a dispersed state by the active agents of transcription-translation, such as ribonucleic acid polymerase molecules and ribosomes.