Ivar Lossius

Purification and characterization of the 17 K protein, a DNA-binding protein from Escherichia coli

A basic protein of molecular mass 17 kDa (protein 17 K) which binds to relaxed DNA has been isolated and purified to homogeneity from Escherichia coli cells. The protein behaves as a tetramer in solution and there are 4800 monomers per cell in exponentially growing cells. The amino-acid composition and N-terminal sequence were determined. No effect of the protein on in vitro transcription was observed. The protein was shown to be different from the Ssb protein (Sigal, N. et al. (1972) Proc. Natl. Acad. Sci. USA 69, 3537-3541), protein H1 (Cukier-Kahn et al. (1972) Proc. Natl. Acad. Sci. USA 69, 3643-3647) and the HLP-1 protein (Lathe, R. et al. (1980) Proc. Natl. Acad. Sci. USA 77, 3548-3552).

DNA- and RNA-binding proteins of chromatin from Escherichia coli

The different proteins present in chromatin of Escherichia coli have been analyzed by a variety of techniques. The chromatin was isolated using a previously published procedure (Sjåstad, K., Fadnes, P., Krüger, P.G. Lossius, I. and Kleppe, K. (1982) J. Gen. Microbiol. 128, 3037) and solubilized by the action of micrococcal nuclease or DNAase I. The DNA-protein and RNA-protein complexes thus obtained were purified by sucrose gradient centrifugation and isopycnic gradient centrifugation in metrizamide in low ionic strength. The protein: DNA ratio of the DNA-protein complexes was estimated from the latter method and found to be approx. 1.75. The protein components were analyzed further by one- and two-dimensional gel electrophoresis. Approx. 15 major polypeptides were detected in the DNA-protein complex, whereas 10 were present in the RNA-protein complex. The majority of the polypeptides in both complexes had acidic isoelectric pH. The polypeptides in the two complexes differed markedly and only two polypeptides, having molecular weights of 57,000 and 37,000, respectively, were found to be common in both complexes. In agreement with earlier studies, the basic protein HU was not present in the DNA-protein complex. Affinity studies of the proteins from chromatin using DNA- and RNA-Sepharose columns in general confirmed the above conclusions. The two-dimensional gel electrophoretic patterns of the proteins in the different complexes were compared with those of proteins in the inner and outer membranes. Only one of the major polypeptides present in the inner membrane, having a molecular weight of 57,000, was enriched in the DNA-protein complex.

Isolation, Properties and Nucleolytic Degradation of Chromatin from Escherichia coli

A new procedure has been developed for the isolation of the chromosome complex, termed chromatin, from Escherichia coli. The bacteria were subjected to low ionic strength and T4 lysozyme, followed by detergent treatment analogous to that employed for the isolation of eukaryotic chromosomes. The chromatin was an insoluble viscous material which contained approximately equal amounts of DNA and RNA. The protein content of the chromatin was almost three times greater than the nucleic acid content. Electron microscopy revealed that the chromatin was highly condensed, having multiple loops and beaded structures with various diameters. The chromatin could be completely solubilized by both micrococcal nuclease and DNAase I, whereas RNAase had no effect. The initial degradation by micrococcal nuclease resulted in the production of a DNA-protein particle, sedimentation coefficient 10S, and an RNA-protein complex of 24S. Further degradation led to a decrease in sedimentation coefficient of the DNA-protein complex, but not of the RNA-protein particle. The peak size of the DNA of the initial DNA-protein particle was approximately 2400 bp. The action of micrococcal nuclease also resulted in the production of several discrete RNA species of various sizes. Several low molecular weight proteins (12000-27000) were found in the DNA-protein complex. The DNA-binding protein HU was present in the undigested chromatin; varying amounts of HU were, however, detected in the DNA-protein and RNA-protein particles.

Effect of Methyl Methanesulphonate on the Nucleoid Structure of Escherichia coli

Incubation of a strain of Escherichia coli K12 with 25 mM-methyl methanesulphonate (MMS) for 1 h changed the sedimentation coefficient of the nucleoids from 1600S to 850S. When isolated nucleoids were treated with MMS under identical conditions in vitro there was no change in the sedimentation coefficient. Alkaline sucrose-gradient centrifugation of DNA from cells treated with 25 mM-MMS for 1 h indicated that there were approximately 100 breaks plus apurinic sites per chromosome. Titration with ethidium bromide of nucleoids from MMS-treated cells showed that almost all supercoiling had been lost, suggesting that the breaks plus apurinic sites consisted mostly of breaks. Further experiments showed that the apurinic sites were probably created by non-enzymic depurination and that little non-enzymic strand breakage had occurred. The depurinated sites thus created could then serve as substrates for the apurinic-specific endonucleases of the cell, with the result that strand breakage occurred. MMS treatment did not cause any changes in the DNA:RNA ratio of the nucleoids. Removal of MMS followed by a period of incubation resulted in a decrease in the number of breaks plus apurinic sites and an increase in the sedimentation coefficient of the nucleoids. After 2 h incubation in MMS-free medium the sedimentation coefficient of the nucleoids from MMS-treated cells was the same as that of the control; the supercoiling was also partially restored. The effect of MMS on two MMS-sensitive mutants of E. coli, one a polA and the other a recA mutant, was also studied. In both cases MMS caused complete collapse of the nucleoid structure.

Mechanism of caffeine-induced inhibition of DNA synthesis in Escherichia coli

Caffeine inhibited DNA synthesis in toluene‐treated Escherichia coli K 12 strains to the same extent as in intact cells using the incorporation of [3H]thymidine as a measure of DNA synthesis. The inhibition was found to be competitive with ATP, and it was not influenced by the concentrations of deoxynucleoside triphosphates to any extent. When caffeine was added together with other DNA synthesis inhibitors such as novobiocin, nalidixic acid or actinomycin D, the inhibition in all cases was non‐additive. It is suggested that caffeine inhibits one of the ATP‐requiring enzymes in the DNA replication machinery, possibly DNA polymerase III or one of the DNA helicases.

Two-dimensional Gel Electrophoretic Separation of the Proteins Present in Chromatin of Escherichia coli

The polypeptides present in 35S-labelled chromatin prepared from Escherichia coli cells, and polypeptides present in the DNA and RNA complexes obtained by micrococcal nuclease digestion of the chromatin, were analysed by two-dimensional non-equilibrium polyacrylamide gel electrophoresis. Three hundred and thirty-five 35S-labelled polypeptides were detected in the chromatin whereas the DNA- and RNA-containing fractions of the micrococcal nuclease digest contained 126 and 183 polypeptides respectively. The major basic low-molecular-weight polypeptides were found in the DNA-containing fractions.

The Structure of the Bacterial Nucleoid

In prokaryotic organisms the chromosome is present in a nucleuslike body termed the nucleoid (1, 2). The nuclear membrane is, however, absent in prokaryotic cells. Most of our knowledge concerning the structure and organization of the nucleoid comes from studies with Escherichia coli. The condensed form of the chromosome can be visualized by phase contrast microscopy directly in living prokaryotic cells (3–5). The mode of division of the nucleoid can also clearly be seen. Escherichia coli cells growing in a minimal medium contain one or two separate nucleoids per cell. When this organism is grown in a rich medium the cells possess two nucleoids per cell.

Influence of Alkylating Agents on the Structure of the Bacterial Nucleoid

Alkylating agents such as methyl methane sulfonate (MMS) and mitomycin C cause large changes in the nucleoid structure of Escherichia coli. In the presence of high concentrations of these compounds, 25 and 0.1 mM respectively, relaxation of the supercoiled structure takes place. This can be demonstrated both by centrifugation studies as well as by phase contrast microscopy of the cells. Low concentrations of mitomycin C, 1–10 μM, on the other hand Cause a rec A dependent increase in the nucleoid mass. During repair, in the absence of the alkylating agents, the number of breaks decreases and supercoiling is introduced again into the nucleoid. The data suggest that consideration of the 3-dimensional structure may be important both during mutagenesis and repair.

Mitomycin-C-induced changes in the nucleoid of Escherichia coli K12

The influence of low concentrations of mitomycin-C on the structure of the envelope-free nucleoid was studied in several strains of Escherichia coli K12. The wild-type strain AB1157 uvr+ rec+ and 3 mitomycin-C-sensitive derivatives carrying mutations in the uvrA, uvrB and recA genes, were used. Treatment of the control strain with mitomycin-C, 0.5 microgram/ml, followed by incubation in drug-free medium resulted in the formation of a transient fast-sedimenting nucleoid with a sedimentation coefficient of 2200 S. A fraction of 25% of the nucleoids had attained the normal sedimentation coefficient of 1570 S 3 h after removal of mitomycin-C. With the uvr- strains, mitomycin-C induced a slow, almost linear increase in the S value of the envelope-free nucleoid. In these cases the S value continued to increase during post-incubation and was 2050 S 3 h after removal of the drug. Post-incubation of recA- cells resulted in loss of supercoiling, decrease in S value of the nucleoid and degradation of DNA. Results obtained with phase-contrast and electron microscopy were in good agreement with the hydrodynamic data.