The deoxyribonucleic acid unwinding protein of Escherichia coli. Properties and functions in replication

The product of the lexC gene of Escherichia coli is single-stranded DNA-binding protein

Extracts from lexC113 cells could not support phage G4 DNA-dependent replication unless supplemented with single-stranded DNA-binding protein. Purified lexC113 binding protein supported synthesis in a reconstituted replication assay, using purified proteins at 30 but not at 42 degrees C, indicating that the product of the lexC113 gene is an altered single-stranded DNA-binding protein.

Variable expression of the ssb--1 allele in different strains of Escherichia coli K12 and B: differential suppression of its effects on DNA replication, DNA repair and ultraviolet mutagenesis

We have transduced the mutant allele ssb-1, which encodes a temperature-sensitive single-strand DNA binding protein (SSB), into several Escherichia coli strains, and have examined colony-forming ability, DNA replication, sensitivity to ultraviolet light (UV) and UV-induced mutability at the nonpermissive temperature. We have found: 1) that the degree of ssb-1-mediated temperature-sensitivity of colony-forming ability and of DNA replication is strain-dependent, resulting in plating efficiencies at 42 degrees C (relative to 30 degrees C) ranging from 100% to 0.002%; 2) that complete suppression of the temperature-sensitivity caused by ssb-1 occurs only on nutrient agar, and not in any other medium tested; 3) that strains in which ssb-1-mediated temperature-sensitivity is completely suppressed show moderate UV sensitivity and normal UV mutability at 30 degrees C, but much more extreme UV sensitivity and drastically reduced UV mutability at 42 degrees C; and 4) that defects in excision repair or in other Uvr+-dependent processes are not responsible for most of the UV sensitivity promoted by ssb-1. We discuss our results in relation to the known properties of SSB and its possible role in the induction of DNA damage-inducible (SOS) functions.

Proteins that shape DNA

During the last five years, considerable accumulation of data on nucleic acids metabolism leads to the discovery of a number of proteins designed to change the conformation of DNA and to "shape" it. Experimental results emphasize the importance of the conformation and the flexibility of DNA itself in such interactions. The mutual recognition of nucleic acids by proteins may be or not dependent on the nnucleotide sequence and in most cases is accompanied by conformational changes in the proteins involved. Among these are proteins that bind in stoichiometric amounts to DNA, proteins that promote the separation of the two strands in a duplex, and finally proteins that change the topology of DNA.

Studies on Escherichia coli chromosome proteins. I. Analysis of the proteins by two-dimensional gel electrophoresis

As an approach for studying the function of chromosome proteins in DNA replication and gene expression, proteins remaining attached to Escherichia coli nucleoids were analyzed by two-dimensional polyacrylamide slab gel electrophoresis. Nucleoids were isolated by gentle lysis of the cells in the presence of a DNA counter-ion such as 1 M NaCl or 5 mM spermidine. In exponentially growing cells, about 100 proteins have been found to exist in the nucleoids. Kinetic studies indicated that the number of chromosome proteins remaining attached varied with time after synchronization. Based on the pattern of the variation, appearance, increase or disappearance of the 29 major proteins, nucleoid proteins were shown to be classified in six different groups (groups A--F). A strong correlation was observed between the variation of proteins belonging to group D and initiation of DNA synthesis or cell division.

Purification from Tetrahymena thermophila of DNA polymerase and a protein which modifies its activity

Two proteins, which may be involved in DNA replication, have been isolated and characterized from the eukaryote Tetrahymena thermophila. One of these proteins, DNA polymerase, has been purified to apparent homogeneity. The enzyme has a native molecular weight of approximately 90 000 in the presence of salt and aggregates to higher-molecular-weight forms in the absence of salt. Purified preparations of the enzyme yield a major subunit of Mr 45 000 when the protein is analyzed by denaturing electrophoresis. Tetrahymena DNA polymerase requires a divalent cation for catalysis and prefers gapped template-primers over denatured and native DNAs. A template-primer such as poly(dT) . oligo(A) can also be elongated by the DNA polymerase. However, the enzyme will not use poly(A) . oligo(dT) as a template-primer. Sulfhydryl-blocking reagents, such as N-ethylmaleimide, inhibit Tetrahymena DNA polymerase. The DNA polymerase lacks assayable levels of both single and double-stranded deoxyribonuclease activity. Throughout the early stages of purification the DNA polymerase chromatographs together with a protein of molecular weight 100 000. This protein, which yields a single major polypeptide of Mr 25 000 when analyzed by denaturing electrophoresis, has single-stranded-DNA-binding properties and has the ability to stimulate both the rate and extent of DNA-polymerase-catalyzed DNA synthesis in vitro. By virtue of this latter ability, the protein has been referred to as the M (for 'modifying') protein. Maximum stimulation of DNA polymerase was achieved with template-primers, which contained large stretches of single-stranded template such as poly(dA) . (dT)10 mixed in a template-to-primer ratio of one to one. Stimulation of DNA polymerase activity by M protein in vitro appears to involve formation of longer product DNA.

Unwinding and rewinding of DNA by the RecBC enzyme

Under physiological conditions the initial action of the RecBC enzyme (exonuclease V) on duplex DNA is unwinding of the DNA strands. We have examined by electron microscopy the initial products of this unwinding reaction. When such reactions are carried out in the presence of DNA binding protein, unwinding structures are seen both at the terminus of the duplex DNA and at locations remote from the ends of the DNA molecule. Both terminal and internal unwinding structures proceed along DNA at about 300 nucleotides per second, and the single-stranded loops in both types of structure enlarge at about 100 nucleotides per second. In the internal unwindings DNA must be rewound behind the enzyme at about 200 nucleotides per second. The structures do not occur on supercoiled or nicked circular DNA, indicating that free ends are needed for their formation. In the absence of DNA binding protein only internal unwinding structures are seen, suggesting that the internal structures are formed from the terminal unwindings by base-pairing of their unwound single-strand tails. We present a model which incorporates these structures and is consistent with previous observations on the unwinding and degradative actions of the enzyme. In this model the enzyme travels through duplex DNA by unwinding the DNA ahead of itself and rewinding it behind itself. The internal unwindings produced by the RecBC enzyme could be active in initial synapsis step in genetic recombination.

Stimulation of deoxyribonucleic acid replication fork movement by spermidine analogs in polyamine-deficient Escherichia coli

We examined the rate of deoxyribonucleic acid (DNA) replication fork movement in polyamine-deficient cells of Escherichia coli by two independent techniques. DNA autoradiography was used to directly visualize the length of DNA produced during a given time interval, and replication rates were calculated. The amount of DNA synthesized after blocking protein synthesis also allowed calculation of replication rates. We found that the DNA chain elongation rate in polyamine-deficient cells was about half that of putrescine- or spermidine-supplemented cells. We also found that spermidine homologs of increasing chain length, when present at equal intracellular concentrations, exhibited a decreasing ability to support growth and the rate of DNA replication fork movement. The kinetics of recovery of DNA synthesis from the polyamine-deficient state were also investigated. A new rate of DNA synthesis was reached about 20 min after addition of spermidine to polyamine-limited cells. The rise in the rate of DNA synthesis was preceded by a rise in the intracellular concentration of spermidine.

Physical chemical studies of the structure and function of DNA binding (helix-destabilizing) proteins

Binding of proteins to DNA is fundamental to the mechanisms of replication, recombination and gene expression. The specific molecular features of DNA recognized by complementary features of the three-dimensional structure of the DNA binding proteins are under intensive investigation. Two large classes of DNA binding proteins have emerged. One class includes enzymes such as the RNA polymerases and restriction endonucleases and the nonenzymatic repressor proteins which recognize unique sequences present in only one or a few copies per genome. A second group is made up of non-sequence-specific DNA binding proteins which bind to DNA at high density and modulate subsequent enzymatic transformations of the DNA. Among the latter group are those proteins originally termed "unwinding proteins", which have in common a higher affinity for single-stranded than for double-stranded DNA and thus promote the melting of double-stranded DNA. They are better termed helix-destabilizing proteins to distinguish them from the enzymes which "unwind" the helix by making and breaking phosphodiester bonds. Because the helix-destabilizing proteins form complexes with all single-stranded DNA regardless of base sequence, the molecular details of complex formation have been much more accessible to direct physicochemical measurements. Structural conclusions derived with techniques which include chemical modification, ultraviolet spectroscopy, circular dichroism, NMR, and X-ray diffraction will be reviewed. The following proteins will be discussed in detail; the gene 32 protein of bacteriophage T4, the gene 5 protein from bacteriophage fd, and the helix-destabilizing protein from E. coli. The largest amount of specific structural information is available for the gene 5 protein and specific models for this protein and its complexes with DNA based on NMR and X-ray diffraction data are presented. A number of other helix-destabilizing proteins from both prokaryotes and eukaryotes have been described and a survey of these will be given. Some of the basic molecular features of DNA-protein interactions emerging from studies of the helix-destabilizing proteins are likely to be shared by the more highly specific binding proteins like the RNA polymerases and repressors. Properties of some of these more complex systems which suggest this will be discussed.

The enzymatic replication of DNA

Enzymatic mechanisms of DNA replication have been investigated using small bacteriophages as probes to illuminate the cellular systems upon which they must rely during infection. Conversion of the circular, single-stranded DNAs of phages M13, G4, and phi X174 to their duplex forms has revealed the participation of diverse ways to start a new chain and a complex DNA polymerase III holoenzyme upon which all these systems depend for chain elongation. The phi X174 system, which is the most exacting and revealing of the host chromosomal replication pattern, includes at least twenty polypeptides for making the viral DNA into a duplex and multiplying the duplex. Resolution and purification of these numerous proteins is in train and their reconstitution into a "replisome"-like structure is envisioned.

Mutant single-strand binding protein of Escherichia coli: genetic and physiological characterization

A mutation in the Escherichia coli gene for single-strand binding protein results in temperature-sensitive deoxyribonucleic acid replication (R. R. Meyer, J. Glassberg, and A. Kornberg, Proc. Natl. Acad. Sci. U.S.A. 76:1702-1705, 1979). The mutant (ssb-1) is also more sensitive to ultraviolet irradiation and about one-fifth as active in recombination. Single-strand binding protein is thus implicated in repair and recombination as well as in replication. The mutation in ssb is located between uvrA and melA at 90.8 min on the genetic map. The ssb gene appears to be allelic with lexC, a gene with a proposed role in regulating inducible deoxyribonucleic acid repair.

Modulation of gene expression by drugs affecting deoxyribonucleic acid gyrase

Nalidixic acid (Nal), a drug which affects deoxyribonucleic acid gyrase activity, inhibits the expression of catabolite-sensitive genes: the three maltose operons, the lactose and galactose operons, and the tryptophanase gene. A correlation between the degree of sensitivity to Nal and that to catabolite repression has been observed. The expression of the threonine and tryptophan operons, insensitive to catabolite repression, is insensitive to Nal. The expression of the lacZ gene under the control of the IQ promoter is activated by Nal. Strains carrying a mutation in the nalA locus are resistant to these effects. Novobiocin, which inhibits the negative supercoiling activity of deoxyribonucleic acid gyrase, affects expression of the operons similarly to Nal. The involvement of promoters in Nal and novobiocin action, as well as a possible role of in vivo negative supercoiling in the selectivity of gene expression, are discussed.

Replication of M13 duplex DNA in soluble extracts of Escherichia coli. Effect of helix-destabilising proteins

Soluble extracts of M13-am5-infected Escherichia coli cells can carry out multiple rounds of M13 duplex DNA replication when supplemented with helix-destabilising protein of E. coli. Similarly addition of the helix-destabilising M13 gene 5 protein in low concentrations (up to 30 micrograms/ml) stimulates the replication of double-stranded M13 DNA. In contrast, higher concentrations of gene 5 protein (but not of E. coli helix-destabilising protein) cause a preferential inhibition of complementary strand synthesis resulting in a switch from double-strand replication to single-strand synthesis. Depending on the addition of the appropriate amounts of these two helix-destabilising proteins either stage of M13 DNA replication can now be studied with cell-free preparations.

Interaction of DNA with DNA-binding proteins: protein exchange and complex stability

The competition of the DNA-binding proteins I and II of Escherichia coli and of the phage fd DNA-binding protein for single-stranded DNA was investigated. Their roles in cells might be judged from their binding affinities to DNA and their mutual exchange in the DNA . protein complexes. Strongest binding on single strands was found for the phage protein. DNA-binding protein II displaced half of the protein I in the complex with single-stranded DNA when no double-stranded DNA was present. Protein-complexed single strands were protected against degradation. The protection is less pronounced for protein II which can increase the stability of the fd DNA complex with DNA-binding protein I against nucleolytic cleavage.