Y-family DNA polymerases in Escherichia coli

The observation that mutations in the Escherichia coli genes umuC+ and umuD+ abolish mutagenesis induced by UV light strongly supported the counterintuitive notion that such mutagenesis is an active rather than passive process. Genetic and biochemical studies have revealed that umuC+ and its homolog dinB+ encode novel DNA polymerases with the ability to catalyze synthesis past DNA lesions that otherwise stall replication--a process termed translesion synthesis (TLS). Similar polymerases have been identified in nearly all organisms, constituting a new enzyme superfamily. Although typically viewed as unfaithful copiers of DNA, recent studies suggest that certain TLS polymerases can perform proficient and moderately accurate bypass of particular types of DNA damage. Moreover, various cellular factors can modulate their activity and mutagenic potential.     

Breakdown of DNA in X-Irradiated Escherichia coli

A comparison of differences in incorporation and loss of radio-activity between two strains of Escherichia coli shows that: (a) three times as much irradiation is necessary to produce the same reduction in incorporation of H³-thymidine in B/r, the resistant strain, as in B_{s - 1}, the sensitive one; (b) radioactivity is lost from the DNA of previously labeled bacteria during the first few cell generations after X-ray exposure, and even though the initial rate of loss is similar for all strains, the sensitive one loses much more label; (c) loss of DNA is a complicated function of dose. Losses increase with dose up to 25 or 50 kr in both strains; with higher doses, losses decrease in B_{s - 1} but are unchanged in B/r. Since in both strains labeled RNA is retained in irradiated cells, lysis has not occurred but the DNA is broken down into small pieces which leak from each cell. Losses from either strain do not occur at ice-bath temperature, indicating that breakdown is a function of metabolic processes. A proposed mechanism for X-ray damage and repair is advanced.     

Purification of Escherichia coli DNA photolyase

Escherichia coli photolyase is a DNA repair enzyme which monomerizes pyrimidine dimers, the major UV photoproducts in DNA, to pyrimidines in a light-dependent reaction. We recently described the construction of a tac-phr plasmid that greatly overproduces the enzyme (Sancar, G. B., Smith, F. W., and Sancar, A. (1983) Nucleic Acids Res. 11, 6667-6678). Using a strain carrying the overproducing plasmid as the starting material, we have developed a purification procedure that yields several milligrams of apparently homogeneous enzyme. The purified protein is a single polypeptide that has an apparent Mr of 49,000 under both denaturing and nondenaturing conditions. The enzyme has no requirement for divalent cations and it restores the biological activity of irradiated DNA only in the presence of photoreactivating light. The purified photolyase has a turnover number of 2.4 dimers/molecule/min; this value agrees well with the in vivo rate of photoreactivation in E. coli.     

A DNA damage checkpoint in Escherichia coli

An early attempt to find out if the DNA double helix is actively unwound before being replicated was not conclusive, but it did disclose the existence of a unique moment in the life cycle of Escherichia coli when the cell registers whether or not its DNA is intact. If not, the cell embarks on rapid breakdown of its DNA, like "apoptosis" in eukaryotic cells.     

Methyl-directed DNA mismatch repair in Escherichia coli

Some of the molecular aspects of methyl-directed mismatch repair in E. coli have been characterized. These include: mismatch recognition by mutS protein in which different mispairs are bound with different affinities; the direct involvement of d(GATC) sites; and strand scission by mutH protein at d(GATC) sequences with strand selection based on methylation of the DNA at those sites. In addition, communication over a distance between a mismatch and d(GATC) sites has been implicated. Analysis of mismatch correction in a defined system (Lahue et al., unpublished) should provide a direct means to further molecular aspects of this process.     

DNA synthesis in Escherichia coli in the presence of cyanide

The addition of cyanide to an exponentially growing culture of Escherichia coli causes an immediate, but spontaneously reversible, inhibition of DNA synthesis. The small amount of DNA which is synthesized appears to be the product of the chromosomal replication fork. However, a substantial number of single-strand interruptions persist in the newly synthesized DNA, so that covalent linkage to the preformed DNA does not occur for many minutes. Since the presence of cyanide causes a shift from DPN to DPNH, it is suggested that the DPN-linked joining activity in these cells is inhibited because of the lowered DPN concentration.     

Amplification of Hot DNA segments in Escherichia coli

In Escherichia coli, a replication fork blocking event at a DNA replication terminus (Ter) enhances homologous recombination at the nearby sister chromosomal region, converting the region into a recombination hotspot, Hot, site. Using a RNaseH negative (rnhA-) mutant, we identified eight kinds of Hot DNAs (HotA-H). Among these, enhanced recombination of three kinds of Hot DNAs (HotA-C) was dependent on fork blocking events at Ter sites. In the present study, we examined whether HotA DNAs are amplified when circular DNA (HotA plus a drug-resistance DNA) is inserted into the homologous region on the chromosome of a rnhA- mutant. The resulting HotA DNA transformants were analysed using pulsed-field gel electrophoresis, fluorescence in situ hybridization and DNA microarray technique. The following results were obtained: (i) HotA DNA is amplified by about 40-fold on average; (ii) whereas 90% of the cells contain about 6-10 copies of HotA DNA, the remaining 10% of cells have as many as several hundred HotA copies; and (iii) amplification is detected in all other Hot DNAs, among which HotB and HotG DNAs are amplified to the same level as HotA. Furthermore, HotL DNA, which is activated by blocking the clockwise oriC-starting replication fork at the artificially inserted TerL site in the fork-blocked strain with a rnhA+ background, is also amplified, but is not amplified in the non-blocked strain. From these data, we propose a model that can explain production of three distinct forms of Hot DNA molecules by the following three recombination pathways: (i) unequal intersister recombination; (ii) intrasister recombination, followed by rolling-circle replication; and (iii) intrasister recombination, producing circular DNA molecules.