DNA synthesis involving a complexes form of DNA polymerase I in extracts of Escherichia coli

chi sequences switch the RecBCD helicase-nuclease complex from degradative to replicative modes during the completion of DNA replication

Accurately completing DNA replication when two forks converge is essential to genomic stability. The RecBCD helicase-nuclease complex plays a central role in completion by promoting resection and joining of the excess DNA created when replisomes converge. chi sequences alter RecBCD activity and localize with cross-over hotspots during sexual events in bacteria, yet their functional role during chromosome replication remains unknown. Here, we use two-dimensional agarose gel analysis to show that chi induces replication on substrates containing convergent forks. The induced-replication is processive, but uncoupled with respect to leading and lagging strand synthesis, and can be suppressed by ter sites which limit replisome progression. Our observations demonstrate that convergent replisomes create a substrate that is processed by RecBCD, and that chi, when encountered, switches RecBCD from a degradative to replicative function. We propose that chi serves to functionally differentiate DNA ends created during completion, which require degradation, from those created by chromosomal double-strand breaks, which require resynthesis.

RecBCD is required to complete chromosomal replication: Implications for double-strand break frequencies and repair mechanisms

Several aspects of the mechanism of homologous double-strand break repair remain unclear. Although intensive efforts have focused on how recombination reactions initiate, far less is known about the molecular events that follow. Based upon biochemical studies, current models propose that RecBCD processes double-strand ends and loads RecA to initiate recombinational repair. However, recent studies have shown that RecBCD plays a critical role in completing replication events on the chromosome through a mechanism that does not involve RecA or recombination. Here, we examine several studies, both early and recent, that suggest RecBCD also operates late in the recombination process - after initiation, strand invasion, and crossover resolution have occurred. Similar to its role in completing replication, we propose a model in which RecBCD is required to resect and resolve the DNA synthesis associated with homologous recombination at the point where the missing sequences on the broken molecule have been restored. We explain how the impaired ability to complete chromosome replication in recBC and recD mutants is likely to account for the loss of viability and genome instability in these mutants, and conclude that spontaneous double-strand breaks and replication fork collapse occur far less frequently than previously speculated.

Chromosomal lesion suppression and removal in Escherichia coli via linear DNA degradation

RecBCD is a DNA helicase/exonuclease implicated in degradation of foreign linear DNA and in RecA-dependent recombinational repair of chromosomal lesions in E. coli. The low viability of recA recBC mutants vs. recA mutants indicates the existence of RecA-independent roles for RecBCD. To distinguish among possible RecA-independent roles of the RecBCD enzyme in replication, repair, and DNA degradation, we introduced wild-type and mutant combinations of the recBCD chromosomal region on a low-copy-number plasmid into a DeltarecA DeltarecBCD mutant and determined the viability of resulting strains. Our results argue against ideas that RecBCD is a structural element in the replication factory or is involved in RecA-independent repair of chromosomal lesions. We found that RecBCD-catalyzed DNA degradation is the only activity important for the recA-independent viability, suggesting that degradation of linear tails of sigma-replicating chromosomes could be one of the RecBCD's roles. However, since the weaker DNA degradation capacity due a combination of the RecBC helicase and ssDNA-specific exonucleases restores viability of the DeltarecA DeltarecBCD mutant to a significant extent, we favor suppression of chromosomal lesions via linear DNA degradation at reversed replication forks as the major RecA-independent role of the RecBCD enzyme.

Clustering of chi sequence in Escherichia coli genome

An 8-mer DNA sequence called chi (5'-GCTGGTGG) is present on the Escherichia coli chromosome at a high frequency. It is responsible for both the attenuation of RecBCD exonuclease activity and the promotion of RecABCD-mediated homologous recombination. chi was first identified as a site that increased plaque size of bacteriophage lambda. lambda containing chi makes very small plaques on a recC* (recC1004) mutant because chi is poorly recognized by the RecBC*D mutant enzyme. We cloned E. coli chromosomal fragments in lambda that allowed lambda to form larger plaques on this recC* mutant as well as on the rec+ parent. One identified fragment contained a cluster of two copies of chi and several chi-like sequences with the same orientation. It increased recombination in the rec+ strain more than a fragment with one chi did. This fragment was within the rep gene, whose helicase product is known to be required for growth in the absence of functional RecBCD enzyme. The possibility that RecBCD enzyme might interact both with the rep gene and its product is discussed. Many of the other chi clusters identified in the E. coli genome database lie within genes for membrane proteins. The possible significance of these findings is discussed.

Biochemistry of homologous recombination in Escherichia coli

Homologous recombination is a fundamental biological process. Biochemical understanding of this process is most advanced for Escherichia coli. At least 25 gene products are involved in promoting genetic exchange. At present, this includes the RecA, RecBCD (exonuclease V), RecE (exonuclease VIII), RecF, RecG, RecJ, RecN, RecOR, RecQ, RecT, RuvAB, RuvC, SbcCD, and SSB proteins, as well as DNA polymerase I, DNA gyrase, DNA topoisomerase I, DNA ligase, and DNA helicases. The activities displayed by these enzymes include homologous DNA pairing and strand exchange, helicase, branch migration, Holliday junction binding and cleavage, nuclease, ATPase, topoisomerase, DNA binding, ATP binding, polymerase, and ligase, and, collectively, they define biochemical events that are essential for efficient recombination. In addition to these needed proteins, a cis-acting recombination hot spot known as Chi (chi: 5'-GCTGGTGG-3') plays a crucial regulatory function. The biochemical steps that comprise homologous recombination can be formally divided into four parts: (i) processing of DNA molecules into suitable recombination substrates, (ii) homologous pairing of the DNA partners and the exchange of DNA strands, (iii) extension of the nascent DNA heteroduplex; and (iv) resolution of the resulting crossover structure. This review focuses on the biochemical mechanisms underlying these steps, with particular emphases on the activities of the proteins involved and on the integration of these activities into likely biochemical pathways for recombination.

Prophage inactivation in recB-proficient Escherichia coli K12 (lambda) lysogens after ultraviolet irradiation

If ultraviolet irradiated, lambda-lysogenic Escherichia coli K12 bacteria are incubated for 4 to 6 h at 30 degrees C, lambda prophage becomes inactive in the non-surviving cells. This was demonstrated by the use of lambda cIts857ind1 prophage which can be induced by heat but not by ultraviolet light. An analysis with various bacterial mutants showed that RecBC recombination enzyme is required in conjunction with RecA protein for prophage inactivation.

Degradation of Escherichia coli DNA synthesized after ultraviolet irradiation in the absence of repair

DNA degradation in Escherichia coli uvrA recA bacteria exposed to a low dose (0.07 J/m2) of ultraviolet radiation was studied. A considerable amount of the newly-synthesized DNA, which contains gaps opposite pyrimidine dimers, is broken down. In contrast, parental, dimer-containing DNA is resistant to radiation-induced degradation.

Purification and properties of an endonuclease from the mitochondrion of Saccharomyces cerevisiae

An endonuclease, which is found only in the mitochondrion of the yeast Saccharomyces cerevisiae, has been purified. The protein has a sedimentation coefficient of 6.3 S, equivalent to a molecular weight of 105,000. The enzyme is active at pH 7.6, when it degrades single-stranded DNA about 10-times faster than double-stranded DNA, but at pH 5.4 only double-stranded DNA is degraded. In both cases the enzyme acts endonucleolytically, breaking a single phosphodiester bond at a random location within the DNA substrate. Mn2+ or Mg2+ are required for activity; Ca2+ and Zn2+ are ineffective cofactors. Enzyme activity at pH 7.6 is severely inhibited by low concentrations of NaCl or KCl, while activity at pH 5.4 is unaffected by salt. Ethidium bromide inhibits both the DNase activity at pH 5.4 and the activity with single-stranded DNA at pH 7.6, but has no effect on the DNase activity with double-stranded DNA at pH 7.6.

Studies on the mechanism of action of the ATP-dependent DNAase from Alcaligenes faecalis

An ATP-dependent DNAase has been purified to homogeneity from extracts of Alcaligenes faecalis, and has been shown to couple the degradation of DNA to the hydrolysis of ATP. Enzyme activity also requires divalent ions, with Mn2+, Mg2+ and Co2+ being effective cofactors for both DNAase and ATPase activities. We have studied the intermediates formed by the enzyme during the degradation of duplex DNA with each of these cofactors using sedimentation velocity, binding to nitrocellulose filters and sensitivity to a nuclease specific for single-stranded DNA. With Mn2+ or Co2+, the enzyme acts processively to produce mostly acid-soluble material and acid-insoluble single-strand fragments up to 400-nucleotides long. However, with Mg2+ present, the enzyme produces intermediates comprising a duplex region with one or more single-strand tails, while little acid-soluble oligonucleotide is formed. From these results, we propose a model to describe the mechanism by which the ATP-dependent DNAase from A. faecalis degrades duplex DNA.

DNA polymerase I and recBC enzyme support the covalent closing of hydrogen-bonded lambda DNA circles in extracts of Escherichia coli cells

The covalent closing of hydrogen-bonded lambda DNA circles in Escherichia coli extract was observed to require DNA polymerase I, recBC enzyme and ATP. This covalent closing activity was lost in strains harbouring a mutation in one of the genes responsible for production of the enzymes mentioned above, and was recovered by combining these mutant extracts. ATP could be replaced with dATP, but not appreciably with any of the other nucleoside triphosphates. High concentrations of ATP inhibited the closure. K+ or NH4+ (0.2M) was required for optimal activity and NMN was a strong inhibitor.

An endonuclease isolated from Epstein-Barr virus-producing human lymphoblastoid cells

An endonuclease has been isolated from human B lymphoblastoid cells that copurifies with an exonucleolytic activity and has been shown to produce double-strand breaks and a high proportion of single-strandedness in phage lambda DNA in vitro. The data are consistent with a model in which single-strand cuts are made by the endonucleolytic activity, possibly in A+T-rich regions of the DNA, followed by creation of single-stranded regions (gaps) precessing from the site of a cut. Generation of overlapping gaps on opposite strands or of a gap opposite a nick would lead to the creation of the banding patterns that we have seen on electrophoretic gels. This endonucleolytic activity copurifies with other enzymes induced by Epstein-Barr virus that relate to the process of viral DNA replication in productively infected cells. However, a more general role is proposed for this class of eukaryotic endonuclease activities. A marked degree of single-strandedness has been found in the replicating DNAs of many eukaryotes, ad these gaps could be generated by endonucleases with associated exonucleolytic activity such as that reported here. This Epstein-Barr virus-induced nuclease activity has been shown to resemble the recBC nuclease isolated from the prokaryote Escherichia coli and also the endonuclease isolated from the eukaryote Chlamydomonas.

Enhancement of post-ultraviolet killing in Escherichia coli K-12 through the action of gyrase inhibitors: evidence for associated gyrase-recBC deoxyribonuclease function

This work in conjunction with the results presented in an earlier report (M. A. Purdy and K. L. Yielding, Antimicrob. Agents Chemother. 10:182--184, 1976) showed the following. (i) Nalidixic acid and novobiocin could inhibit post-ultraviolet and post-X-ray survival, implicating gyrase function in deoxyribonucleic acid repair. (ii) The inhibition of post-ultraviolet survival requires the action of functional recBC deoxyribonuclease. (iii) Structural changes in the gyrase could (a) cause recBC mutants to exhibit enhancement of post-ultraviolet killing in the presence of novobiocin, (b) increase the ultraviolet sensitivity of recBC mutants, and (c) enhance the thermal lability of a recBCts mutant.

The 'DNA-membrane complex' of Escherichia coli B/r. Its composition and properties and the fate of nascent and genome DNA during DNA synthesis

The composition and properties of 'DNA-membrane complex' of Escherichia coli B/r have been investigated. The 'complexes' contain most of the DNA and membrane of the cells, and about 50% and 25% of the RNA and protein respectively. The properties of DNA synthesized by the 'complexes' are described and the process is concluded to be largely mediated through polymerase I. Nascent DNA synthesized by the 'DNA-membrane complexes' was of two main classes, one of molecular weight around 600,000--800,000 and the other of higher molecular weight. Polynucleotide ligase activity was not detectable. The onset of synthesis coincided with the dissociation of at least 70% of the genome DNA and all of the nascent DNA from the 'complexes' and was concomitant with the action of a nuclease on parental DNA. This nuclease activity was not ATP-dependent.

Inactivation of phage repressor in a permeable cell system: role of recBC DNase in induction

UV light causes inactivation of phage (phi80) repressor molecules in a plasmolyzed, permeable cell preparation of Escherichia coli. Induction without UV irradiation occurs when the permeable cells are incubated in the presence of four deoxyribonucleoside triphosphates and ATP. The induction triggered by dNTP's requires a functional recBC gene product and is associated with degradation of the DNA replication fork. The role of recBC DNase in the induction of prophage and SOS functions in general is discussed.

Mutator mutations in bacteriophage T4 gene 42 (dHMC hydroxymethylase)

Temperature-sensitive mutations of bacteriophage T4 gene 42 produce diverse effects upon spontaneous mutation rate. G:C vector A:T transition rates are increased, often strongly; frameshift mutation rates are weakly increased; A:T vector G:C transition rates (and perhaps also A:T vector Py:Pu transversion rates) are decreased; and one G:C vector Py:Pu transversion rate is also decreased. These results, together with certain interactions between gene-42 mutator effects and both base analogue mutagenesis and the viral error-prone repair system, suggest that the dHMC hydroxymethylase coded by gene 42 affects mutation rates in a more complex manner than by the simple regulation of the concentration of the DNA precursor dHMCTP.

The recBC enzyme of Escherichia coli K12: premature cessation of catalytic activities in vitro and reactivation by potassium ions

It is shown that in vitro the degradation of native and single-stranded DNA as well as the hydrolysis of ATP by purified recBC enzyme ceases 2-3 min after the start of the reaction. The presence of potassium ions (60-100 mM), bovine serum albumin (1 mg/ml) or protein from cell-free Escherichia coli extract (10 microgram/ml) prevents the cessation of the activity. Once the cessation has occurred, the activity of the enzyme can be completely restored by the addition of potassium ions, but not by bovine serum albumin. Sedimentation studies revealed that, in contrast to the active recBC enzyme, the 'silent' enzyme is no longer associated with substrate DNA of high molecular weight. On the basis of these results and other observations it is hypothesized that during the degradation of DNA in the absence of potassium ions or bovine serum albumin the recBC enzyme is subject to an alteration of its molecular conformation which results in an inactive form.

Novikoff hepatoma deoxyribonucleic acid polymerase. Identification of a stimulatory protein bound to the beta-polymerase

The Novikoff hepatoma DNA polymerase-beta sediments as a 7.3S form in crude extracts but during purification sediments as a 4.1S form (after diethylaminoethyl-Sephadex chromatography) or as a 3.3S form (after DNA-cellulose chromatography). If 0.25 M ammonium sulfate or 0.5 M NaCl is included in the sucrose gradients, the 7.3S form sediments at 3.3 S; after removal of the salt, it sediments again at 7.3 S, indicating the reversibility of the aggregation phenomenon. By careful adjustment of ionic strength in the gradient, four distinct and reproducible forms of the enzyme sedimenting at 7.3, 5.8, 4.1, and 3.3 S can be generated. The isoelectric point of the DNA polymerase also changes during purification; the 7.3S form has a pI of 7.5, while the 4.1S form isoelectrically focuses at a pH of 8.5. During DNA-cellulose chromatography, the Novikoff beta-polymerase is separated from a stimulatory factor designated as Novikoff factor IV. Factor IV is a protein as shown by its sensitivity to protease and resistance to nucleases. It is responsible for converting the 3.3S enzyme to the 4.1S form since the 3.3S homogeneous DNA polymerase-beta sediments at 4.1 S in the presence of factor IV. Factor IV confers stability to the polymerase in low ionic strength buffers as well as stability to heat denaturation. Factor IV has the ability to increase the activity of the 3.3S homogeneous polymerase by about fourfold.

REPLICAtion of small plasmids in extracts of Escherichia coli: requirement for both DNA polymerases I and II

The role of the three E. coli DNA polymerases (pol I, II, and III) in the replication of Col E1 DNA and other small plasmids with similar replicative properties was investigated in a soluble in vitro system prepared by freeze-thaw lysis of chloramphenicol-treated cells (Staudenbauer, 1976). Extracts from isogenic mutants of the polA, polB and polC gene loci deficient in pol I, II, and III respectively were examined for their replicative capacity. It was found that polA and polC extracts are deficient in the synthesis of supercoiled plasmid DNA, whereas the polB mutation has not effect. Deficient extracts could be complemented by addition of purified pol I and pol III holoenzyme. Analysis of the in vitro synthesized DNA by alkaline gradient centrifugation indicates that pol I is involved in an early step of the replication cycle whereas pol III is required at a later stage. These conclusions are confirmed by inhibition studies employing arabionsylcytosine triphosphate (aCTP) which is shown to interfere with pol III as well as pol II. The strong inhibitory effect of aCTP on plasmid replication is not influenced by the polB mutation and mimicks the effects of thermal inactivation of polC extracts. It is suggested that aCTP blocks plasmid ENA replication in vitro by interfering with pol III function

Excision repair of ultraviolet-irradiated deoxyribonucleic acid in plasmolyzed cells of Escherichia coli

A system of cells made permeable by treatment with high concentrations of surcrose (plasmolysis) has been exploited to study the excision repair of ultraviolet-irradiated deoxyribonucleic acid in Escherichia coli. It is demonstrated that adenosine 5'-triphosphate is required for incision breaks to be made in the bacterial chromosome as well as in covalently closed bacteriophage lambda deoxyribonucleic acid. After plasmolysis, uvrC mutant strains appear as defective in the incision step as the uvrA-mutated strains. This is in contrast to the situation in intact cells where uvrC mutants accumulate single-strand breaks during postirradiation incubation. These observations have led to the proposal of a model for excision repair, in which the ultraviolet-specific endonuclease, coded for by the uvrA and uvrB genes, exists in a complex with the uvrC gene product. The complex is responsible for the incision and possibly also the excision steps of repair. The dark-repair inhibitors acriflavine and caffeine are both shown to interfere with the action of the adenosine 5'-triphosphate-dependent enzyme.