Properties of four mutants of Escherichia coli defective in genetic recombination

λ Recombination and Recombineering

The bacteriophage λ Red homologous recombination system has been studied over the past 50 years as a model system to define the mechanistic details of how organisms exchange DNA segments that share extended regions of homology. The λ Red system proved useful as a system to study because recombinants could be easily generated by co-infection of genetically marked phages. What emerged from these studies was the recognition that replication of phage DNA was required for substantial Red-promoted recombination in vivo, and the critical role that double-stranded DNA ends play in allowing the Red proteins access to the phage DNA chromosomes. In the past 16 years, however, the λ Red recombination system has gained a new notoriety. When expressed independently of other λ functions, the Red system is able to promote recombination of linear DNA containing limited regions of homology (∼50 bp) with the Escherichia coli chromosome, a process known as recombineering. This review explains how the Red system works during a phage infection, and how it is utilized to make chromosomal modifications of E. coli with such efficiency that it changed the nature and number of genetic manipulations possible, leading to advances in bacterial genomics, metabolic engineering, and eukaryotic genetics.

Phage recombinases and their applications

The homologous recombination systems of linear double-stranded (ds)DNA bacteriophages are required for the generation of genetic diversity, the repair of dsDNA breaks, and the formation of concatemeric chromosomes, the immediate precursor to packaging. These systems have been studied for decades as a means to understand the basic principles of homologous recombination. From the beginning, it was recognized that these recombinases are linked intimately to the mechanisms of phage DNA replication. In the last decade, however, investigators have exploited these recombination systems as tools for genetic engineering of bacterial chromosomes, bacterial artificial chromosomes, and plasmids. This recombinational engineering technology has been termed "recombineering" and offers a new paradigm for the genetic manipulation of bacterial chromosomes, which is far more efficient than the classical use of nonreplicating integration vectors for gene replacement. The phage λ Red recombination system, in particular, has been used to construct gene replacements, deletions, insertions, inversions, duplications, and single base pair changes in the Escherichia coli chromosome. This chapter discusses the components of the recombination systems of λ, rac prophage, and phage P22 and properties of single-stranded DNA annealing proteins from these and other phage that have been instrumental for the development of this technology. The types of genetic manipulations that can be made are described, along with proposed mechanisms for both double-stranded DNA- and oligonucleotide-mediated recombineering events. Finally, the impact of this technology to such diverse fields as bacterial pathogenesis, metabolic engineering, and mouse genomics is discussed.

The HSV-1 exonuclease, UL12, stimulates recombination by a single strand annealing mechanism

Production of concatemeric DNA is an essential step during HSV infection, as the packaging machinery must recognize longer-than-unit-length concatemers; however, the mechanism by which they are formed is poorly understood. Although it has been proposed that the viral genome circularizes and rolling circle replication leads to the formation of concatemers, several lines of evidence suggest that HSV DNA replication involves recombination-dependent replication reminiscent of bacteriophages λ and T4. Similar to λ, HSV-1 encodes a 5′-to-3′ exonuclease (UL12) and a single strand annealing protein [SSAP (ICP8)] that interact with each other and can perform strand exchange in vitro. By analogy with λ phage, HSV may utilize viral and/or cellular recombination proteins during DNA replication. At least four double strand break repair pathways are present in eukaryotic cells, and HSV-1 is known to manipulate several components of these pathways. Chromosomally integrated reporter assays were used to measure the repair of double strand breaks in HSV-infected cells. Single strand annealing (SSA) was increased in HSV-infected cells, while homologous recombination (HR), non-homologous end joining (NHEJ) and alternative non-homologous end joining (A-NHEJ) were decreased. The increase in SSA was abolished when cells were infected with a viral mutant lacking UL12. Moreover, expression of UL12 alone caused an increase in SSA, which was completely eliminated when a UL12 mutant lacking exonuclease activity was expressed. UL12-mediated stimulation of SSA was decreased in cells lacking the cellular SSAP, Rad52, and could be restored by coexpressing the viral SSAP, ICP8, indicating that an SSAP is also required. These results demonstrate that UL12 can specifically stimulate SSA and that either ICP8 or Rad52 can function as an SSAP. We suggest that SSA is the homology-mediated repair pathway utilized during HSV infection.

The repair of DNA damage is essential to maintain genomic stability. Cells have at least four distinct DNA repair pathways, and defects in any of them can lead to tumor formation and cancer progression. Herpes Simplex Virus-1 (HSV-1) manipulates components of the host DNA repair pathways. In this paper we showed that DNA repair by the single strand annealing (SSA) pathway was increased during HSV infection and that other pathways were inhibited. We also show that a viral nuclease in conjunction with either a viral or cellular single strand annealing protein can stimulate the SSA pathway. We suggest that viral DNA synthesis occurs via an SSAdependent mechanism that is reminiscent of that used by bacterial viruses such as λ. Interestingly, λ has evolved an SSA-mediated repair mechanism to exchange genetic information that has also been used to enhance gene targeting in bacteria. It is thus possible that HSV proteins could be similarly used as tools to stimulate gene targeting in human cells leading to more effective strategies for gene therapy. Furthermore, the diversity of HSV reported in human populations, combined with the high rate of genetic exchange during infection, suggests that SSA may play a role in viral evolution and pathogenesis.

Homologous Recombination-Experimental Systems, Analysis, and Significance

Homologous recombination is the most complex of all recombination events that shape genomes and produce material for evolution. Homologous recombination events are exchanges between DNA molecules in the lengthy regions of shared identity, catalyzed by a group of dedicated enzymes. There is a variety of experimental systems in Escherichia coli and Salmonella to detect homologous recombination events of several different kinds. Genetic analysis of homologous recombination reveals three separate phases of this process: pre-synapsis (the early phase), synapsis (homologous strand exchange), and post-synapsis (the late phase). In E. coli, there are at least two independent pathway of the early phase and at least two independent pathways of the late phase. All this complexity is incongruent with the originally ascribed role of homologous recombination as accelerator of genome evolution: there is simply not enough duplication and repetition in enterobacterial genomes for homologous recombination to have a detectable evolutionary role and therefore not enough selection to maintain such a complexity. At the same time, the mechanisms of homologous recombination are uniquely suited for repair of complex DNA lesions called chromosomal lesions. In fact, the two major classes of chromosomal lesions are recognized and processed by the two individual pathways at the early phase of homologous recombination. It follows, therefore, that homologous recombination events are occasional reflections of the continual recombinational repair, made possible in cases of natural or artificial genome redundancy.

Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda

Although homologous recombination and DNA repair phenomena in bacteria were initially extensively studied without regard to any relationship between the two, it is now appreciated that DNA repair and homologous recombination are related through DNA replication. In Escherichia coli, two-strand DNA damage, generated mostly during replication on a template DNA containing one-strand damage, is repaired by recombination with a homologous intact duplex, usually the sister chromosome. The two major types of two-strand DNA lesions are channeled into two distinct pathways of recombinational repair: daughter-strand gaps are closed by the RecF pathway, while disintegrated replication forks are reestablished by the RecBCD pathway. The phage lambda recombination system is simpler in that its major reaction is to link two double-stranded DNA ends by using overlapping homologous sequences. The remarkable progress in understanding the mechanisms of recombinational repair in E. coli over the last decade is due to the in vitro characterization of the activities of individual recombination proteins. Putting our knowledge about recombinational repair in the broader context of DNA replication will guide future experimentation.

Double-strand end repair via the RecBC pathway in Escherichia coli primes DNA replication

To study the relationship between homologous recombination and DNA replication in Escherichia coli, we monitored the behavior of phage lambda chromosomes, repressed or not for lambda gene activities. Recombination in our system is stimulated both by DNA replication and by experimentally introduced double-strand ends, supporting the idea that DNA replication generates occasional double-strand ends. We report that the RecBC recombinational pathway of E. coli uses double-strand ends to prime DNA synthesis, implying a circular relationship between DNA replication and recombination and suggesting that the primary role of recombination is in the repair of disintegrated replication forks arising during vegetative reproduction.

Recombination in phage lambda: one geneticist's historical perspective

Several features of bacteriophage lambda suit it for the study of genetic recombination. Central among them are those that make it possible to correlate inheritance of DNA with the inheritance of information encoded by DNA through density-label equilibrium centrifugation. Such studies have revealed relationships between DNA replication and recombination, have identified roles for double-strand breaks in the initiation of recombination, and have elucidated the role of the recombination-stimulating sequence, chi.

recA mutants of E. coli K12: a personal turning point

A first year graduate student, Ann Dee Margulies, changed my research career in 1962 by challenging me to direct her in the isolation of recombination-deficient mutants of Escherichia coli K-12. She succeeded in isolating two mutants, which conjugated with donor strains and received the donor DNA, but could not recombine that DNA with their own chromosomes. Ann Dee showed that both mutants were much more sensitive to UV radiation than was the wild type. Furthermore, she showed that one of these mutants carried a single mutation affecting both recombination and resistance. This work, published in 1965, was the first demonstration of the recA gene of E. coli. Subsequent work led to the discovery of many more recombination genes, the phenomenon of post replication-recombination repair, the invention of the SOS hypothesis and the discovery of genes encoding proteins with similar primary structure and function in all major groups of organisms. This article honors the memory of Ann Dee.

Amber suppressors of Erwinia chrysanthemi

Mutations trp1 and thyA1, both of a polyauxotrophic derivative of the Erwinia chrysanthemi strain B374, were characterized as amber mutations with an Escherichia coli suppressor, supA1P2, which inserts a glutamine in response to UAG. Simultaneous reversion of both mutations allowed us to isolate amber suppressor mutants of E. chrysanthemi. These suppressors were tested with a set of amber mutants of bacteriophage Mu which had been previously characterized on E. coli. The two independently isolated suppressors behaved as supD and supE mutants, respectively, of E. coli.

recD: the gene for an essential third subunit of exonuclease V

Exonuclease V (EC 3.1.11.5) of Escherichia coli, an enzyme with multiple activities promoting genetic recombination, has previously been shown to contain two polypeptides, the products of the recB and recC genes. We report here that the enzyme contains in addition a third polypeptide (alpha) with a molecular mass of about 58 kDa. The alpha polypeptide is not synthesized by a class of mutants (previously designated recB) lacking the nuclease activity of exonuclease V but retaining recombination proficiency. The gene, recD, coding for the alpha polypeptide is located near recB in the order thyA-recC-ptr-recB-recD-argA on the E. coli chromosome. The recB and recD genes appear to be governed by a common promoter to the left of recB; a weaker promoter appears to govern recD alone. In the light of these results we discuss the relation between the structure and function of the three polypeptides of exonuclease V, hereby alternatively designated RecBCD enzyme.

A third defective lambdoid prophage of Escherichia coli K12 defined by the lambda derivative, lambdaqin111

We describe the isolation and characterization of a new Q-independent substitution mutant of lambda, lambdaqin111, which differs from other characterized Q-independent lambda phages. This mutant defines a new lambda-like prophage in the bacterial chromosome, as seen by homologous recombination between lambdaqin111 and the host DNA and by DNA/DNA hybridization methods. Genetic and electron microscopy data show that this new prophage carries, at least, genes analogous to Q-S-R of lambda and also a cos site functionally identical to lambda cos. It is located near 34 min on the Escherichia coli K12 map, i.e. in the same region but at a different site from the defective Rac prophage.

Genetic analysis of mu or mini-mu containing F' pro lac episomes after prophage induction

We have investigated the fate of different F pro lac episomes carrying a Mu or mini-Mu, after induction of the Mu or mini-Mu prophage, by looking at the frequencies of transfer of the episome and of one chromosomal marker. During the first 10 min after induction the frequency of chromosome mobilization increases while the frequency of episome transfer decreases. This suggests that the F interacts with the chromosome through some kind of Mu mediated process. Later the transfer of both the episome and chromosomal markers is inhibited. Possible reasons for this inhibition are discussed.

Mini-muduction: a new mode of gene transfer mediated by mini-mu

We compared the transducing properties of Mucts62 and Mucts62/mini-Mu lysates, using Mu immune and non immune Recqnd recA recipient strains. The Mu/mini-Mu lysates transduced all bacterial markers tested 10 times more efficiently than the Mucts62 lysates in Rec + recipients. Most of the transductants obtained after infection with the Mu/mini-Mu lysates result from the substitution of the mutated gene of the recipient by the wild type allele from the donor, most probably carried on the gigantic variable end linked to the mini-Mu genome. Moreover the Mu/mini-Mu lysates gave a new type of Rec-independent transduction that we called mini-muduction. Mini-muduction requires the activity of Mu gene A and provides transductants which carry the transduced marker surrounded by two mini-Mu genomes similarly oriented, and inserted at random location in the recipient chromosome. The mini-Mu/transduced DNA/mini-Mu structures are able to transpose spontaneously, for instance into a transmissible plasmid, in the presence of Mu gene A product.

The genetic characterization of lexB32, lexB33 and lexB35 mutations of Escherichia coli: location and complementation pattern for UV resistance

Mutants of LexB have been isolated by their resistance to lysogenic induction by thymine starvation, their resistance to thymine starvation and on the basis of their UV sensitivity. Here, three mutations identified originally in strains lacking mutagenic response to UV-irradiation, unmB (Kato and Shinoura, 1977), have been further characterized, mapped by P1-mediated transduction with srl into the recA-tif-zab-lexB cluster at the lexB position and analysed for complementation with various lexB and recA mutations. From the results it was concluded that unmB mutations are identical to lexB mutations; consequently these mutations have been termed lexB32, lexB33 and lexB35. The mutations lexB33 and lexB35 do not complement any of the other lexB mutations and define therefore a new complementation type. The lexB32 mutation, which like the lexB34 mutation, results in moderate UV sensitivity has a complementation pattern similar to that of lexB34. However, unlike lexB34 the lexB32 behaves like a leaky mutation. The results are discussed in relation to the recA gene product and its control.

Characterization of lexB mutations in Escherichia coli K-12

Two mutations have been located at the recA locus and phenotypically characterized along with a third one, previously called rec-34. The three mutants behaved similarly to lexA mutants. They were sensitive to ultraviolet (UV) light and X rays, and lambdaFec- phages were able to plate on them. The three mutations were called lexB because they could be distinguished from recA mutations by the last property. lexB mutants were less sensitive to UV and X irradiations than were recA mutants and were, to various degrees, recombination proficient. UV light failed to induce prophage lambda in all three lexB lysogens. In contrast, thymine starvation induced lexB31 and lexB34 lysogens. In lexB34 mutants, but not in lexB30 and lexB31 mutants, UV reactivation occurred at a low level. In Escherichia coli K-12, the recA gene has basic functions in the repair of deoxyribonucleic acid lesions, deoxyribonucleic acid recombination, and prophage induction. The three lexB mutations alter unequally and independently the three functions. This suggests that the recA and lexB mutations affect the same gene.

Mutation of lambda during prophage induction by nitrosamides

Approximately 6% of Escherichia coli K12 (lambda wild-type) cells whose prophage was induced by treatment with N-methyl-N-nitrosourea initiated plaques on E. coli K12S which contained wholly or mostly clear plaque-forming mutants (lambdac). "Fuzzy" plaque-forming mutants (lambdaf) were also recognised, at lesser frequencies. Less marked mutation occurred during prophage induction by N-ethyl-N-nitrosourea, and no apparent mutation occurred during induction by methyl and iso-propyl methanesulphonates, or by a non-inducing treatment of the lysogen with ethyl methanesulphonate. Mutagenic effects of treatment of susceptible host cells or of phage alone, prior to infection, seem not to account for the phenomenon described.

Genetics and complementation of Haemophilus influenzae mutants deficient in adenosine 5'-triphosphate-dependent nuclease

Eight different mutations in Haemophilus influenzae leading to deficiency in adenosine 5'-triphosphate (ATP)-dependent nuclease have been investigated in strains in which the mutations of the originally mutagenized strains have been transferred into the wild type. Sensitivity to mitomycin C and deoxycholate and complementation between extracts and deoxyribonucleic acid (DNA)-dependent ATPase activity have been measured. Genetic crosses have provided information on the relative position of the mutations on the genome. There are three complementation groups, corresponding to three genetic groups. The strains most sensitive to mitomycin and deoxycholate, derived from mutants originally selected on the basis of sensitivity to mitomycin C or methyl methanesulfonate, are in one group. Apparently all these sensitive strains lack DNA-dependent ATPase activity, as does a strain intermediate in sensitivity to deoxycholate, which is the sole representative of another group. There are four strains that are relatively resistant to deoxycholate and mitomycin C, and all of these contain the ATPase activity. Three of these are in the same genetic and complementation group, whereas the other incongruously belongs in the same group as the sensitive strains. It is postulated that there are three cistrons in H. influenzae that code for the three known subunits of the ATP-dependent nuclease.

Fate of transforming DNA after uptake by competent Bacillus subtilis: failure of donor DNA to replicate in a recombination-deficient recipient

The fate of radioactively-labeled transforming DNA was studied in a recombination-deficient strain of Bacillus subtilis that carried the recB2 mutation (Rec(-)) and was sensitive to radiation. Experiments performed with extracts of this strain after transformation showed that the recovery of donor transforming activity and the appearance of recombinant transforming activity occurred to the same extent as in the Rec(+) strain. Sucrose gradient analyses revealed that donor-recipient complex is also formed to the same extent in the Rec(-) and Rec(+) strains, but that 80-90% of the donor genetic material in the complex failed to replicate in the Rec(-) mutant.

Survival, DNA-breakdown and induction of prophage lambda in a Escherichia coli K 12 recA uvrB double mutant

Cellular functions of a double mutant ofEscherichia coliK 12 deficient in recombination (recA) and defective in excision of pyrimidine dimers (uvrB) have been compared to those of isogenicrecAoruvrBsingle mutants and ‘wild type’ bacteria. A combined effect of the two mutations on cell survival both under normal conditions of growth and after exposure to ultraviolet light or mitomycin C was demonstrated. The ratio of optical density to the number of colony formers in growing cultures of the double mutant is three times greater than in similar cultures of therecAsingle mutant and 9 times greater than in eitheruvrBor in ‘wild type’ cultures. The doubling time in growingrecA uvrBcultures is 90 min, compared to 60 min, for therecAsingle mutant and 40 min for theuvrBsingle mutant and ‘wild type’ bacteria. Growing cultures ofrecA uvrB(λcI857) bacteria contain a substantial fraction of cells which are unable to form colonies at 32 °C, but produce phage when heated to 42 °C. No such cells were found in cultures of the single mutants or the ‘wild type’ bacteria lysogenic for λc1857. The double mutant is 10 times more sensitive to ultraviolet light and twice more sensitive to mitomycin C than therecAsingle mutant. In contrast torecAbacteria, exposure of the double mutant to mitomycin C induces little additional breakdown of cellular DNA. Induction of the prophage by mitomycin C is, however, prevented in bothrecA uvrB(λ) andrecA(λ) bacteria. Exposure to mitomycin C creates conditions which render the prophage inducible by a newly transducedree Agene. This effect of mitomycin C persists and can be revealed in complete medium at 37 °C after 100 min of incubation. The decay of the prophage, in cells exposed to mitomycin C, proceeds at a similar rate in both the double mutant and therecAsingle mutant. The inability ofrecAlysogens to be induced to phage production is discussed in the light of the present findings.

Genetic analysis of recombination-deficient mutants of Escherichia coli K-12 carrying rec mutations cotransducible with thyA

The rec mutations carried by 20 strains of Escherichia coli K-12 which are defective in genetic recombination and sensitive to ultraviolet light and X rays, and whose lambda lysogens show spontaneous phage production, have been mapped near thyA. In 15 of the strains, the rec mutation fails to complement recB21 but complements rec-22. The other five strains carry a rec mutation which complements recB21 but not rec-22. These mutations map closer to thyA than those which fail to complement recB21. They therefore appear to be defective in a different recombination gene, denoted recC. The order of recB and recC on the linkage map of E. coli K-12 is thyA-recC-recB-argA.

Identification of closely linked loci controlling ultraviolet sensitivity and refractivity to colicin E2 in Escherichia coli

Mutants (phenotypic symbol Ref-II) refractory to colicin E2 have been isolated in several strains of Escherichia coli K-12, and a refII locus has been mapped 1 to 2 min counter clockwise to thr. A small number of Ref-II mutants are also ultraviolet (UV)-sensitive and the uv(s) locus in one such strain has been mapped close to the refII locus near thr. The Ref-II mutation alone does not affect recombinant formation in F(-) strains, but the Ref-II, UV(s) strains behave in many respects like Rec(-) mutants, giving reduced recombination frequencies in crosses with male strains. It is suggested that the refII and uv(s) loci correspond to closely linked if not identical genes, concerned in some way in the activity of one or more deoxyribonucleases, and that the Ref-II, UV(s) mutants arise as the pleiotropic expression of a single gene or of a deletion or polar mutation affecting linked genes.

Spontaneous lethal sectoring, a further feature of Escherichia coli strains deficient in the function of rec and uvr genes

Eight recombination-deficient (Rec(-)) mutants of Escherichia coli were studied. Progeny lines were obtained on solid media, by means of micromanipulation, and the colony-forming ability of individual cells was analyzed. Cells of all eight strains gave rise to colony-forming as well as non-colony-forming descendants ("lethal sectoring"). Lethal sectors, i.e., groups of non-colony-forming cells which originate from a common ancestor, appeared with frequencies per generation ranging between 4 and 20% in Rec(-) strains, whereas lethal sectors were rare in Rec(+) strains (less than 1%). A strain carrying a mutation (uvrA6) in one of the genes involved in pyrimidine dimer excision from deoxyribonucleic acid (DNA) showed twice as many lethal sectors per generation as a strain with the genotype uvrA(+). Similarly, a double mutant (AB2480, uvrA6, recA13) showed twice as much spontaneous lethal sectoring as the corresponding Rec(-) strain (uvrA(+), recA13). The kinetics of growth curves obtained in nutrient broth and the frequency of non-colony-forming units in stationary-phase broth cultures indicate clearly that lethal sectors occur in liquid cultures too. The causes for spontaneous lethal sectoring are unknown at present. It seems reasonable to assume that gene uvrA and the rec genes are somehow involved in the repair of spontaneously occurring DNA lesions, since a deficiency in this type of repair may cause lethal sectors. The extent to which spontaneous lethal sectoring (observed in all Rec(-) strains of E. coli studied) may contribute indirectly to the failure to form recombinants is discussed.

Selective stimulation of one of the mechanisms for genetic recombination of bacteriophage S13

In certain recombination-deficient (Rec(-)) bacterial strains genetic recombination of bacteriophage S13 is reduced, but the existence of some residual recombination has suggested that there is a secondary mechanism of phage recombination that is still functioning. In these Rec(-)strains it is found that there is no stimulation of recombination by irradiation of the parental phage with ultraviolet light, in contrast to the large increase found when irradiated phage particles infect a Rec(+) host. This selective stimulation of phage recombination in the Rec(+) but not in the Rec(-) strains supports the view that the phage uses at least two mechanisms of genetic recombination.

Mutator factor in Neisseria meningitidis associated with increased sensitivity to ultraviolet light and defective transformation

A variant of Neisseria meningitidis was found to carry a mutator factor which endowed the bacteria with generalized genetic instability. The reversion frequencies of several biochemical mutants were increased up to 1,000-fold when the factor was introduced. The factor is not unidirectional in preference, since the mutator induced mutants generally reverted with increased frequency in its presence. There could be found no indication of insufficient synthesis of nucleic acid precursors. Attempts to demonstrate an unusual, mutagenic base incorporated in deoxyribonucleic acid (DNA) were negative. Strains carrying the mutator factor had significantly increased sensitivity to ultraviolet light. A mutation to a more ultraviolet-resistant type coincided with a disappearance of the mutator property. The presence of the mutator factor in a competent strain resulted in a reduction of the transformation frequency to between 0.5 and 5% of that in the parental strain. A mutation to the more ultraviolet-resistant type resulted in simultaneous loss of the mutator property and reestablishment of a normal transformation efficiency. It has been suggested that this mutator factor may represent a defect in the DNA repair mechanism, which is also of importance for genetic recombination. The mutator factor showed cotransformation with the locus for streptomycin resistance, but a true linkage could not be proved.