The Effect of Lysogenic Induction on the Deoxyribonucleases of Escherichia coli K12λ

Half a century of bacteriophage lambda recombinase: In vitro studies of lambda exonuclease and Red-beta annealase

DNA recombination, replication, and repair are intrinsically interconnected processes. From viruses to humans, they are ubiquitous and essential to all life on Earth. Single‐strand annealing homologous DNA recombination is a major mechanism for the repair of double‐stranded DNA breaks. An exonuclease and an annealase work in tandem, forming a complex known as a two‐component recombinase. Redβ annealase and λ‐exonuclease from phage lambda form the archetypal two‐component recombinase complex. In this short review article, we highlight some of the in vitro studies that have led to our current understanding of the lambda recombinase system. We synthesize insights from more than half a century of research, summarizing the state of our current understanding. From this foundation, we identify the gaps in our knowledge and cast an eye forward to consider what the next 50 years of research may uncover.

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.

Instantiating a vision: creating the new pathology department at Stanford Medical School

This review represents my best effort to recreate and memorialize events that occurred 44 years ago, when I was invited to join the Stanford University faculty to create, essentially de novo, what rapidly became and remains today one of the very best and most admired departments of pathology in the world. That I was able to accomplish this challenging task I attribute to my holding fast to a somewhat inchoate vision of where the science and practice of pathology would go in future decades, a little bit to my gut instincts and innate ability to spot up-and-coming talent, but a lot to circumstances and good fortune in leading me to a small nucleus of wonderful young professionals of outstanding promise who were willing to join me in "betting the house" that, working together, we could pull off this once-in-a-lifetime opportunity--and we did.

Functional characterization of an alkaline exonuclease and single strand annealing protein from the SXT genetic element of Vibrio cholerae

BACKGROUND

SXT is an integrating conjugative element (ICE) originally isolated from Vibrio cholerae, the bacterial pathogen that causes cholera. It houses multiple antibiotic and heavy metal resistance genes on its ca. 100 kb circular double stranded DNA (dsDNA) genome, and functions as an effective vehicle for the horizontal transfer of resistance genes within susceptible bacterial populations. Here, we characterize the activities of an alkaline exonuclease (S066, SXT-Exo) and single strand annealing protein (S065, SXT-Bet) encoded on the SXT genetic element, which share significant sequence homology with Exo and Bet from bacteriophage lambda, respectively.

RESULTS

SXT-Exo has the ability to degrade both linear dsDNA and single stranded DNA (ssDNA) molecules, but has no detectable endonuclease or nicking activities. Adopting a stable trimeric arrangement in solution, the exonuclease activities of SXT-Exo are optimal at pH 8.2 and essentially require Mn2+ or Mg2+ ions. Similar to lambda-Exo, SXT-Exo hydrolyzes dsDNA with 5'- to 3'-polarity in a highly processive manner, and digests DNA substrates with 5'-phosphorylated termini significantly more effectively than those lacking 5'-phosphate groups. Notably, the dsDNA exonuclease activities of both SXT-Exo and lambda-Exo are stimulated by the addition of lambda-Bet, SXT-Bet or a single strand DNA binding protein encoded on the SXT genetic element (S064, SXT-Ssb). When co-expressed in E. coli cells, SXT-Bet and SXT-Exo mediate homologous recombination between a PCR-generated dsDNA fragment and the chromosome, analogous to RecET and lambda-Bet/Exo.

CONCLUSIONS

The activities of the SXT-Exo protein are consistent with it having the ability to resect the ends of linearized dsDNA molecules, forming partially ssDNA substrates for the partnering SXT-Bet single strand annealing protein. As such, SXT-Exo and SXT-Bet may function together to repair or process SXT genetic elements within infected V. cholerae cells, through facilitating homologous DNA recombination events. The results presented here significantly extend our general understanding of the properties and activities of alkaline exonuclease and single strand annealing proteins of viral/bacteriophage origin, and will assist the rational development of bacterial recombineering systems.

Lambda bacteriophage gene produces and X-ray sensitivity of Escherichia coli: comparison of red-dependent and gam-dependent radioresistance

When gene products of lambda bacteriophage are introduced into a cell by transient induction of a lysogen, increased resistance of the cells to X rays results. This phenomenon has been called phage-induced radioresistance. Genetic studies show at least two classes of induced radioresistance. The first type depends on the products of the lambda red genes and is observed in bacteria that are mutated in the recB gene. It is thought that the lambda red products compensate for the missing RecBC nuclease in the repair of X-ray damage. An optimal effect is obtained even when the lambda red products are supplied 1 h after irradiation. The lesions that are affected by the red-dependent process are probably not deoxyribonucleic acid strand breaks because the extent of deoxyribonucleic acid strand rejoining is not altered by the red products. The second type of phage-induced radioresistance requires the gam product of lambda and is observed in wild-type and polA strains. The lambda gam+ gene produce must be present immediately after irradiation to exert its full effect. In its presence, DNA breakdown is decreased, and a greater fraction of DNA is converted back to high molecular weight. Strains carrying lex, recA, or certain other combinations of mutations do not show any detectable phage-induced radioresistance.

Thymineless death in Bacillus subtilis: correlation between cell lysis and deoxyribonucleic acid breakdown

Bacillus subtilis carrying an inducible defective phage is several times more sensitive to thymineless death than a mutagenized derivative that behaves as a nonlysogen. When the integrity of the deoxyribonucleic acid (DNA) of both strains was examined during thymine starvation by transformation experiments, sedimentation studies, and measurements of acid-soluble DNA degradation products, it was shown that extensive DNA breakdown occurred only in the lysogenic strain. During thymine starvation of this strain, there is a progressive proclivity to lysis, followed by leakage of DNA and DNA degradation products. Such leakage was not observed in the nonlysogen. A correlation between proclivity to lysis and extensive DNA degradation is indicated.

Loss of deoxyribonucleic acid-thymine during thymine starvation of Escherichia coli

A substantial loss of deoxyribonucleic acid-thymine occurs during thymine starvation of several thymine auxotrophs derived from Escherichia coli strains B, 15, and K-12.

Degradation of bacteriophage lambda deoxyribonucleic acid after restriction by Escherichia coli K-12

Wild-type bacteria which restrict the deoxyribonucleic acid (DNA) of infecting phage when the phage do not carry the proper host modification rapidly degrade that restricted DNA to acid-soluble products. The purified restriction enzyme acts as an endonuclease in vitro to cleave restrictable DNA and does not further degrade the DNA fragments produced. We have examined mutants of Escherichia coli K-12 which lack various nucleases in order to determine which nucleases are involved in the rapid acid solubilization in vivo of unmodified lambda DNA following restriction. Bacteria which are wild type, recA(-), or polA1(-) degrade about 50% of the unmodified phage DNA within 10 min of infection, with little subsequent degradation. Mutants which are recB(-) or recC(-) degrade unmodified DNA very slowly, solubilizing about 15% of the DNA by 10 min after infection. Two classes of phenotypic revertants of recB(-)/C(-) mutants were also tested. Bacteria which are sbcA(-) restrict poorly and do not degrade much of the restricted DNA. Bacteria which are sbcB(-) restrict normally. This mutation does not appear to affect degradation of restricted phage DNA in recB(-)/C(-) mutants, but such degradation is decreased in recB(+)/C(+) bacteria. The presence of a functional lambda exonuclease gene is not required for degradation after restriction.

Repression of λ-Associated Enzyme Synthesis After λ vir Superinfection of Lysogenic Hosts

Lisio, Arnold L. (National Institutes of Health, Bethesda, Md.), and Arthur Weissbach . Repression of λ-associated enzyme synthesis after λ vir superinfection of lysogenic hosts. J. Bacteriol. 90: 661–666. 1965.—Phage λ vir is a multiple mutant of λ which is capable of overcoming the immunity of a host lysogenic for λ, and initiating normal vegetative replication of the superinfecting phage genome. Superinfection of Escherichia coli K-112 (λ 22 ) with λ vir results in a normal phage yield, lysis time, and H 3 -thymine incorporation compared with infection of the sensitive host, K-112 (S). However, the production of the λ phage-specific early protein, λ-exonuclease, after superinfection of E. coli K-112 (λ 22 ) with λ vir is only 25 to 50% of that obtained from corresponding infection of a nonlysogenic host, E. coli K-112 (S). This repression of λ-exonuclease synthesis is dependent on the C 1 cistron of the prophage and is overcome if the lysogenic host cells are induced prior to superinfection. The data are interpreted as evidence for partial repression of λ vir by the host immunity.