Conjugal transfer of UV-damaged F-prime sex factors and indirect induction of prophage-

At the birth of molecular radiation biology

Rational thinking builds on feelings, too. This article starts with a tribute to Richard Setlow, an eminent scientist; it retraces as well some studies in molecular genetics that helped to understand basic questions of radiation biology. In the mid-1950s, the induction of a dormant virus (prophage) by irradiation of its host was an intriguing phenomenon. Soon, it was found that prophage induction results from the inactivation of the prophage repressor. Similarly, a score of induced cellular SOS functions were found to be induced when the LexA repressor is inactivated. Repressor inactivation involves the formation of a newly formed distinctive structure: a RecA-polymer wrapped around single-stranded DNA left by the arrest of replication at damaged sites. By touching this RecA nucleofilament, the LexA repressor is inactivated, triggering the sequential expression of SOS functions. The RecA nucleofilament acts as a chaperone, allowing recombinational repair to occur after nucleotide excision repair is over. The UmuD'C complex, synthesized slowly and parsimoniously, peaks at the end of recombinational repair, ready to be positioned at the tip of a RecA nucleofilament, placing the UmuD'C complex right at a lesion. At this location, UmuD'C prevents recombinational repair, and now acts as an error-prone paucimerase that fills the discontinuity opposite the damaged DNA. Finally, the elimination of lesions from the path of DNA polymerase, allows the resumption of DNA replication, and the SOS repair cycle switches to a normal cell cycle.

Quantitation of the inhibition of Hfr x F- recombination by the mutagenesis complex UmuD'C

The UmuD'C complex and RecA protein are two essential components in mutagenic repair of gaps produced by the replication of damaged DNA. In this process, the UmuD'C complex might help DNA polymerase to synthesize DNA across a lesion. Besides, a RecA polymer wrapping around single-stranded DNA could function as a directional chaperone to target the UmuD'C complex at the lesion. It was shown in our laboratory that the UmuD'C complex prevents homologous recombination and recombinational repair when expressed at elevated levels. To find out whether the UmuD'C complex inhibits recombination by interfering directly with RecA, we measured the kinetics of inhibition of Hfr x F- recombination in F- recipients in which either RecA or UmuD'C were made to vary. The cell concentrations of RecA and UmuD'C proteins were adjusted by having the recA and the umuD'C genes regulated by the arabinose P(BAD) promoter. In the absence of the UmuD'C complex, recombination was a function of RecA concentration and then reached a plateau when the RecA concentration was above 9000 monomers/cell. At a fixed RecA concentration, the yield of Hfr x F- recombinants decreased as a function of the UmuD'C cell concentration. At a given UmuD'C/RecA ratio, recombination inhibition by UmuD'C was reversed by increasing the RecA cell concentration. RecA1730, a mutant protein impaired in the chaperone activity, was insensitive to UmuD'C inhibition. We propose a model accounting for the RecA chaperone function in SOS mutagenesis and for the UmuD'C inhibitory effect on homologous recombination. We suggest that the UmuD'C complex is placed at the tip of a RecA polymer as a result of a treadmilling process. This would position the UmuD'C complex right at a lesion while the capping by UmuD'C would destabilize a RecA polymer and thereby abort the recombination process.

The appearance of the UmuD'C protein complex in Escherichia coli switches repair from homologous recombination to SOS mutagenesis

The process of SOS mutagenesis in Escherichia coli requires (i) the replisome enzymes, (ii) RecA protein, and (iii) the formation of the UmuD'C protein complex which appears to help the replisome to resume DNA synthesis across a lesion. We found that the UmuD'C complex is an antagonist of RecA-mediated recombination. Homologous recombination in an Hfr x F- cross decreased as a function of the UmuD'C cell concentration; this effect was challenged by increasing RecA concentration. Recombination of a u.v.-damaged F-lac with the lac gene of an F- recipient was reduced by increasing the UmuD'C concentration while lac mutagenesis increased, showing an inverse relationship between recombination and SOS mutagenesis. We explain our data with the following model. The kinetics of appearance of the UmuD'C complex after DNA damage is slow, reaching a maximum after an hour. Within that period, excision and recombinational repair have had time to occur. When the UmuD'C concentration relative to the number of residual RecA filaments, not resolved by recombinational repair, becomes high enough, UmuD'C proteins provide a processive factor for the replisome to help replication bypass and repel the standing RecA filament. Thus, at a high enough concentration, the UmuD'C complex will switch repair from recombination to SOS mutagenesis.

New mutations in and around the L2 disordered loop of the RecA protein modulate recombination and/or coprotease activity

The RecA protein plays a key role in Escherichia coli recombination and DNA repair. We have created new recA mutants with mutations in the vicinity of the recA430 mutation (Gly-204----Ser) which is known to affect RecA coprotease activity. Mutants carrying recA659 or recA611, located 3 and 7 amino acids downstream of residue 204, respectively, lose all RecA activities, while the mutant carrying recA616, which is located at 12 amino acids from this residue, keeps the coprotease activity but is unable to promote recombination. Complementation experiments show that both mutations recA611 and recA659 are dominant over the wild-type or recA430 allele while recA616 seems to be recessive to recA+ and dominant over recA430. It is suggested that these mutations are located in RecA domains which direct conformational modifications.

PsiB, and anti-SOS protein, is transiently expressed by the F sex factor during its transmission to an Escherichia coli K-12 recipient

PsiB, an anti-SOS protein, shown previously to prevent activation of RecA protein, was purified from the crude extract of PsiB overproducing cells. PsiB is probably a tetrameric protein, whose subunit has a sequence-deduced molecular mass of 15741 daltons. Using an immuno-assay with anti-PsiB antibodies, we have monitored PsiB cell concentrations produced by F and R6-5 plasmids: the latter type produces a detectable level of PsiB protein while the former does not. The discrepancy can be assigned to a Tn10 out-going promoter located upstream of psiB. When we inserted a Tn10 promoter upstream of F psiB, the F PsiB protein concentration reached the level of R6-5 PsiB. We describe here the physiological role that PsiB protein may have in the cell and how it causes an anti-SOS function. We observed that PsiB protein was transiently expressed by a wild-type F sex factor during its transmission to an Escherichia coli K-12 recipient. In an F+ x F- cross, PsiB concentration increased at least 10-fold in F- recipient bacteria after 90 minutes and declined thereafter; the psiB gene may be repressed when F plasmid replicates vegetatively. PsiB protein may be induced zygotically so as to protect F single-stranded DNA transferred upon conjugation. PsiB protein, when overproduced, may interfere with RecA protein at chromosomal single-stranded DNA sites generated by discontinuous DNA replication, thus causing an SOS inhibitory phenotype.

Mini-F plasmid-induced SOS signal in Escherichia coli is RecBC dependent

Dispensable replicons such as F plasmid [95 kilobases (kb)] or its mini-derivatives such as mini-F (9.3 kb) or lambda mini-F efficiently induced cellular SOS genes such as sfiA (sulA) when they were damaged by UV irradiation and then introduced into a recipient bacterium. To generate an SOS signal, UV light-damaged mini-F or mini-F conditional mutants deficient in replication required that the bacterial RecBC enzyme retained some activity different from the nuclease activity that was dispensable. In contrast, UV light-damaged F plasmid produced an SOS signal independently of the activity of the RecBC enzyme and of the expression of the mini-F, -H, and -G proteins. Our findings are consistent with a picture in which the SOS signal is constituted by stretches of single-stranded DNA on a replicon. Moreover, our present data combined with other data previously published lead to the hypothesis that the SOS signal induced by mini-F plasmid is located in trans on the host chromosome, whereas the one generated by UV light-damaged F plasmid is in cis on the transferred DNA.

Differential effect of ultraviolet light on the induction of simian virus 40 and a cellular mutator phenotype in transformed mammalian cells

UV irradiation of simian virus 40 (SV40)-transformed human and hamster cells induced them both to express a mutator phenotype and to produce SV40. The mutator could also be activated indirectly by transfecting unirradiated cells with UV-damaged calf thymus DNA. In contrast, UV-damaged exogenous DNA failed to rescue SV40 from unirradiated transformed cells. These results suggest that the expression of transforming viruses and of cellular mutator functions is regulated by at least partially independent mechanisms. Unlike the activation of a cellular mutator phenotype, the rescue of SV40 from virus-transformed mammalian cells by UV light might require that the integrated viral DNA and/or specific cellular sequences are directly damaged.

SOS induction by thermosensitive replication mutants of miniF plasmid

MiniF, a 9.3 kb fragment of the dispensable F plasmid, carries genes necessary for its replication and partition as well as for the expression of an SOS signal. The arrest of replication of a thermo-sensitive miniFts at 42 degrees C induced SOS functions such as prophage lambda, sfiA expression, W-reactivation of UV-irradiated phage lambda. Two miniF ts9 and ts17 mutations were located within the KpnI fragment (43.6-46.9) in the minimal oriS replicon. Blocking miniF replication by incBC+ incompatibility genes situated in trans on a second plasmid also induced SOS functions. In contrast, if miniFts17 plasmid escaped the replication block at 42 degrees C by being inserted into pR325, there was no SOS induction. SOS induction by the arrest of miniF replication required the miniF lynA+ locus in cis, the host recA+ and lexA+ genes. We found that SOS induction was increased greatly near the stationary phase and that cell viability declined. During host cell exponential growth, miniFts9 and miniFts17 plasmids were lost rapidly, although SOS induction persisted for several cell generations. We postulate that lynA expresses a persistent product that may lead to the unwinding of chromosomal DNA.

Indirect SOS induction is promoted by ultraviolet light-damaged miniF and requires the miniF lynA locus

Indirect prophage induction is produced by transfer to recipients of u.v.-damaged F plasmid (95 kb). We tested whether the SOS signal can be produced by miniF, a 9.3 kb restriction fragment, coding for the replication and segregation functions of plasmid F. We used lambda miniF, a hybrid phage-plasmid. u.v.-irradiated lambda miniF induced prophages phi 80 or lambda and sfiA, a chromosomal SOS gene, in more than 50% of the infected cells. The maximal inducing dose produced about 0.5 pyrimidine dimers per kb and left 1% of lambda miniF survivors. Thus, the SOS signal produced by u.v.-damaged lambda miniF was almost as potent as that resulting from direct u.v.-irradiation of the lysogens. The u.v.-damaged vector lambda, devoid of miniF, failed to promote SOS induction. In contrast, efficient induction was observed when u.v.-damaged lambda miniF infected a lambda immune host, in which replication and expression of the phage genome were repressed. When replication and expression of the miniF genome was repressed by Hfr incompatibility, SOS induction was largely prevented. All these facts indicate that, in the hybrid lambda-miniF, it is the u.v.-damaged miniF that generates an SOS signal. To locate on the miniF genome the loci that are involved in the production of the SOS signal, we isolated deletions spanning all the miniF restriction fragments. We characterized six mutant phenotypes (Par+, Rep-, Fid-, Par-2, Par-1 and SOS-) related to four functions; partition, copy number, replication and SOS induction. A locus, we call lynA, 800 bp long, located by deletion mapping between the two origins of replication oriP and oriS is required for the production of an inducing signal. We postulate that indirect SOS induction by u.v.-damaged miniF results from the disturbance of the lynA function that may be involved in the co-segregation of F plasmid with the host chromosome.

Gratuitous induction

We describe a novel mode of SOS induction, called gratuitous indirect induction, which is elicited when the maintenance of an intact lambda miniF introduced into a recipient was inhibited by a resident plasmid or by mutations in miniF that impaired partition or replication. Gratuitous induction required the presence of the lynA locus on miniF and was dependent on the host recA and lexA alleles. To account for gratuitous induction, we postulate that impairment of the normal co-regulation between partition and replication of miniF affects lynA functions whose disturbance leads to the production of an SOS signal.

The role of pyrimidine dimers as premutagenic lesions: a study of targeted vs. untargeted mutagenesis in the lacI gene of Escherichia coli

We have employed conjugal transfer of an F' lac episome to examine targeted and untargeted mutagenesis in the lacI gene of Escherichia coli and to determine the relative importance of pyrimidine dimers as premutational UV lesions compared to (6-4) photoproducts that also may have a mutational role. This conjugal system allowed us to assess the premutagenic role of UV lesions independently from any role as inducers of SOS functions. F' DNA was transferred to an SOS-induced recipient strain from: unirradiated donor cells, UV-treated donor cells or donor cells that were irradiated and then exposed to photoreactivating light. The results indicate that SOS-related, untargeted events may account for as much as one-third of the nonsense mutations (i.e., base substitutions) recovered after undamaged F' DNA is transferred to UV-irradiated recipients. When the donor strain also is irradiated, in excess of 90% of the mutations detected following conjugation appear to be targeted. Photoreactivation of the UV-treated donors cells, prior to F' transfer to the SOS-induced recipient strain, demonstrated that in this experimental system virtually all recovered UV-induced mutations are targeted by photoreactivable lesions. We presume that these lesions are pyrimidine dimers because (6-4) photoproducts are not photoreactivable.

DNA replication and indirect induction of the SOS response in Escherichia coli

The SOS response can be induced indirectly in Escherichia coli by infection with UV irradiated bacteriophage P1, lambda or M13. Induction, monitored quantitatively by means of a sfiA::lac operon fusion, was stronger with the plasmid phage P1 than with lambda, but the kinetics were similar, showing that plasmid and non-plasmid phages are not fundamentally different in their ability to produce indirect induction. In the absence of lambda DNA replication the level of induction was strongly reduced, indicating that the attempt to replicate damaged DNA results in induction of the SOS response. The slight residual induction observed in the absence of DNA replication suggests the existence of a second pathway leading from DNA lesions to induction of the SOS response.

Cleavage of lambda repressor and synthesis of RecA protein induced by transferred UV-damaged F sex factor

Transfer of a UV-damaged F sex factor to a recipient lambda lysogen induces prophage lambda development. Under these conditions RecA protein synthesis was induced and lambda repressor cleaved, as observed upon direct induction, that is, when the recipient lambda lysogen was directly exposed to UV-light. The efficiency of induction of RecA protein synthesis in recipient bacteria which had received an irradiated F-lac factor was about 80% of that measured upon direct induction. We observed the simultaneous disappearance of lambda repressor and a slight production of cleavage fragments; quantitation by densitometric scanning of the autoradiogram after correction for the efficiency of transfer indicated that 55% of lambda repressor was cleaved. Transfer of UV-damaged Hfr DNA failed to induce RecA protein synthesis. A lambda phage vector carrying oriF, the cloned origin of F plasmid replication, after exposure to UV-light and infection of a recipient lysogen, induced RecA protein synthesis and a moderate but significant cleavage of lambda repressor. Indirect induction by UV-damaged F sex factor or phage lambda oriF resulted in biochemical cellular reactions similar to those observed upon direct induction. LexA repressor that negatively controls RecA protein synthesis appeared more susceptible to cleavage than did lambda repressor.

Suppression of induction of SOS functions in an Escherichia coli tif-1 mutant by plasmid R100.1

The tif-1 mutation in the recA gene of Escherichia coli caused, at 40 degrees C, lethal cell filamentation, induction of the recA protein, mutagenesis, and, in lambda lysogens, prophage induction. The presence of plasmid R100.1 in tif-1 strains suppressed tif-mediated cell filamentation and killing, recA protein induction, and prophage induction in lysogens. It also reduced mutagenesis in a tif-1 sfiA11(R100.1) strain. Plasmids F'lac, P1, and pMB9, in contrast, had little or no effect on tif-mediated induction of lambda. The presence of R100.1 did not inhibit the induction of the recA protein or of lambda by ultraviolet irradiation or mitomycin C treatment of tif-1(R100.1) or tif-1(lambda)(R100.1) strains.

Ultraviolet mutagenesis and inducible DNA repair in Escherichia coli

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Inducible, error-free DNA Repair in tsl recA mutants of E. coli

Host of cell reactivation and UV reactivation and mutagenesis of UV-irradiated phage mu were measured in tsl recAplus and tsl recA host mutants. Host cell reactivation was slightly more efficient in the tsl recA strain. Phage was UV-reactivated in the tsl recA strain with about one-half the efficiency of that in the wild type strain, but there was no corresponding mutagenesis of phage. UV-reactivation was also slightly lower and mutagenesis several-fold lower than normal in the tsl recAplus strain. To account for these observations, we propose that there is an inducible, error-free pathway of DNA repair in E. coli that competes with error-prone repair for repair of phage lesions.

The kinetics of derepression of prophage lambda following ultraviolet irradiation of lysogenic cells

Double lysogens for prophages lambda cI+ and lambda cI ind-ts-857 are induced only by the combined effects of ultraviolet (UV) irradiation and high temperature, not by either treatment alone (Sussman and Jacob, 1962). We have followed the kinetics of inactivation of the cI+ repressor brought about by irradiation in asynchronously and synchronously growing cultures of B/r (lambda cI ind- ts-857). Assays of the yield of phage released as a result of temporary thermal inactivation of the UV-resistant ind- ts-857 repressor at intervals after the irradiation accurately reflect the time course of UV-induced inactivation of the cI+ repressor. The results show that UV-induced derepression takes place in all cells of the population approximately 20 min after the irradiation whether the cells were growing asynchronously or synchronously. Hence UV induction of prophage lambda is not triggered at a particular stage in the cell cycle.

Induction of prophage lambda during the division cycle of Escherichia coli

When synchronous populations of Escherichia coli B/r (lambda) were exposed to low doses of ultraviolet light, the yield of infective centres varied with cell age. The yield was highest if the lysogenic bacteria were irradiated at a time which coincides approximately with the termination of rounds of DNA replication and it was lowest when dividing cells were irradiated. No such variation was detected following either irradiation of excision-defective lysogenic cells or thermal induction of lambdacI857 prophage in irradiated bacteria. It is suggested that the variation reflects a relationship between prophage induction and inhibition of cell division. This hypothesis is supported by data showing that irradiation promoted induction and curtailed division in E. coli K12 dnaA mutants which were dividing in the absence of DNA replication.

Repair by genetic recombination in bacteria: overview

DNA molecules that have been damaged in both strands at the same level are not subject to repair by excision but instead can be repaired through recombination with homologous molecules. Examples of two-strand damage include postreplication gaps opposite pyrimidine dimers, two-strand breaks produced by X-rays, and chemically induced interstrand cross-links. In ultraviolet-irradiated bacteria, the newly synthesized DNA is of length equal to the interdimer spacing. With continued incubation, this low-molecular-weight DNA is joined into high-molecular-weight chains (postreplication repair), a process associated with sister exchanges in bacteria. Recombination is initiated by pyrimidine dimers opposite postreplication gaps and by interstrand cross-links that have been cut by excision enzymes. The free ends at the resulting gaps presumably initiate the exchanges. Postreplication repair in Escherichia coli occurs in recB- AND RECC but is greatly slowed in recF- mutants. RecB and recC are the structural genes for exonuclease V, which digests two-stranded DNA by releasing oligonucleotides first from one strand and then from the other. The postreplication sister exchanges in ultra-violet-irradiated bacteria result in the distribution of pyrimidine dimers between parental and daughter strands, indicating that long exchanges involving both strands of each duplex occur. The R1 restriction endonuclease from E. COli has been used to cut the DNA of a bacterial drug-resistance transfer factor with one nuclease-sensitive site, and also DNA from the frog Xenopus enriched for ribosomal 18S and 28S genes. The fragments were annealed with the cut plasmid DNA and ligated, producing a new larger plasmid carrying the eukaryotic rDNA and able to infect and replicate in E. coli.

Recovery of phage lambda from ultraviolet damage

Recovery of phage lambda from ultraviolet damage can occur, in the dark, through three types of repair processes as defined by microbiological tests: (1) host-cell reactivation, (2) prophage reactivation, and (3) UV reactivation. This paper reviews the properties of the three repair processes, analyzes their dependence on the functioning of bacterial and phase genes, and discusses their relationship. Progress in the understanding of the molecular mechanisms underlying the three repair processes has been relatively slow, particularly for UV reactivation. It has been shown that host-cell reactivation is due to pyrimidine dimer excision and that prophage reactivation is due to genetic recombination (prereplicative). We provide evidence showing that neither of these mechanisms accounts for UV reactivation of phage lambda. Furthermore, UV reactivation differs from the other repair processes in that it is inducible and error-prone. Whether UV-damaged bacterial DNA is subject to a similar repair process is still an open question.

Indirect ultraviolet-reactivation of phage lambda

When an F(-) recipient Escherichia coli K12 bacterium receives Hfr or F-lac(+) DNA from an ultraviolet-irradiated donor, its capacity to promote DNA repair and mutagenesis of ultraviolet-damaged phage lambda is substantially increased. We call this phenomenon indirect ultraviolet-reactivation, since its features are essentially the same as those of ultraviolet-reactivation; this repair process occurs in pyrimidine dimer excision-deficient strains and produces clear plaque mutations of the restored phage. Moreover, this process is similar to indirect ultraviolet-induction of prophage lambda, since it is promoted by conjugation. However, contrarily to indirect induction, it is produced by Hfr donors and occurs in recipients restricting the incoming ultraviolet-damaged donor DNA. The occurrence of indirect ultraviolet-reactivation provides evidence for the existence in E. coli of an inducible error-prone mechanism for the repair of DNA.

Genetic studies of class 2 nonsense suppressors in Escherichia coli

Three genetically distinct ochre suppressors have been identified in a strain ofEscherichia coliB/r, all of which suppress a tyrosine auxotrophy and classify as class 2 by phage suppression pattern. One ochre suppressor, which was obtained by conversion from a class 2 amber suppressor, and a second ochre suppressor obtained directly from the non-suppressing parent, were found to have separate map locations, though a peculiar phenotype with regard to a leucine auxotrophy is exhibited by strains carrying either suppressor. We suggest that both suppressors correspond to separate genes for glutamine-insertingtRNA. A Leu+mutant of a strain carrying one of these suppressors was studied and was found to contain a further nonsense suppressor having amber-suppressing activity at a reduced level. We suggest that this suppressor might result from a mutation in another part of the translational machinery concerned with glutamine insertion. The third ochre suppressor has no effect on the leucine auxotrophy and mapping data suggest that it may besupL, an ochre suppressor probably inserting a different amino acid, from glutamine.