Isolation and characterization of Tn5 insertion mutations in the lexA gene of Escherichia coli

Regulatory role of recF in the SOS response of Escherichia coli: impaired induction of SOS genes by UV irradiation and nalidixic acid in a recF mutant

We isolated a new recF mutant of Escherichia coli K-12 by insertion of transposon Tn5 into the recF gene. This recF400::Tn5 allele displayed the same phenotypic characteristics as the classic recF143 mutation. By using Mu d(Ap lac) fusions, the induction of nine SOS genes, including recA, umuC, dinA, dinB, dinD, dinF, recN, and sulA, by UV irradiation and nalidixic acid was examined. Induction of eight genes by the two agents was impaired by recF400::Tn5 to different extents. The ninth fused SOS gene, dinF, was no longer inducible by UV when combined with recF400::Tn5. The generally impaired SOS response in recF strains did not result from weak induction of recA protein synthesis, since a recA operator-constitutive mutation did not alleviate the inhibitory effect of the recF mutation. The results suggest that recF plays a regulatory role in the SOS response. It is proposed that this role is to optimize the signal usage by recA protein to become a protease.

Differential repression of SOS genes by unstable lexA41 (tsl-1) protein causes a "split-phenotype" in Escherichia coli K-12

The lexA41 (formerly tsl-1) mutant was isolated as an ultraviolet light-resistant, temperature-sensitive derivative of its ultraviolet light-sensitive lexA3(Ind-) parent. Cells exhibit a so-called "split-phenotype", a phenomenon in which only a subset of the SOS responses can be detected physiologically following inducing treatments. lexA41 has been cloned and sequenced; the mutant gene retains the lexA3 mutation (Gly to Asp at position 85) and has a second mutation, lexA41 (Ala to Thr at position 131). We show that LexA41 protein is not cleaved by the RecA protein-catalyzed pathway in vivo, but the mutant protein is degraded by the Lon protease at both 32 degrees C and 42 degrees C. beta-Galactosidase activities of lac fusions to 13 different SOS promoters were measured at 30 degrees C and 42 degrees C to determine levels of expression and were found to vary considerably. The temperature-sensitive phenotype is a result of increased expression of sulA, which encodes a division inhibitor, at 42 degrees C. Excision repair genes, including uvrA, uvrB and uvrD, are constitutively expressed at 30 degrees C accounting for the ultraviolet light resistance of the lexA41 mutant, but the SOS mutagenesis operon, umuD,C, is not adequately derepressed, thereby explaining the failure to induce mutagenesis in this background. This differential expression of SOS genes gives a plausible explanation of the split-phenotype associated with lexA41.

Derepression of single-stranded DNA-binding protein genes on plasmids derepressed for conjugation, and complementation of an E. coli ssb- mutation by these genes

Plasmid single-stranded DNA-binding protein genes complement the E. coli ssb-1 mutation, and partially restore capacity for DNA synthesis, DNA repair (direct role as well as role in SOS induction) and general recombination. Plasmid mutants derepressed for fertility derived from R1, R64 and R222 show a higher level of complementation compared to the parental repressed plasmids. Derepressed mutants of R222 synthesize more RNA which hybridizes with the ssb gene of the F factor than does the original R222 plasmid. This indicates that plasmid ssb genes are regulated coordinately with fertility genes.

Role of the RecF gene product in UV mutagenesis of lambda phage

E. coli recF mutants have a greatly reduced capacity for Weigle mutagenesis of ultraviolet light-irradiated lambda phage. A recF 332::Tn3 mutation was introduced into an E. coli recA441 lexA51 strain which constitutively expresses SOS functions. Weigle mutagenesis of phage lambda could occur in the resulting strain in the absence of host cell irradiation, and was increased when the recA441 (tif) allele was activated by increased temperature and excess adenine. The inability of recF strains to support Weigle mutagenesis can therefore be ascribed to a defect in expression of SOS functions after irradiation.

Role of RecA protein in untargeted UV mutagenesis of bacteriophage lambda: evidence for the requirement for the dinB gene

Untargeted UV mutagenesis of bacteriophage lambda--i.e., the increased recovery of lambda mutants when unirradiated lambda infects UV-irradiated Escherichia coli--is thought to be mediated by a transient decrease in DNA replication fidelity, generating mutations in the newly synthesized strands. Using the bacteriophage lambda cI857----lambda c mutation system, we provide evidence that the RecA protein, shown previously to be required for this mutagenic pathway, is no longer needed when the LexA protein is inactivated by mutation. We suggest that the error-prone DNA replication responsible for UV-induced untargeted mutagenesis is turned on by the presence of replication-blocking lesions in the host cell DNA and that the RecA protein is required only to derepress the relevant din gene(s). This is in contrast to mutagenesis of irradiated bacteria or irradiated phage lambda, in which activated RecA protein has a second role in mutagenesis in addition to the cleavage of the LexA protein. Among the tested din genes, the dinB gene product (in addition to the uvrA and uvrB gene products) was found to be required for untargeted mutagenesis of bacteriophage lambda. To our knowledge, a phenotype associated with the dinB gene has not been reported previously.

Weigle reactivation and mutagenesis of bacteriophage lambda in lexA(Def) mutants of E. coli K12

The SOS response in UV-irradiated bacteria enhances the survival and mutagenesis of infecting damaged bacteriophage lambda. In a lexA(Def) strain, SOS bacterial genes are fully derepressed by an inactivating mutation in the LexA repressor gene. We tested several lexA(Def) derivative strains for their capacity to constitutively promote high survival and mutagenesis of irradiated lambda. We showed that UV irradiation of the lexA(Def) host bacteria is still necessary for optimal efficiency of both these SOS functions, which are dependent on the umuC gene product and an activated form of RecA protein.

UV-induced mutagenesis of phage S13 can occur in the absence of the RecA and UmuC proteins of Escherichia coli

The UV-induced mutagenesis of phage S13 that accompanies Weigle repair is known to require the products of the recA and umuDC genes, as does the UV-induced mutagenesis of the Escherichia coli chromosome. I found that UV-induced mutagenesis of phage S13 occurred in the absence of both the RecA and UmuC functions when the irradiated phage was photoreactivated. Furthermore, UV-induced phage mutations were produced in a recA- umuC- cell even without photoreactivation and in the absence of any other known UV repair mechanism, at a frequency 29% of that found after photoreactivation and 7% of that found after Weigle repair, implying that DNA synthesis can proceed past a dimer at an unexpectedly high frequency even when unaided by the UmuC-RecA SOS repair functions. The unaided DNA synthesis appears capable of producing mutations in the vicinity of a pyrimidine dimer; by aiding synthesis past a dimer, a repair mechanism may disclose a mutation without having any active role in producing it.

Genetic recombination of bacterial plasmid DNA: effect of RecF pathway mutations on plasmid recombination in Escherichia coli

Tn5 insertion mutations in the recN gene, and in what appears to be a new RecF pathway gene designated recO and mapping at approximately 55.4 min on the standard genetic map, were isolated by screening Tn5 insertion mutations that cotransduced with tyrA. The recO1504::Tn5 mutation decreased the frequency of recombination during Hfr-mediated crosses and increased the susceptibility to killing by UV irradiation and mitomycin C when present in a recB recC sbcB background, but only increased the sensitivity to killing by UV irradiation when present in an otherwise Rec+ background. The effects of these and other RecF pathway mutations on plasmid recombination were tested. Mutations in the recJ, recO, and ssb genes, when present in otherwise Rec+ E. coli strains, decreased the frequency of plasmid recombination, whereas the lexA3, recAo281, recN, and ruv mutations had no effect on plasmid recombination. Tn5 insertion mutations in the lexA gene increased the frequency of plasmid recombination. These data indicate that plasmid recombination events in wild-type Escherichia coli strains are catalyzed by a recombination pathway that is related to the RecF recombination pathway and that some component of this pathway besides the recA gene product is regulated by the lexA gene product.

Plaque color method for rapid isolation of novel recA mutants of Escherichia coli K-12: new classes of protease-constitutive recA mutants

As a prerequisite to mutational analysis of functional sites on the RecA protein of Escherichia coli, a method was developed for rapid isolation of recA mutants with altered RecA protease function. The method involves plating mutagenized lambda recA+ cI ind on strains deleted for recA and containing, as indicators of RecA protease activity, Mu d(Ap lac) fusions in RecA-inducible genes. The lambda recA phages were recognized by their altered plaque colors, and the RecA protease activity of the lambda recA mutant lysogens was measured by expression of beta-galactosidase from dinD::lac. One class of recA mutants had constitutive protease activity and was designated Prtc; in these cells the RecA protein was always in the protease form without the usual need for DNA damage to activate it. Some Prtc mutants were recombinase negative and were designated Prtc Rec-. Another class of 65 recA mutants isolated as being protease defective were all also recombinase defective. Unlike the original temperature-dependent Prtc Rec+ mutant (recA441), the new Prtc Rec+ mutants showed constitutive protease activity at any growth temperature, with some having considerably greater activity than the recA441 strain. Study of these strong Prtc Rec+ mutants revealed a new SOS phenomenon, increased permeability to drugs. Use of this new SOS phenomenon as an index of protease strength clearly distinguished 5 Prtc mutants as the strongest among 150. These five strongest Prtc mutants showed the greatest increase in spontaneous mutation frequency and were not inhibited by cytidine plus guanosine, which inhibited the constitutive protease activity of the recA441 strain and of all the other new Prtc mutants. Strong Prtc Rec+ mutants were more UV resistant than recA+ strains and showed indications of having RecA proteins whose specific activity of recombinase function was higher than that of wild-type RecA. A Prt+ Rec- mutant with an anomalous response to effectors is described.

Colicin synthesis and cell death

Colicin E1 is a small plasmid, containing the cea gene for colicin, the most prominent product of the plasmid. Colicin is a 56-kilodalton bacteriocin which is especially toxic to Escherichia coli cells that do not contain the plasmid. Under normal growth conditions very low levels of the plasmid are produced as a result of cea gene repression by the host LexA protein. Conditions that lower the concentration of LexA protein result in elevated levels of colicin synthesis. The LexA protein concentration can be lowered by exposing the cells to DNA-damaging reagents such as UV light or mitomycin C. This is because DNA damage signals the host SOS response; the response leads to activation of the RecA protease which degrades the LexA protein. DNA-damaging reagents result in very high levels of colicin synthesis and subsequent death of plasmid-bearing cells. Elevated levels of colicin are also produced in mutants of E. coli that are deficient in LexA protein. We found that comparably high levels of colicin can be produced in such mutants in the absence of cell death. In lexA strains carrying a defective LexA repressor, colicin synthesis shows a strong temperature dependence. Ten to twenty times more colicin is synthesized at 42 degrees C. This sharp dependence of synthesis on temperature suggests that there are factors other than the LexA protein which regulate colicin synthesis.

Mitomycin-induced lethality of Escherichia coli cells containing the ColE1 Plasmid: involvement of the kil gene

Escherichia coli cells containing the ColE1 plasmid or related plasmids are killed by considerably lower levels of mitomycin C (MTC) than are plasmid-free cells. Since exposure to MTC induces high levels of synthesis of the plasmid-encoded colicin toxin, it was originally thought that the killing effect was due to the increased levels of colicin. This possibility was discounted when it was shown that deletion mutations in the plasmid lacking most of the colicin (cea) gene still sensitized host cells to MTC. Only when the region containing the cea gene promoter was deleted did the killing effect disappear. This led to the suggestion that transcription originating from the cea gene promoter and not the colicin protein itself was required for killing. Transcription-blocking mutations in the cea gene support this suggestion. It was proposed that there is a gene (kil) located downstream from the cea gene in the same operon that is responsible for MTC killing and colicin transport. The precise location of the kil gene in ColE1 can be predicted by piecing together published sequence information. We used available sequence data to construct a number of well-defined plasmid mutants to further examine the relevance of transcription from the cea promoter and the kil gene to drug-induced killing and colicin transport. The most informative mutant had a small insertion in the kil gene. This mutant behaved as predicted; cells containing it had a greatly lowered sensitivity to MTC and were severely inhibited in the transport of colicin.

Dual role for Escherichia coli RecA protein in SOS mutagenesis

Induction of the Escherichia coli SOS system increases the ability of the cells to perform DNA repair and mutagenesis. Previous work has shown that this increased mutagenesis is the result of derepression of specific genes through a complex regulatory mechanism controlled by LexA and RecA proteins. One role of RecA protein in this process is to facilitate proteolytic cleavage of LexA protein (the repressor) in response to an inducing signal that reversibly activates RecA protein to perform this function. We show that activated RecA protein plays a second role in SOS mutagenesis, as revealed by analyzing repair of UV-damaged phage lambda in host mutants with alterations in the SOS regulatory system. First, phage mutagenesis was not expressed constitutively in a mutant that is derepressed through lack of functional LexA protein; activated RecA protein was still required. Second, phage mutagenesis was constitutively expressed in the presence of recA mutations that alter RecA protein so that it is activated in normally growing cells. There was also RecA-dependent constitutive expression of SOS mutagenesis in host mutants that lack functional LexA protein and carry plasmids. We discuss several possible biochemical mechanisms for this second role of activated RecA protein in SOS mutagenesis.

Cold sensitivity induced by overproduction of UmuDC in Escherichia coli

The UmuD and UmuC proteins of Escherichia coli are essential for mutagenesis by UV and most chemicals. Their mode of action is presently unknown. Strains which lack the LexA repressor [lexA(Def)] and contain a pBR322-derived plasmid carrying the umuDC operon overexpress UmuD and UmuC and become cold sensitive (growth at 42 degrees C but not at 30 degrees C). Deletion mapping showed that the umuDC locus on the plasmid is responsible for conferring cold sensitivity. The conditional lethality appeared due to a rapid and reversible inhibition of DNA synthesis at the nonpermissive temperature. Cold sensitivity was enhanced by the increase of NaCl in the medium to 1% and eliminated by 4% ethanol in the medium. Cold sensitivity was partially suppressed by the lon-100 mutation and completely suppressed by the htpR165 mutation.

Deletions within a hinge region of a specific DNA-binding protein

Many proteins are organized as a set of compact functional domains connected by flexible, exposed segments of the polypeptide chain. To study one of these connector regions, we isolated a series of functional in-frame deletions in the central portion of a specific DNA-binding protein, the LexA repressor of Escherichia coli. These mutant proteins fell into two main classes: those with small deletions of two to eight amino acids functioned as repressor about as well as did wild type, while those with large deletions of 17-22 amino acids functioned well only at considerably higher concentrations. The mutant proteins were resistant to the specific cleavage reaction that triggers the SOS response. These data suggest that the conformation of the hinge region in LexA protein is important for cleavage. By contrast, the hinge plays a topological role in repressor function, connecting the two functional halves of the protein; in the SOS response, this function of the hinge is inactivated by cleavage, leading to inactivation of the repressor.

groEL and dnaK genes of Escherichia coli are induced by UV irradiation and nalidixic acid in an htpR+-dependent fashion

Two proteins with molecular weights of 61,000 and 73,000 were found to be induced by UV light in Escherichia coli mutants in which the SOS responses are constitutively expressed. The induction of these proteins by UV light and nalidixic acid was shown to be independent of the recA+ lexA+ regulatory system. Analysis of these proteins by two-dimensional gel electrophoresis and comparison with the "heat-shock" proteins of E. coli revealed that the Mr 61,000 protein comigrated with the groEL gene product, that the Mr 73,000 protein comigrated with the dnaK gene product, and that other heat-shock proteins were also induced. The induction of groEL and dnaK by UV light and nalidixic acid is controlled by the htpR locus. The results suggest that the regulatory response of E. coli to agents such as UV light and nalidixic acid is more complex than previously thought.

UV inducible UV protection and mutation functions on the I group plasmid TP110

The UV protection and mutation properties of the I group plasmid TP110 have been investigated. It is demonstrated that the genes responsible for these effects are able to complement the deficiency in umuC36 mutants of E. coli, as are the similar genes carried by the B group plasmid R16. Mu-lac inserts into TP110 have been isolated which abolish the UV protection and mutation functions. Restriction mapping of these inserts locates them within a single region of the genome. A comparison of the restriction sites of this region with the muc region of pKM101 reveals very little similarity. Expression of beta-galactosidase in those Mu-lac inserts in which the lacZ gene is fused to the promoter for the protection and mutation functions is inducible by DNA damaging agents, and induction in mutant strains suggests that these genes are under the direct control of the lexA repressor.

Transcription analysis of the lexA gene of Escherichia coli: attenuation and cotranscription with the neighboring region

The lexA gene of Escherichia coli encodes a repressor of the genes whose expression is induced by the agents that result in DNA damage. In vivo transcripts of the lexA gene consisted of two species; mRNA-1 of 673 bases and mRNA-2 of approximately 3,000 bases. The transcription in vivo started at a site which was two-base pairs downstream from the in vitro initiation site reported previously. The majority of the transcription stopped at a series of T residues preceeded by a dyad symmetry located immediately after the lexA gene. A small fraction of the transcription passed through the termination site to form the mRNA of downstream gene(s) which would be related to the "SOS functions".

The Escherichia coli uvrD gene is inducible by DNA damage

The product of the uvrD gene of Escherichia coli is involved in the repair of DNA damage, mismatch repair, and recombination. Phage Mud(Amp, Lac) was used to form a uvrD-lacZ fusion allowing uvrD expression to be followed by measuring the activity of beta-galactosidase, the product of the lacZ gene. uvrD expression was inducible by DNA damage and was under the control of lexA-recA regulatory system. Mutations in the uvrD gene that result in different phenotypes in respect to DNA repair and spontaneous mutation have been previously found. The phenotype of the uvrD::Mud(Amp, Lac) mutant was mutator and UV-sensitive but not as deficient in host cell reactivation or repair of methyl methanesulfonate damage as the previously described uvrD3 mutant.