Dissociation of tsl-tif-induced filamentation and recA protein synthesis in Escherichia coli K-12

DdrO is an essential protein that regulates the radiation desiccation response and the apoptotic-like cell death in the radioresistant Deinococcus radiodurans bacterium

Deinococcus radiodurans is known for its extreme radioresistance. Comparative genomics identified a radiation-desiccation response (RDR) regulon comprising genes that are highly induced after DNA damage and containing a conserved motif (RDRM) upstream of their coding region. We demonstrated that the RDRM sequence is involved in cis-regulation of the RDR gene ddrB in vivo. Using a transposon mutagenesis approach, we showed that, in addition to ddrO encoding a predicted RDR repressor and irrE encoding a positive regulator recently shown to cleave DdrO in Deinococcus deserti, two genes encoding α-keto-glutarate dehydrogenase subunits are involved in ddrB regulation. In wild-type cells, the DdrO cell concentration decreased transiently in an IrrE-dependent manner at early times after irradiation. Using a conditional gene inactivation system, we showed that DdrO depletion enhanced expression of three RDR proteins, consistent with the hypothesis that DdrO acts as a repressor of the RDR regulon. DdrO-depleted cells loose viability and showed morphological changes evocative of an apoptotic-like response, including membrane blebbing, defects in cell division and DNA fragmentation. We propose that DNA repair and apoptotic-like death might be two responses mediated by the same regulators, IrrE and DdrO, but differently activated depending on the persistence of IrrE-dependent DdrO cleavage.

The promoter of the recA gene of Escherichia coli

The growth defect of a lambda phage carrying a recA-lacZ fusion was used to select mutations that reduced recA expression. Nine single base changes in the recA promoter were isolated that reduced both induced and basal (repressed) levels of expression. Deletion analysis of the promoter region and mapping of transcripts indicated that there is one main promoter responsible for both basal and induced expression. Some of the mutants displayed a lowered induction ratio, raising the possibility that there is a second, weak promoter that is not regulated by the SOS response. When one of the mutants was examined, it showed normal affinity for LexA repressor binding to the operator site. Binding of RNA polymerase to this mutant promoter, however, was much reduced. Further binding experiments suggested that LexA does not block RNA polymerase binding to the recA promoter, but inhibits a later step in initiation.

Reversibility of SOS-associated division inhibition in Escherichia coli

In Escherichia coli the SOS response, induced by DNA-damaging treatments, includes two systems of cell division inhibition, SfiA and SfiC, which are thought to prevent cell division by interacting with the division protein FtsZ. It is shown here that SfiA-mediated division inhibition is readily reversible, even in the absence of de novo protein synthesis, suggesting that functional FtsZ molecules can be recovered from SfiA-FtsZ complexes. The action of SfiC, on the other hand, is essentially irreversible; induction by expression of the recA (Tif) mutation for 60 min results in division inhibition that continues for at least 180 min after the end of the induction period. An excess of the presumed target molecule FtsZ, furnished by a multicopy plasmid, suppresses the action of SfiA but not SfiC. Simultaneous induction of SfiA and SfiC results in irreversible division inhibition, showing that SfiC is epistatic to SfiA. The irreversibility of SfiC action is most readily accounted for by assuming that the SfiC product, unlike SfiA, is stable. The reversibility of SfiA action is slower in a lon mutant, in which the SfiA protein is partially stabilized. From the kinetics of division resumption in the absence of protein synthesis, we estimated the in vivo half-life of the SfiA protein to be 10 min in a lon+ strain and 170 min in a lon mutant.

Direct selection of mutations reducing transcription or translation of the recA gene of Escherichia coli with a recA-lacZ protein fusion

When a recA-lacZ protein fusion was cloned into phage lambda, the resulting transducing phage grew normally on wild-type Escherichia coli, but its growth was severely inhibited in lexA(Def) mutant strains that express recA constitutively at high levels. Mutants of the transducing phage that grew on the lexA(Def) strains were isolated and were found to affect production of the RecA-beta-galactosidase hybrid protein. Most mutants, including a number of nonsense mutants, were phenotypically LacZ-. LacZ+ mutants were also isolated; most of these expressed lower basal and induced levels of beta-galactosidase activity. DNA sequence analysis revealed that some of the LacZ+ mutations were in the recA promoter. One of these was found to prevent induction. Unexpectedly, three of the mutations that reduced expression were located in the recA structural gene, at codons 10, 11, and 12. Further analysis of the codon 10 mutant showed that it most likely affected translation since it had little effect on transcription as measured by beta-galactosidase synthesis from a recA-lacZ operon fusion. This expression defect was not limited to the protein fusion, since the codon 10 mutation also reduced synthesis of RecA protein when present in a complete recA gene. Analysis of the recA DNA sequence in the fusion revealed that each of the mutations at codons 10, 11, and 12 increases the homology between this region of the mRNA and a sequence found at codons 1 to 4. Thus, the secondary structure of the mutant recA mRNAs may be affecting translation.

Novel mechanism of cell division inhibition associated with the SOS response in Escherichia coli

Certain Escherichia coli strains were shown to possess a novel system of cell division inhibition, called the SfiC+ phenotype. SfiC+ filamentation had a number of properties similar to those of sfiA-dependent division inhibition previously described: (i) both are associated with the SOS response induced by expression of the recA(Tif) mutation, (ii) both are associated with cell death, (iii) both are amplified in mutants lacking the Lon protease, and (iv) both are suppressed by sfiB mutations. SfiC+ filamentation and sfiA-dependent division inhibition differed in (i) the physiological conditions under which loss of viability is observed, (ii) the extent of amplification in lon mutants, (iii) their genetic regulation (SfiC+ filamentation is not under direct negative control of the LexA repressor), and (iv) their genetic determinants (SfiC+ filamentation depends on a locus, sfiC+, near 28 min on the E. coli map and distinct from sfiA).

Two pathways of division inhibition in UV-irradiated E. coli

We have investigated the mechanism of division inhibition in E. coli following UV-irradiation or nalidixic acid treatment. After UV, two separate mechanisms, both dependent upon recA+, appear to block division. One mechanism is dependent upon sfiA and sfiB, is inhibited by low levels (4 micrograms/ml) of rifamycin and is expressed in tif mutants at 42 degrees C. The second mechanism is independent of sfiA, and sfiB, is resistant to rifamycin and does not occur in cells lacking DNA replication forks. We suggest that this second mechanism is the result of the failure to terminate DNA replication in inhibited cells. Nalidixic acid inhibition of cell division also appears to involve both mechanisms but as found previously replication forks are also necessary to induce the sfi pathway.

Two pathways of division inhibition in UV-irradiated E. coli

We have investigated the mechanism of division inhibition in E. coli following UV-irradiation or nalidixic acid treatment. After UV, two separate mechanisms, both dependent upon recA, appear to block division. One mechanism is dependent upon sfiA and sfiB, is inhibited by low levels (4 micrograms/ml) of rifamycin and is expressed in tif mutants at 42 degrees C. The second mechanism is dependent on sfiA, B, is resistant to rifamycin and does not occur in cells lacking DNA replication forks. We suggest that this second mechanism is the result of the failure to terminate DNA replication in inhibited cells. Nalidixic acid inhibition of cell division also appears to involve both mechanisms but as found previously replication forks are also necessary to induce the sfi pathway.

Effect of suppressors of SOS-mediated filamentation on sfiA operon expression in Escherichia coli

In Escherichia coli, the cell division block observed during the SOS response requires the product of the sfiA gene, whose expression is regulated negatively by the LexA repressor and positively by the RecA protease. We have studied the effect on sfiA expression of sfiA, sfiB, infA, and infB mutations, which are known to affect SOS-associated filamentation. To measure sfiA expression in the different strains, we first constructed a lambda transducing phage carrying an sfiA::lac operon fusion. Mutations at the sfiA locus (dominant and recessive) and the sfiB locus (recessive) had no effect on sfiA expression. The mutations tif (at the recA locus) and tsl (at the lexA locus) are known to induce filamentation and a high level of sfiA expression at 42 degrees C. The infB1 mutation, which suppresses filamentation in a tif tsl strain at 42 degrees C, reduced sfiA expression at 42 degrees C in tif tsl infB1 and tsl infB1 strains but not in a tif infB1 strain. The infA3 mutation, which suppresses tif-mediated filamentation, reduced induction of sfiA expression in a tif infA3 strain at 42 degrees C or after UV irradiation. The isolation and characterization of sfiA constitutive strains revealed only lexA-linked mutations in a sfiA-background, suggesting that LexA is the only readily eliminated repressor of the sfiA gene. Nevertheless, the infA and infB mutations could define elements involved in the regulation of sfiA expression.

Cell survival, UV-reactivation and induction of prophage lambda in Escherichia coli K12 overproducing RecA protein

The effect of the cellular level of RecA protein on the ability of E. coli K12 bacteria to (i) survive UV-irradiation (ii) promote UV-reactivation of UV-damaged phage lambda (iii) induce prophage lambda was determined in bacterial mutants with discrete increasing levels of RecA protein. The various levels of RecA protein were obtained by combining lexA and recA alleles. Except for the double mutant lexA3 recAo98, whose repair ability was 25% less than that observed in wild type bacteria, bacterial survival was proportional to the level of RecA protein measured after 90 min of incubation. In lexA3 recAo98 bacteria, RecA protein, at a constitutive high basal level, failed to compensate totally for the lack of LexA repressor cleavage; UV-reactivation of UV-damaged phage lambda was not restored; yet, prophage lambda was induced with 35% efficiency. Efficient UV-induction of prophage lambda is linked to the induction of lexA-controlled host processes that repair the UV-damaged prophage.

Isolation and characterization of an operator-constitutive mutation in the recA gene of E. coli K-12

The recA gene of E. coli is regulated by a specific repressor, the lexA protein, which binds to an operator in the recA regulatory region. We describe in this paper the isolation and characterization of a mutant thought to carry an operator-constitutive mutation in the recA gene. This mutation has the following properties: 1) It partially suppresses the UV sensitivity of lexA- strains. 2) It maps near the recA gene. 3) It allows constitutive high-level synthesis of recA protein in both lexA- and lexA+ backgrounds. 4) It allows constitutive synthesis of the recA messenger RNA. 5) It is cis-acting. The mutation does not restore induced cellular mutagenesis in a lexA- background. The expression of induced repair and mutagenesis of UV irradiated phage lambda or the regulation of the lexA gene is not affected by the presence of the mutation in either a lexA+ or lexA- strain. These observations confirm other findings that high levels of recA protein synthesis per se is not sufficient for the expression of UV inducible functions and that the lexA protein represses other genes besides the recA gene.

Quantitative evaluation of recA gene expression in Escherichia coli

A recA::lac operon fusion was constructed using the phage Mu d(Ap, lac) in Escherichia coli to obtain precise measurements of the level of recA gene expression in various genetic backgrounds. The RecA protein normally represents 0.02% of total protein. This value is known to increase dramatically after treatments interrupting DNA synthesis; kinetic experiments showed that the rate of recA expression increases 17-fold within 10 min after UV irradiation or thymine starvation. In mutants affected in SOS regulation or repair the following observations were made: (i) the tif-1 mutation in the recA gene does not alter the basal level of recA expression, suggesting that it improves the protease activity of RecA; (ii) the lexA3 mutation does not create a "super-repressor" of recA; (iii) the tsl-1 mutation in the lexA gene makes the LexA protein a poor repressor of recA at 30 degrees C (2.5-fold derepression) and a poor substrate for RecA protease (3-fold stimulation of recA expression by UV); (iv) the spr-55 amber mutation in the lexA gene causes a 30-fold increase in recA expression, higher than all inducing treatments, and this level cannot be further increased by nalidixic acid; (v) the zab-53 mutation at the recA locus, known to abolish tsl-mediated induction of recA expression, is trans-recessive and thus probably affects a regulatory site on the DNA; (vi) uvrA, B and C, recB and recF mutations do not increase the basal level of recA expression, suggesting that there are not sufficient spontaneous lesions to cause induction even when any one of these three repair pathways is inoperative.

Further characterization of sfiA and sfiB mutations in Escherichia coli

The sfiA and sfiB mutations, originally isolated in thermoresistant ultraviolet-resistant revertants of a tif lon strain, also suppressed filamentation in tsl strains (mutated at the lexA locus). When deoxyribonucleic acid synthesis was arrested, however, sfi-independent filamentation occurred. Other SOS functions were not affected by sfiA and sfiB mutations; in particular, ultraviolet-induced repair and mutagenesis of bacterial deoxyribonucleic acid were normal, as was tsl-tif-induced synthesis of recA protein. Genetic studies (i) established the identity of map location of the sfiA and sulA loci, (ii) showed that the two sfiB mutations are recessive, and (iii) showed that of six independent sfiA mutations, three are recessive and three are dominant. One sfiB strain was shown to have a 6% growth disadvantage relative to a sfi+ or sfiA strain. It is proposed that the sfiA locus may define the structural gene of a hypothetical inducible SOS-associated division inhibitor.