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RecA protein in the SOS response: milestones and mysteries.

The role of RecA protein in the SOS response of Escherichia coli is traced from the isolation of the first recA mutant to our current understanding of the scope and regulation of this DNA damage-inducible system. In addition, possible RecA protein activities that may be essential in the expression of several SOS phenotypes (stable DNA replication, DNA replication recovery, SOS mutagenesis and RecA association with the cell membrane) are discussed.

DNA Repair↗

Suppressive effects of urine on the SOS responses induced by UV and chemical mutagens.

We studied the antimutagenic effects of urine on the SOS-inducing activity of mutagenic substances by using a novel test system (umu-test) for detecting DNA damaging agents, which uses a new tester strain (Salmonella typhimurium TA1535/pSK1002). The SOS-inducing activity of chemicals was detected in terms of the level of umu operon expression by measuring beta-galactosidase activity. We first examined the effects of various amounts of urine on SOS responses caused by mitomycin C (MMC). As a result, the urine suppressed beta-galactosidase activity of MMC dose-dependently. A urine concentration of 50 microliters/ml in the medium also suppressed 89.9% of SOS response induced by 0.1 microgram/ml of PEP, 75.6% of that induced by 0.02 microgram/ml of AF2 and 60.9% of that induced by 0.1 microgram/ml of AFB1. In addition, a urine concentration of 50 microliters/ml in the medium also suppressed 85.6% of SOS response by 5 J/m2 of UV irradiation. The observed suppression seemed to be directly related to the SOS responses at a cellular level, rather than to interaction between urine and mutagens, because the urine suppressed SOS responses induced not only by various mutagens but also by UV irradiation. These results suggest that urine works as a strong antimutagen against UV and chemical substances.

Antimutagenic Agents↗

Enhanced induction of tissue-type plasminogen activator in normal human cells compared to cancer-prone cells following ionizing radiation.

Normal human fibroblast (i.e., GM2936B, GM2907A, and IMR-90) and cancer-prone human fibroblast (i.e., Fanconi's anemia, Bloom's syndrome, and Ataxia telangiectasia) cells demonstrated the induction of intracellular and extracellular levels of tissue-type plasminogen activator (t-PA) at 6 and 12 hr, respectively, following ionizing radiation. Induced t-PA enzymatic activities following ionizing radiation were blocked by actinomycin D treatments. t-PA enzymatic activities were induced over 14-fold in Ataxia telangiectasia cells, over 9-fold in Bloom's syndrome cells, and over 6-fold in Fanconi's anemia cells, as compared to normal human fibroblasts. Similarly, the induction of t-PA mRNA levels in cancer-prone cells were between 5- to 10-fold higher than those observed in normal cells following equitoxic doses of ionizing radiation. Temporal induction of t-PA mRNA levels for normal and cancer-prone human cells were consistent with quantifiable enzymatic activities. The elevated induction of an intracellular protease (i.e., t-PA) in cancer-prone human cells is reminiscent of an "SOS"-like response observed in yeast and bacteria.

Ataxia Telangiectasia↗

sulA-independent division inhibition in his-constitutive strains of Salmonella typhimurium.

Constitutive expression of the S. typhimurium histidine operon causes multiple phenotypic changes including strong filamentation. However, the SOS regulatory network is not involved in the inhibition of cell division. The possibility of SOS-independent activation of sulA gene transcription has been ruled out using sulA-lacZ fusions. These results suggest the existence of a pathway of division inhibition unrelated to sulA and not regulated by the SOS system.

Cell Division↗

Construction and evaluation of a cea-lacZ gene fusion for the detection of environmental mutagens and carcinogens.

The cea-kil operon of the ColE1 plasmid is negatively regulated by the LexA-repressor and therefore, it is under the control of SOS regulation. We constructed a gene fusion between the cea and lacZ genes. Expression of the translational fusion can be easily detected by monitoring the levels of beta-galactosidase. Since the whole detection system is plasmid-based, it can be used in both Escherichia coli and Salmonella typhimurium strains. The SOS-function-inducing activities of 14 chemical mutagens were investigated in E. coli K12 and in two S. typhimurium Ames-strains and compared with results obtained by the SOS-chromotest and by the Umu-test. To correct for the inhibitory effects of test chemicals on mRNA and/or protein synthesis, the level of the constitutive chloramphenicol acetyl transferase was assayed in parallel.

Bacillus subtilis↗

Molecular cloning of a recA-like gene of Methylophilus methylotrophus and identification of its product.

A recombinant plasmid, pPF5, has been constructed which contains a 5.5-kb fragment of Methylophilus methylotrophus DNA inserted into pAT153, and which confers resistance to UV and mitomycin C (MC) upon Escherichia coli recA mutants. Hybridisation analysis indicates that sequence homology exists between the cloned DNA and a fragment of E. coli chromosomal DNA that contains the recA gene. Tn1000 insertions have been isolated within pPF5 that inactivate its ability to complement recA mutations, and the site of each insertion has been determined by restriction mapping. A 36-kDa protein is synthesised by pPF5 but not by any of the Tn1000 derivatives, indicating that this protein is the product of the gene responsible for the complementation. Comparison of the size of truncated polypeptides produced by selected pPF5::Tn1000 derivatives with the position of the insertion sites of the transposon, gave the direction of transcription of the M. methylotrophus recA+ gene. SOS proteins are induced in E. coli recA mutants harbouring pPF5 following MC treatment.

Cloning, Molecular↗

Evolution of the enterobacterial sulA gene: a component of the SOS system encoding an inhibitor of cell division.

The LexA-regulated sulA (sfiA) gene of Escherichia coli encodes an unstable protein which inhibits cell division. By determining the nucleotide sequences of the corresponding genes from the related bacteria Salmonella typhimurium, Enterobacter aerogenes and Serratia marcescens it was found that the regulatory region and the LexA binding site (SOS box) have been better conserved during evolution than the coding sequence. The N terminus of the SulA protein [amino acid (aa) residues 1-30] has diverged extensively during the evolution of Enterobacteriaceae, whereas the central region (aa residues 31-149) has been well conserved. At the C terminus a sequence showing some homology to the N protein of phage lambda was detected that may represent a recognition site for the Lon protease, which is known to degrade both polypeptides. When expressed in E. coli, the foreign sulA genes did not block cell division suggesting that their products are inactive. This may indicate that the N terminus of the SulA protein is involved in recognizing the cell division apparatus.

Amino Acid Sequence↗

Identification of a unique specificity determinant of the colicin E3 immunity protein.

Plasmid immunity to a nuclease-type colicin is defined by the specific binding of an immunity (or inhibitor) protein, Imm, to the C-terminal nuclease domain, T2A, of the colicin molecule. Whereas most regions of colicin operons exhibit extensive sequence identity, the small plasmid region encoding T2A and Imm is exceptionally varied. Since immunity is essential for the survival of the potentially lethal colicin plasmid (Col), we inferred that T2A and Imm must have co-evolved, retaining their mutual binding specificities. To evaluate this co-evolution model for the col and imm genes of ColE3 and ColE6, we attempted to obtain a stabilized clone from a plasmid which had been destabilized with a non-cognate immunity gene. A hybrid Col, in which the immE3 gene of the ColE3 was replaced with immE6 from ColE6, was lethal to the host cells upon SOS induction. From among this suicidal cell population, we isolated a stabilized, i.e., evolved, clone which produced colicin E3 (E3) stably and exhibited immunity to E3. This change arose from only a single mutation in ImmE6, from Trp48 to Cys, the same residue as in the ImmE3 sequence. In addition, we constructed a series of chimeric genes through homologous recombination between immE3 and immE6. Characterization of these chimeric immunity genes confirmed the above finding that colicins E3 and E6 are mostly distinguished by only Cys48 of the ImmE3 protein.

Amino Acid Sequence↗

SOS induction as an in vivo assay of enzyme-DNA interactions.

We have constructed strains which are convenient and sensitive indicators of DNA damage and describe their use. These strains utilize an SOS::lac Z fusion constructed by Kenyon and Walker [Proc. Natl. Acad. Sci. USA 77 (1980) 2819-2823] and respond to DNA damage by producing beta-galactosidase. They can be used to characterize restriction systems and screen for restriction endonuclease mutants. Applications include the study of other enzymes involved in DNA metabolism, such as DNA methyltransferases, topoisomerases, recombinases, and DNA replication and repair enzymes.

DNA↗

Cloning of a gene from Thermus filiformis and characterization of the thermostable nuclease.

A gene coding for a thermostable nuclease was cloned from the thermophilic microorganism, Thermus filiformis (Tf), using an indicator strain containing a dinD::lacZ fusion. The gene, designated nuc17, has been mapped within a 2300-bp fragment. The 55-kDa Tf nuclease was purified to over 95% homogeneity. Single-stranded (ss) DNA is the preferred substrate for the Tf nuclease, although double-stranded (ds) DNA can also be digested. Nuclease activity increases with increasing temperature up to 80 degrees C and requires the metal ions Ca++ or Mg++ for catalysis. Tf nuclease is primarily an endonuclease that leaves 5' phosphates in the digested products. The ssDNA extensions remaining after exonuclease III digestion of dsDNA can be removed by the Tf nuclease, making it a useful reagent to generate unidirectional deletions.

Bacterial Proteins↗

A putative SOS repair gene (dinF-like) in a hyperthermophilic archaeon.

The hyperthermophilic archaeon, Pyrococcus (strain IFREMER AL585), contains an ORF that encodes a polypeptide with a high similarity to the Escherichia coli dinF (DNA damage-inducible) gene product. The conservation of this protein between Archaea and Bacteria suggests that a SOS repair system might operate in Archaea.

Amino Acid Sequence↗

Induction of sfiA SOS function by peroxides using three different E. coli strains.

Five peroxides and two related compounds were tested for genotoxicity by the SOS Chromotest using 3 different E. coli strains (PQ37, PM21, GC4798). All tested hydroperoxides (hydrogen peroxide, tert-butylhydroperoxide, cumene hydroperoxide) were clearly positive in all strains. From a comparison of results obtained from the different strains it can be concluded that neither DNA lesions leading to the induction of excision repair nor covalent binding of radicals to DNA is responsible for the induction of sfiA-SOS function by hydroperoxides. Among the remaining compounds tested, only dibenzoylperoxide gave a clearly positive result in strain PQ37 whereas di-tert-butylperoxide and azobisisobutyronitrile showed only borderline activity. When using strains PM21 and GC4798, none of the latter compounds was positive. Paraquat was inactive in all strains.

DNA↗

The possible role of alpha, beta-unsaturated carbonyl compounds in mutagenesis and carcinogenesis.

alpha, beta-Unsaturated carbonyl compounds are industrially important compounds, ubiquitous in the environment and are formed endogenously. They interact with proteins and enzymes. Genotoxicity was found in eucaryotic cells and some compounds were carcinogenic. Unsaturated carbonyl compounds are considered to play an important role in human cancer. Insufficient and contradictory results were reported on mutagenicity. We demonstrated a clear mutagenic potential for these compounds and have shown interference of their bacterial toxicity with an adequate testing. Structure-mutagenicity relationships were confirmed by the results of the SOS-chromotest. The compounds induce DNA-strand breaks. However, we did not find indications for cross linking. With mutagenic alpha, beta-unsaturated carbonyl compounds we isolated and characterized 1,N2-cyclic deoxyguanosine adducts, 7,8-cyclic and 7-linear guanine adducts as well as 1,N2-7,8-biscyclic adducts and 1,N2-cyclic, 7-linear bisadducts. Reactivity of these compounds towards nucleosides runs in parallel with their mutagenic potential. Mutagenic and carcinogenic activities most probably depend on these reactions with DNA, and DNA adducts can be utilized as indicators for the role of these compounds in human carcinogenicity.

Aldehydes↗

A comparative study of five nitro musk compounds for genotoxicity in the SOS chromotest and Salmonella mutagenicity.

Five nitro musk compounds widely used in cosmetics and detergents were examined for DNA-damaging and mutation-inducing properties. For this purpose two short-time assays were used, the SOS chromotest and the Salmonella/mammalian microsome test. Musk ambrette showed mutagenicity in Salmonella typhimurium TA 100 requiring metabolic activation by rat liver postmitochondrial supernatant (S9) but it lacked mutagenicity in the absence of S9 and genotoxicity in the SOS chromotest. Musk xylene, musk ketone, musk moskene and musk tibetene showed neither mutagenicity nor genotoxicity in the presence and absence of S9.

Alkaline Phosphatase↗

Application of the SOS umu-test in detection of pollution using fish liver S9 fraction.

1. The possibility of Aroclor 1254 and beta-naphthoflavone treated fish Mugil auratus and fish sampled in low and high polluted areas to convert some premutagens to active intermediers in the SOS umu-test have been investigated. 2. Genotoxicity of Aflatoxin b1 differed markedly upon activation with liver S9 fractions from fish with different pollution histories, with the highest activation potency in fish living near a fish cannery. 3. Inhibition of umu gene expression by 7,8-benzoflavone in vitro clearly demonstrates a cytochrome P-450 mediated activation of aflatoxin b1. 4. 2-Aminoanthracene and 2-aminofluorene were weakly activated to genotoxic products and the induction of umu gene expression could be detected only in the presence of S9 fractions from fish treated with beta-naphthoflavone and Aroclor 1254 in the laboratory. 5. The capability of S9 from fish living near a fish cannery to convert 2-aminoanthracene and 2-aminofluorene was not observed.

Animals↗

The LexA protein does not bind specifically to the two SOS box-like sequences immediately 5' to the phr gene.

There are two SOS box-like sequences located at the regions -161 to -142 and -69 to -50 with regard to the initiation codon of phr. Ihara et al. (1987) constructed a phr'-'lacZ fusion plasmid in which these sequences and the amino terminal end of the phr gene was fused to lacZ and therefore lacZ was under the regulatory control of phr promoter-operator. The authors found that in cells carrying this plasmid beta-galactosidase was inducible by UV and UV-mimetic agents and concluded that phr was controlled by the LexA repressor. We wished to confirm these results by theoretical analysis of the SOS-like sequences by the method developed by Berg (1987) as well as by measuring the binding of LexA protein to the putative SOS boxes by a novel gel retardation assay. Both theoretical analysis and experimental results indicate that the putative SOS boxes immediately 5' to phr have no specific affinity for LexA protein.

Bacterial Proteins↗

Expression of DNA damage-inducible genes of Escherichia coli upon treatment with methylating, ethylating and propylating agents.

Several alkylation-inducible genes have been identified by construction of Mu-d1 (Apr lac) fusions to genes whose expression is increased in response to alkylation treatment, but not UV treatment. We have examined the induction of 4 different alkylation-inducible genes by treatment with a variety of methylating and ethylating agents, and a propylating agent. We have compared the induction of the alkylation-inducible genes with the induction of the sulA gene, which is a component of the SOS response to DNA damage. We find that the Ada-regulated adaptive response genes (ada-alkB, alkA and aidB) are induced primarily in response to methylation treatment. The ada-independent aidC gene is induced upon treatment with agents that alkylate predominantly by SN1 nucleophilic attack. aidC induction occurs only when cells are not aerated during treatment. The SOS response, as indicated by sulA induction, is strongly induced by all types of alkylating agents used.

Aerobiosis↗

Conditional lethality of the recA441 and recA730 mutants of Escherichia coli deficient in DNA polymerase I.

E. coli strains bearing the recA441 mutation and various mutations in the polA gene resulting in enzymatically well-defined deficiencies of DNA polymerase I have been constructed. It was found that the recA441 strains bearing either the polA1 or polA12 mutation causing deficiency of the polymerase activity of pol I are unable to grow at 42 degrees C on minimal medium supplemented with adenine, i.e., when the SOS response is continuously induced in strains bearing the recA441 mutation. Under these conditions the inhibition of DNA synthesis is followed in recA441 polA12 by DNA degradation and loss of cell viability. A similar lethal effect is observed with the recA730 polA12 mutant. The recA441 strain bearing the polA107 mutation resulting in the deficiency of the 5'-3' exonuclease activity of pol I shows normal growth under conditions of continuous SOS response. We postulate that constitutive expression of the SOS response leads to an altered requirement for the polymerase activity of pol I.

DNA Polymerase I↗