Lack of single-strand DNA-binding protein amplification under conditions of SOS induction in E. coli

Regulation of ssb Gene Expression in Escherichia coli

Bacterial SSB proteins, as well as their eukaryotic RPA analogues, are essential and ubiquitous. They avidly bind single-stranded DNA and regulate/coordinate its metabolism, hence enabling essential DNA processes such as replication, transcription, and repair. The prototypic Escherichia coli SSB protein is encoded by an ssb gene. Although the ssb gene promoters harbor an SOS box, multiple studies over several decades failed to elucidate whether ssb gene expression is inducible and SOS dependent. The SOS regulon is comprised of about 50 genes, whose transcription is coordinately induced under stress conditions. Using quantitative real-time PCR, we determined the ssb gene expression kinetics in UV- and γ-irradiated E. coli and revealed that ssb gene expression is elevated in irradiated cells in an SOS-dependent manner. Additionally, the expression of the sulA gene was determined to indicate the extent of SOS induction. In a mutant with a constitutively induced SOS regulon, the ssb gene was overexpressed in the absence of DNA damage. Furthermore, we measured ssb gene expression by droplet digital PCR during unaffected bacterial growth and revealed that ssb gene expression was equal in wild-type and SOS^- bacteria, whereas sulA expression was higher in the former. This study thus reveals a complex pattern of ssb gene expression, which under stress conditions depends on the SOS regulon, whereas during normal bacterial growth it is unlinked to SOS induction. The E. coli ssb gene is SOS regulated in such a way that its basal expression is relatively high and can be increased only through stronger SOS induction. The remarkable SOS induction observed in undisturbed wild-type cells may challenge our notion of the physiological role of the SOS response in bacteria.

Are there DNA damage checkpoints in E. coli?

The concept of regulatory 'checkpoints' in the eukaryotic cycle has proved to be a fruitful one. Here, its applicability to the bacterial cell cycle is examined. A primitive DNA damage checkpoint operates in E. coli such that, after exposure to ultraviolet light, while excision repair occurs, chromosome replication continues very slowly with the production of discontinuous daughter strands. The slower the rate of excision of photoproducts, the greater the delay before the normal rate of DNA replication is restored, the additional time for repair ensuring that normal survival is maintained. A model is proposed in which replication rate is controlled by the ratio of RecA-coated to uncoated single stranded regions of DNA in the replication fork. There are also two cell division inhibitors SulA (= SfiA) and SfiC under the control of the SOS system and sensitive to DNA damage, but they are irrelevant to the survival of wild-type bacteria under normal conditions. In strains where SulA and SfiC do not operate, inhibition is not influenced by the rate of excision repair and so fails one of the criteria for a DNA damage checkpoint, namely the monitoring of the DNA for the level of residual damage.

Survival of M13mp18 gapped duplex DNA as a function of gap length

Gaps of various lengths were generated in duplex M13mp18DNA by exonuclease III digestion of nicked DNA. The length of the gap increased essentially linearly with time of digestion. Survival in E. coli, however, was not a linear function of gap length. Similar results were obtained when gaps were produced by stopping the polymerization reaction. The survival (N/No) of the gapped DNA in SOS-induced E. coli cells transformed by electroporation and uninduced cells transformed by the calcium chloride method can be quantitatively accounted for by a kinetic model assuming a single-strand endonucleolytic activity (Pd) in the cell which increases linearly with gap length (L) and a repair activity by a polymerase (Pr) which is independent of gap length (formula 1). With uninduced cells transformed by electroporation the results can be mathematically described if assumptions are made concerning the protection of single-stranded parts of the DNA by single-strand affinic proteins.

Biochemical and biological function of Escherichia coli RecA protein: behavior of mutant RecA proteins

The recA protein of E coli participates in several diverse biological processes and promotes a variety of complex in vitro reactions. A careful comparison of the phenotypic behavior of E coli recA mutations to the biochemical properties of the corresponding mutant proteins reveals a close parallel both between recombination phenotype and DNA strand exchange and renaturation activities, and between inducible phenomena and repressor cleavage activity. The biochemical alterations manifest by the mutant recA proteins are reflected in the strength of their interaction with ssDNA. The defective mutant recA proteins fail to properly assume the high-affinity DNA-binding state that is characteristic of the wild-type protein and, consequently, form less stable complexes with DNA. The mutant proteins displaying an 'enhanced' activity bind ssDNA with approximately the same affinity as the wild-type protein but, due to altered protein-protein interactions, they associate more rapidly with ssDNA. These changes proportionately affect the ability of recA protein to compete with SSB protein, to interact with dsDNA, and, perhaps, to bind repressor proteins. In turn, the DNA strand exchange, DNA renaturation, and repressor cleavage activities mirror these modifications.

The single-stranded DNA-binding protein of Escherichia coli

The single-stranded DNA-binding protein (SSB) of Escherichia coli is involved in all aspects of DNA metabolism: replication, repair, and recombination. In solution, the protein exists as a homotetramer of 18,843-kilodalton subunits. As it binds tightly and cooperatively to single-stranded DNA, it has become a prototypic model protein for studying protein-nucleic acid interactions. The sequences of the gene and protein are known, and the functional domains of subunit interaction, DNA binding, and protein-protein interactions have been probed by structure-function analyses of various mutations. The ssb gene has three promoters, one of which is inducible because it lies only two nucleotides from the LexA-binding site of the adjacent uvrA gene. Induction of the SOS response, however, does not lead to significant increases in SSB levels. The binding protein has several functions in DNA replication, including enhancement of helix destabilization by DNA helicases, prevention of reannealing of the single strands and protection from nuclease digestion, organization and stabilization of replication origins, primosome assembly, priming specificity, enhancement of replication fidelity, enhancement of polymerase processivity, and promotion of polymerase binding to the template. E. coli SSB is required for methyl-directed mismatch repair, induction of the SOS response, and recombinational repair. During recombination, SSB interacts with the RecBCD enzyme to find Chi sites, promotes binding of RecA protein, and promotes strand uptake.

The relative rate of synthesis and levels of single-stranded DNA binding protein during induction of SOS repair in Escherichia coli

Induction of the SOS response in Escherichia coli results in an increase in the relative rate of synthesis of single-stranded DNA binding protein (SSB). In contrast to RecA protein, this increase is slow and does not lead to higher SSB levels. The significance of ssb induction to SOS repair is discussed.

Effects of overproduction of single-stranded DNA-binding protein on RecA protein-dependent processes in Escherichia coli

Overproduction of single-stranded DNA-binding protein (SSB) in Escherichia coli led to a decrease in the basal level of repressor LexA. Expression of the LexA-controlled genes was increased differentially, depending on the affinity of the LexA repressor for each promoter: expression of the recA and sfiA genes was increased 5-fold and 1.5-fold, respectively. Despite only a slight effect on expression of sfiA, which codes for an inhibitor of cell division, bacteria overproducing SSB produced elongated cells. In fact, the effect on cell shape appeared to be essentially independent of the expression of the sfiA and recA genes. Bacteria overproducing SSB were therefore phenotypically similar to bacteria partially starved of thymine, in which filamentation results from both sfiA-dependent and sfiA-recA-independent pathways. These data indicate that excess SSB acts primarily by perturbing DNA replication, thereby favoring gratuitous activation of RecA protein to promote cleavage of LexA protein. When bacteria overproducing SSB were exposed to a DNA-damaging agent such as ultraviolet light or mitomycin C, the recA and sfiA genes were fully induced. Induction of the sfiA gene occurred, however, at higher doses in bacteria overproducing SSB protein than in bacteria with normal levels of SSB. Whereas the efficiency of excision repair was apparently increased by excess SSB, the efficiency of post-replication recombinational repair was reduced as judged by a decrease in the recombination proficiency between a prophage and ultraviolet-irradiated heteroimmune infecting phage. Following induction of ssb+ bacteria with mitomycin C, the cellular content of SSB was slightly increased. These results provide evidence that SSB modulates RecA protein-dependent activities in vivo. It is proposed that SSB favors the formation of short complexes of RecA protein and single-stranded DNA that mediate cleavage of the LexA and lambda repressors, while it delays the formation of long nucleoprotein filaments, thereby slowing down RecA-promoted recombinational events in uninduced as well as in induced bacteria.

Analysis of the regulatory region of the ssb gene of Escherichia coli

The regulation of the ssb gene of E. coli has been studied. We reported earlier that the SOS box of the neighbouring uvrA gene also controls the transcription of the ssb gene. Detailed analysis of the upstream region of ssb by S1 mapping reveals the existence of three in vivo functional promoters of which the most upstream one (PI) is inducible by DNA damage. Measurement of galactokinase synthesis using galK fusion plasmids indicates that the uninduced level of transcription from the PI promoter is low. Ssb multicopy plasmids lacking the PI promoter still complement the UV sensitivity of an Ssb mutant. The role of the three promoters in the regulation of the level of Ssb protein in the cell, is discussed.

The SOS system

In the bacterium Escherichia coli DNA damaging treatments such as ultraviolet or ionizing radiation induce a set of functions called collectively the SOS response, reviewed here. The regulation of the SOS response involves a repressor, the LexA protein, and an inducer, the RecA protein. After DNA damage an effector molecule is produced--possibly single stranded DNA--which activates the RecA protein to a form capable of catalysing proteolytic cleavage of LexA. The repressors of certain temperate prophages are cleaved under the same conditions, resulting in lysogenic induction. SOS functions are involved in DNA repair and mutagenesis, in cell division inhibition, in recovery of normal physiological conditions after the DNA damage is repaired, and possibly in cell death when DNA damage is too extensive. The SOS response also includes several chromosomal genes of unknown function, a number of plasmid encoded genes (bacteriocins, mutagenesis), and lysogenic induction of certain prophages. DNA damaging treatments seem to induce DNA repair and mutagenic activities and proviral development in many species, including mammalian cells. In general, substances which are genotoxic to higher eukaryotes induce the SOS response in bacteria. This correlation is the basis of the numerous bacterial tests for genotoxicity and carcinogenicity.

Quantification of SSB protein in E. coli and its variation during RECA protein induction

Using a two-site immunometric assay (IRMA) we quantified the concentration of single-stranded DNA binding protein (SSB) in several E. coli strains. We found approximately 7,000 monomers of SSB present per bacterium, and this number remained constant throughout the exponential phase of growth. Two ssb- mutants (ssb-1 and ssb-113) are defective in the induction of the S.O.S. pathway. One of the first functions expressed upon induction of the S.O.S. pathway is the amplification of recA protein (RECA), which we monitored by an IRMA assay similar to the one used for SSB quantification. By combining the two assays we determined the level of SSB and RECA in ssb- mutants or in SSB and RECA overproducer strains. We found: a) a normal induction of RECA following UV irradiation of E. coli bacteria overproducing SSB, b) a normal level of SSB in wild type and ssb-1 and ssb-113 mutants either in the absence or in the presence of S.O.S. inducing agents. We confirmed a severe impairment in the induction of RECA in these two mutants after nalidixic acid treatment. Our results suggest that the concentrations of RECA and SSB protein in E. coli are regulated by independent biochemical pathways.

A common regulatory region shared by divergently transcribed genes of the Escherichia coli SOS system

The Escherichia coli single-stranded DNA binding protein (SSB) is implicated in DNA replication, recombination and repair. On the chromosome, the ssb gene is located adjacent to the excision repair gene uvrA, but the two genes are transcribed in opposite directions. uvrA has been shown to be part of the E. coli SOS system by introducing Mud(Ap, lac) insertions distal to the regulatory region of the gene in the chromosome. Recent investigations suggest that SSB is also involved in the SOS response. However, because the SSB protein is essential to the cell, the inducibility of the ssb gene cannot be investigated by the insertion method. Therefore, we used plasmids harbouring the regulatory region of ssb fused to the galK structural gene, while leaving an intact ssb gene in the chromosome. We show here that expression of the ssb gene is dependent on two promoters of which one is damage inducible. Evidence is presented that the divergently transcribed ssb and uvrA genes are controlled by a common LexA binding site.

F sex factor encodes a single-stranded DNA binding protein (SSB) with extensive sequence homology to Escherichia coli SSB

We have determined the sequence of the gene encoding a single-stranded DNA (ss DNA) binding protein (SSB) from the Escherichia coli F sex factor and the amino acid sequence of the protein it encodes. The protein has extensive homology with E. coli SSB, particularly within its NH2-terminal region, where 87 of the first 115 amino acid residues are identical to those of the E. coli protein. We have previously shown that this portion of E. coli SSB contains the DNA binding region. The sequences diverge extensively in their COOH-terminal regions, although small areas of homology exist in several places. Six of the last seven amino acid residues of the two proteins are identical, which may have implications in terms of the direct interactions of these proteins with other proteins required for DNA replication, recombination, and repair. The coding region of the F plasmid ssf gene is 537 base pairs. The protein encoded by the gene contains 178 amino acids (one more than E. coli SSB) and has a calculated molecular weight of 19,505. Other than the presumptive Shine-Dalgarno sequence, the promoter and terminator regions of both genes are not similar. The most significant feature in this regard may be the lack of a region of dyad symmetry within the presumptive promoter of the F plasmid ssf gene as is found in the region of the presumptive E. coli ssb promoter. In this report the predicted secondary structures of both the F plasmid and E. coli SSB proteins are compared and the evolutionary significance of their sequence and structural similarities to the functional domains of the proteins are discussed.