Mutant single-strand binding protein of Escherichia coli: genetic and physiological characterization

Pi exchange mediated by the GlpT-dependent sn-glycerol-3-phosphate transport system in Escherichia coli

The GlpT system for sn-glycerol-3-phosphate transport in Escherichia coli is shown to catalyze a rapid efflux of Pi from the internal phosphate pools in response to externally added Pi or glycerol-3-phosphate. A glpR mutation, which results in constitutive expression of the GlpT system, is responsible for this rapid Pi efflux and the arsenate sensitivity of several laboratory strains, including the popular strain C600. Glucose and other phosphotransferase system sugars inhibit Pi efflux by repressing glpT expression.

Variability in the nucleic acid binding site size and the amount of single-stranded DNA-binding protein in Escherichia coli

The Escherichia coli single-stranded DNA binding protein (SSB), essential for DNA replication, recombination and repair, can undergo a thermally induced irreversible conformational change which does not eliminate its biological activity, but changes the number of nucleotides it covers (binding site size) when binding to a single-stranded nucleic acid lattice. The binding site size of native and conformationally changed SSB was also found to be a function of the molecular mass of the polynucleotide, an observation which is unusual for single-stranded DNA binding proteins and will greatly affect the affinity relationship of this protein for nucleic acids. A radioimmunoassay used to quantitate in SSB level in cells revealed the number of SSB tetramers to be larger than initial estimates by a factor of as much as six. All these data suggest that the biological role of SSB and its mechanism of action is by far more complex than originally assumed.

Lethality of the double mutations rho rep and rho ssb in Escherichia coli

The similarity of rho mutants to rep and ssb mutants in sensitivity to UV light and in recombination deficiency suggested that the function of the Rho protein might be related to that of Rep and Ssb. In support of that idea, we found that rho rep and rho ssb double mutants are either nonviable, or at best only marginally viable. Viability could be restored by suppressor mutations, one of which mapped either in the rho gene or close to its 5'-end. Rho may thus share a role with Rep and Ssb in replication and the structural maintenance of DNA; a multifunctional Rho protein could account for the diversity of the defects seen in rho mutants, some of which appear to have no relation to the defect in transcription termination.

Genetic analysis of essential genes in the ftsE region of the Escherichia coli genetic map and identification of a new cell division gene, ftsS

Several conditional lethal mutants of Escherichia coli have been analysed genetically using generalized transduction and lambda transducing vectors. Three temperature-sensitive ftsE mutants were found as was a cold-sensitive ftsE mutant. A new gene was found which mapped close to ftsE, namely ftsS. Both cell division genes map close to the gene which controls the heat-shock regulon (htpR).

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.

Mechanism of the concerted action of recA protein and helix-destabilizing proteins in homologous recombination

Secondary structure in single-stranded DNA impedes the presynaptic association of recA protein and consequently blocks the formation of joint molecules as evidenced by effects of temperature, nucleotide sequence, and ionic conditions. Escherichia coli single-strand-binding protein eliminates sequence-specific "cold spots" by removing folds even from sites of strong secondary structure. Thus, destabilization of secondary structure in single-stranded DNA is critical for the action of recA protein, whereas specific interactions directly between helix-destabilizing proteins and recA protein are unimportant.

Minor protein content of the gene V protein/phage single-stranded DNA complex of the filamentous bacteriophage f1

The gene V protein/phage single-stranded (SS) DNA complex is an intermediate in the assembly of the filamentous bacteriophage f1. The minor protein content of this complex isolated from wild-type and amber mutant phage-infected Escherichia coli bacteria has been analyzed. Other than the gene V protein, none of the proteins found in purified samples of the complex correspond to any known phage gene products. In particular, the minor coat proteins found in the mature phage particle do not appear to be components of the cytoplasmic gene V protein/f1 SS DNA complex. However, approximately 1-3 molecules of E. coli single-stranded DNA binding protein (SSB) copurify with the complex and may be stably associated with this structure in vivo.

Repair resynthesis in Escherichia coli mutants deficient in single-stranded DNA-binding protein

A series of Escherichia coli strains deficient in single-stranded DNA-binding protein (SSB) and DNA polymerase I was constructed in order to analyze the effects of these mutations on DNA repair resynthesis after UV-irradiation. Since SSB has been suggested to play a role in protecting single-stranded regions which may transiently exist during excision repair and since long single-stranded regions are believed to occur frequently as repair intermediates in strains deficient in DNA polymerase I, studies of repair resynthesis and strand rejoining were performed on strains containing both the ssb-1 and polA1 mutations. Repair resynthesis appears to be slightly decreased in the ssb-1 strain at 42 degrees C relative to the wild-type; however, this effect is not enhanced in a polA1 derivative of this strain. After UV-irradiation, the single-strand molecular weight of the DNA of an ssb-1 strain decreases and fails to recover to normal size. These results are discussed in the context of long patch repair as an inducible component of repair resynthesis and of the protection of intermediates in the excision repair process by SSB. A direct role for SSB in repair resynthesis involving modulation of the proteins involved in this mode of DNA synthesis (particularly stimulation of DNA polymerase II) is not supported by our findings.

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.

Interaction of single-strand binding protein and RecA protein at the single-stranded DNA site

Escherichia coli single-strand binding protein (SSB), which participates in DNA replication, also plays a role in DNA repair and induction of SOS functions. We show that the formation of RecA-dATP-single-stranded DNA complexes is influenced by the presence of SSB. In equilibrium reactions with limiting bacteriophage fd DNA, the mutant SSB113 protein competes more effectively than SSB with RecA protein for sites on the DNA. This result can account for the inability of strain ssb113 to amplify RecA protein synthesis and induce lambda prophage. SSB fails to displace RecA protein completely, even at very high concentrations. Both proteins inhibit the dATPase activity of RecA protein in spite of a large proportion of RecA protein still complexed to single-stranded DNA. Analysis of the multiple RecA protein activities and how they respond to the presence of SSB suggests that they fall into two distinct classes. Those that are enhanced by SSB (proteolysis and strand assimilation) and those inhibited by SSB (NTPase, reannealing of complementary single-stranded DNA). We propose a two-state model of conformational change of RecA protein, affected by the number of available free bases in single-stranded DNA relative to the number of RecA monomers, that would explain the choice of mutually exclusive catalytic activities.

Overproduction of Escherichia coli replication proteins by the use of runaway-replication plasmids

A derivative of the runaway-replication plasmid was constructed. This plasmid, pSY343, has the gene for kanamycin resistance and single sites for EcoRI, BamHI, HindIII, KpnI, and XhoI that can be used as cloning sites without inactivating the kanamycin resistance gene or the replication genes. Three replication genes of Escherichia coli were cloned on the plasmid. The activity of dnaA, dnaZ, and ssb gene products were 200-, 90-, and 60-fold greater, respectively, in the cells containing these plasmids than in normal cells.

Study of the expression of UVRA and SSB proteins in vivo in lambda hybrid phages containing the uvrA and ssbA genes of Escherichia coli

A 9.3-kb Eco RI fragment obtained by partial digestion of the plasmid pDR2000 and containing the uvrA and ssbA genes was subcloned in the insertion vector lambda gt4. Two hybrid bacteriophages carrying this fragment inserted in opposite orientations were isolated and used to lysogenize a uvrA and an ssbA mutant of Escherichia coli. Both phages conferred to these host bacteria the ultraviolet resistance of the wild-type parent indicating full complementation of the uvrA and of the ssbA defect. Two polypeptides corresponding to the molecular weights of the UVRA protein (115 000 dalton) and of the SSB protein (18 500 dalton) were synthesized and amplified after infection of a UV-irradiated lambda ind- lysogen with these 2 hybrid phages. The UVRA protein was not amplified after infection of a lex A3 host while SSB was still produced in large amount. These results establish that uvrA is repressed by lexA in vivo whereas ssbA is not.

DNA degradation, UV sensitivity and SOS-mediated mutagenesis in strains of Escherichia coli deficient in single-strand DNA binding protein: effects of mutations and treatments that alter levels of Exonuclease V or recA protein

Certain strains suppress the temperature-sensitivity caused by ssb-1, which encodes a mutant ssDNA binding protein (SSB). At 42 degrees C, such strains are extremely UV-sensitive, degrade their DNA extensively after UV irradiation, and are deficient in UV mutability and UV induction of recA protein synthesis. We transduced recC22, which eliminates Exonuclease V activity, and recAo281, which causes operator-constitutive synthesis of recA protein, into such an ssb-1 strain. Both double mutants degraded their DNA extensively at 42 degrees C after UV irradiation, and both were even more UV-sensitive than the ssb-1 single mutant. We conclude that one or more nucleases other than Exonuclease V degrades DNA in the ssb recC strain, and that recA protein, even if synthesized copiously, can function efficiently in recombinational DNA repair and in control of post-UV DNA degradation only if normal SSB is also present. Pretreatment with nalidixic acid at 30 degrees C restored normal UV mutability at 42 degrees C, but did not increase UV resistance, in an ssb-1 strain. Another ssb allele, ssb-113, which blocks SOS induction at 30 degrees C, increases spontaneous mutability more than tenfold. The ssb-113 allele was transduced into the SOS-constitutive recA730 strain SC30. This double mutant expressed the same elevated spontaneous and UV-induced mutability at 30 degrees C as the ssb+ recA730 strain, and was three times more UV-resistant than its ssb-113 recA+ parent. We conclude that ssb-1 at 42 degrees C and ssb-113 at 30 degrees C block UV-induced activation of recA protease, but that neither allele interferes with subsequent steps in SOS-mediated mutagenesis.

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

A two site immunoradiometric assay (IRMA) for quantification of the recA protein has been recently described (Paoletti et al. 1982). We have used a similar technique to monitor the possible amplification of the ssb protein in E. coli after induction of the SOS repair process by various DNA damaging agents. Under these conditions, while we have been able to detect a full amplification of recA protein, we failed to observed any amplification of the ssb protein.

Interactions of DNA replication factors in vivo as detected by introduction of suppressor alleles of dnaA into other temperature-sensitive dna mutants

Suppressor mutations located within dnaA can suppress the temperature sensitivity of a dnaZ polymerization mutant, indicating in vivo interaction of the products of these genes. The suppressor allele of dnaA [designated dnaA(SUZ, Cs)] could not be introduced, even at the permissive temperature, by transduction into temperature-sensitive (Ts) dnaC or dnaG recipients; it was transduced into dnaB(Ts) and dnaE(Ts) strains but at very low frequency. Recipient cells which were dnaA+ dnaE(Ts) were killed by the incoming dnaA(SUZ, Cs) allele, and it is presumed that combinations of dnaA(SUZ, Cs) with dnaB(Ts), dnaC(Ts), or dnaG(Ts) are lethal also. In one specific case, the lethality required the presence of three alleles: the incoming dnaA suppressor mutation, the resident dnaA+ gene, and the dnaB(Ts) gene. This was shown by the fact that dnaB(Ts) could readily be introduced into a dnaA(SUZ, Cs) dnaB+ recipient. That is, in the absence of dnaA+, the dnaA suppressor and dnaB(Ts) double mutant was stable. One model to explain these results proposes that the dnaA protein functions not only in initiation but also in the replication complex which contains multiple copies of dnaA and other replication factors.

Induction of prophage lambda in Escherichia coli recA- strain by N-methyl-N'-nitro-N-nitrosoguanidine

Induction of prophage by N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) occurred in a recA- strain lysogenic for lambda phage at a level significantly higher than the spontaneous level although the frequency was much lower than that of induction in a recA+(lambda) strain. The plaque-forming ability of lambda c17 super-infecting the recA-(lambda) strain pretreated with MNNG increased with dose of MNNG as it did for super-infection of the recA+(lambda) strain, indicating that the frequency of maturation of lambda c17 increased owing to a decrease in the immunity of the lambda lysogen with dose of MNNG given to it. Further, the activity of lambda repressor in the recA-(lambda) strain decreased after treatment with MNNG as measured by the decrease of repressor-binding activity to lambda DNA although it decreased at a 3-fold slower rate than that in recA+(lambda) strain. From these results and others previously reported we conclude that inactivation of repressor leading to MNNG-initiated prophage induction takes place through two pathways, one being the recA-dependent normal process and the other a recA-independent process unique to the effect of MNNG.

Suppression of the ssb-1 and ssb-113 mutations of Escherichia coli by a wild-type rep gene, NaCl, and glucose

The ssb-1 mutation confers severe temperature sensitivity and UV sensitivity on many strains of Escherichia coli K-12 and C, including strain C1412. However, ssb-1 confers only slight temperature sensitivity and slight UV sensitivity on strain C1a, suggesting that strain C1a contains extragenic suppressors of ssb-1. We found that introduction of the wild-type rep gene from C1a into strain C1412 ssb-1 gave strong suppression of temperature sensitivity and moderate suppression of UV sensitivity. Also, the C1a rep+ gene mildly suppressed the temperature sensitivity conferred by the ssb-113 mutation, formerly called lexC113. Suppression of the C1412 ssb-1 growth defect by C1a rep+ rendered the cells Gro- for phi X174. In contrast to the positive suppression of ssb-1 and ssb-113 by a wild-type rep gene, mutant rep alleles enhanced the severity of the ssb-1 defect, with several C1a ssb-1 double mutants being either more temperature sensitive or more UV sensitive than C1a ssb-1, depending on which mutant rep allele was used. As a control, the same rep alleles in combination with a dnaB mutation gave an allele-independent increase in temperature sensitivity. Our results on suppression of ssb-1 by rep and on the role of the genetic background in this suppression suggested that the rep and ssb proteins interact to form a subcomplex of the total DNA replication complex and that this subcomplex has some function in repair. The effects of NaCl and glucose on suppression of both the temperature sensitivity and the UV sensitivity conferred by ssb-1 and ssb-113 are described. The degree of suppression of temperature sensitivity by salt or glucose was dependent on the source of the wild-type rep allele, as well as on the genetic background.

Escherichia coli single-strand binding protein organizes single-stranded DNA in nucleosome-like units

Electron microscopy shows that complexes of the single-strand DNA binding protein (SSB) of Escherichia coli and phage fd DNA appear as beaded fiber loops containing an average of 38 beads, 1 per 170 bases of DNA. Extensive digestion of native unfixed SSB-fd DNA complexes with micrococcal nuclease reveals a protected DNA fragment of 145 bases, while shorter digestion periods result in a sequence of fragments in multiples of 160 +/- 25 bases. Digestion of these complexes with DNase I produces a repeating pattern of bands, multiples of approximately 15 bases with strong bands at 60, 105, 118, 130, 145, 150, and 210 bases. Isopycnic banding in CsCl solution yields densities of 1.272 and 1.700 g/ml, respectively, for SSB alone and for fd DNA and, after fixation, of 1.388 g/ml for fd DNA-SSB beaded fibers and 1.373 g/ml for the individual protein-DNA beads. Based on these data and the molecular weights of SSB and fd DNA, we suggest that the nucleoprotein chain consists of eight molecules of SSB bound to 145 bases of DNA, with these units linked by roughly 30 bases of protein-free DNA. The excellent concord between results obtained by enzyme digestion of unfixed native samples and, after fixation, by electron microscopy and density banding supports the conclusion that SSB organizes single-stranded DNA in a manner similar to the organization of duplex DNA by histones.

Effects of the ssb-1 and ssb-113 mutations on survival and DNA repair in UV-irradiated delta uvrB strains of Escherichia coli K-12

The molecular defect in DNA repair caused by ssb mutations (single-strand binding protein) was studied by analyzing DNA synthesis and DNA double-strand break production in UV-irradiated Escherichia coli delta uvrB strains. The presence of the ssb-113 mutation produced a large inhibition of DNA synthesis and led to the formation of double-strand breaks, whereas the ssb-1 mutation produced much less inhibition of DNA synthesis and fewer double-strand breaks. We suggest that the single-strand binding protein plays an important role in the replication of damaged DNA, and that it functions by protecting single-stranded parental DNa opposite daughter-strand gaps from nuclease attack.

Influence of single-stranded DNA-binding protein on recA induction in Escherichia coli

Two ssb mutants of Escherichia coli, which carry a lesion in the single-strand DNA-binding protein (SSB), are sensitive to UV-irradiation. We have investigated the influence of SSB on the "SOS" repair pathway by examining the levels of recA protein synthesis. These strains fail to induce normal levels of recA protein after treatment with nalidixic acid or ultraviolet light. The level of recA protein synthesis in wild-type cells is about three times greater than ssb cells. This deficiency in ssb mutants occurs in all strains and at all temperatures tested (30-41.5 degrees). In contrast, the ssb-1 mutation has no effect on temperature-induced recA induction in a recA441 (tif-1) strain. Cells carrying ssb+ plasmids and overproducing normal DNA-binding protein surprisingly are moderately UV-sensitive and have reduced levels of recA protein synthesis. Together these results establish that single-strand DNA-binding protein is involved in the induction of recA, and accounts, at least in part, for the UV sensitivity of ssb mutants. Three possible mechanisms to explain the role of SSB are discussed.

Suppression of the lexC (ssbA) mutation of Escherichia coli by a mutant of bacteriophage P1

A new mutant of bacteriophage P1 designated lxc that suppresses the phenotype of lexC and ssbA mutants of Escherichia coli was isolated and characterized. The properties of lexC mutants suppressed by the lxc mutation include temperature sensitive growth at 42 degrees C, sensitivity to ultraviolet light and alkylating agents, and a nonmutagenic response following exposure to ultraviolet irradiation. A bac mutant of bacteriophage P1 that suppresses the temperature sensitivity of dnaB mutants does not affect the phenotype of lexC or ssbA mutants. Neither the lxc or bac mutations affect the ultraviolet light sensitivity of strains with the mutations uvrA155, lexA102, or recA56.

Escherichia coli single-strand DNA binding protein from wild type and lexC113 mutant affects in vitro proteolytic cleavage of phage lambda repressor

In Escherichia coli, the single-strand DNA-binding protein (SSB) is required for DNA replication. A mutation of the ssb gene, lexC113, imparts to the cells UV sensitivity and inability to induce lambda prophage and to amplify recA protein, indicating participation of SSB in DNA repair and viral induction processes. We report the effect of purified SSB, isolated from wild-type and lexC113 strains, on the recA-mediated proteolysis of lambda repressor in vitro. (i) These proteins abolished the inhibition produced by excess single-strand DNA and (ii) in the presence of the binding proteins, the apparent stoichiometry--1 monomer of recA to 6 nucleotides of single-strand DNA [Craig, N. L. & Roberts, J. W. (1980) Nature (London) 283, 26-30] was no longer observed. (iii) At the optimal concentration--1 protein monomer to 8 nucleotides--they increased the rate and extent of repressor cleavage at all single-strand DNA concentrations, including that observed at the apparent optimal DNA concentration. (iv) At binding protein/nucleotide ratios greater than or equal to 1:3, SSB from lexC113 inhibited repressor cleavage while that from wild type did not. (v) These results are consistent with the notion that SSB is probably involved in the induction of prophages in vivo.

Enzymatic synthesis of bacteriophage fd viral DNA

An enzyme system with requirements similar to those for replication of phage fd replicative form (RF) DNA in bacteriophage fd-infected cells has been reconstituted with purified fd gene 2 protein, and DNA polymerase III holoenzyme, DNA binding protein I and rep-protein (rep-helicase) of Escherichia coli. The system generates viral circular single strands, which are infective for E. coli spheroplasts. Parental and newly synthesized DNA are covalently connected in early stages of replication, as expected for DNA replication using the rolling circle mechanism. Single-stranded tails of the rolling circle intermediates are cleaved after a full round of replication by gene 2 protein and circularized by the same enzyme molecule.

Effect of lexA and ssb genes, present on a uvrA recombinant plasmid, on the UV survival of Escherichia coli K-12

The recombinant plasmid pJA01 contains, besides the uvrA gene, the genes lexA, ubiA and ssb. This plasmid does not fully complement a uvrA mutation in a Rec+ background. Plasmids which contain the uvrA and ssg genes, but not the lexA gene, show a higher but still only partial complementation. Full complementation achieved when the ssb gene us inactivated by insertion of Tn5. Furthermore, it appears that the presence of the ssb gene on a multicopy plasmid sensitizes wild-type cells to UV light. The effect of Ssb (single-strand DNA binding protein) overproduction on UV survival is discussed.

Biological activity and a partial amino-acid sequence of Escherichia coli DNA-binding protein I isolated from overproducing cells

DNA-binding protein I from Escherichia coli was purified from cells carrying the ssb gene on a multicopy plasmid. In comparison to the strain without the recombinant plasmid the DNA-binding protein was over-produced more than 20-fold. The amount of the protein was measured after the purification steps by gel electrophoresis and radial immunodiffusion. The protein was purified to homogeneity and was active in replication assays like the wild-type DNA-binding protein. The assays were enzymatic replication of single-stranded and double-stranded fd DNA. E. coli DNA-binding protein I was further subjected to amino acid sequence analysis. A monomer of the protein consists of 187 residues which correspond to a molecular weight of 19715 with 5% error in analysis. The sequence of the amino-terminal 40 residues was determined and includes several basic residues of the protein. Sequence comparison between the DNA-binding protein I from E. coli and that coded by bacteriophage fd reveals similarities suggesting that DNA-binding protein I may use amino-terminal residues for binding to DNA like the phage protein.

dnaC-dependent reconstitution of replication forks in Escherichia coli lysates

Lysates of Escherichia coli exhibit a DNA-synthesizing activity that depends on the presence of replication forks and of replication proteins. Replicative activity was reconstituted in vitro by mixing lysates prepared from temperature-sensitive dnaB mutants with wild-type dnaB protein. Lysates of double mutants deficient in both dnaB and dnaC genes could only be complemented by the addition of both dnaB and dnaC proteins, whereas lysates deficient in dnaC protein did not require the addition of any exogenous factor. This shows that the replication machinery, once it is running along the chromosome, is independent of dnaC protein, dnaC activity, however, is required for the replacement of defective dnaB protein at running replication forks.

Visualization of recA protein and its association with DNA: a priming effect of single-strand-binding protein

A stoichiometric interaction of RecA protein with single-stranded DNA promotes homologous pairing of the single strand with duplex DNA and subsequent polar formation of a heteroduplex joint. Escherichia coli single-strand-binding (SSB) protein augments these reactions. Electron microscopic observations suggest structural bases for these interactions. Without triphosphates or DNA, RecA protein forms short linear filaments. With added circular single-stranded DNA, it forms extended circular filaments as well as collapsed and aggregated complexes of protein and DNA. The extended circular filaments are stiff and regular in appearance, contrasting with the convoluted structure formed by SSB protein and single-stranded DNA. Together, these two proteins form mixed filaments, which mostly resemble the extended structures containing RecA protein; moreover, SSB protein accelerates formation of extended filaments more than 50-fold, increasing the yield of these structures at the expense of heterogeneous aggregates. Other observations further define the interactions of RecA protein with partially single-stranded DNA, and the effects of ATP gamma S on the tendency of RecA protein to form polymeric structures even in the absence of DNA.

The product of the lexC gene of Escherichia coli is single-stranded DNA-binding protein

Extracts from lexC113 cells could not support phage G4 DNA-dependent replication unless supplemented with single-stranded DNA-binding protein. Purified lexC113 binding protein supported synthesis in a reconstituted replication assay, using purified proteins at 30 but not at 42 degrees C, indicating that the product of the lexC113 gene is an altered single-stranded DNA-binding protein.

DNA repair in E. coli strains deficient in single-strand DNA binding protein

Weigle reactivation and mutagenesis have been found to be defective in strains of E. coli deficient in single-strand DNA binding protein (SSB). These defects parallel those previously found in prophage induction and amplification of recA protein synthesis in ssb- strains. Together, these results demonstrate a role for SSB in the induction of SOS responses. UV survival studies of ssb- recA- and ssb- uvr- strains are presented which also suggest a role for SSB in recombinational repair processes but not in excision repair. Studies of host cell reactivation support this latter conclusion.

Variable expression of the ssb--1 allele in different strains of Escherichia coli K12 and B: differential suppression of its effects on DNA replication, DNA repair and ultraviolet mutagenesis

We have transduced the mutant allele ssb-1, which encodes a temperature-sensitive single-strand DNA binding protein (SSB), into several Escherichia coli strains, and have examined colony-forming ability, DNA replication, sensitivity to ultraviolet light (UV) and UV-induced mutability at the nonpermissive temperature. We have found: 1) that the degree of ssb-1-mediated temperature-sensitivity of colony-forming ability and of DNA replication is strain-dependent, resulting in plating efficiencies at 42 degrees C (relative to 30 degrees C) ranging from 100% to 0.002%; 2) that complete suppression of the temperature-sensitivity caused by ssb-1 occurs only on nutrient agar, and not in any other medium tested; 3) that strains in which ssb-1-mediated temperature-sensitivity is completely suppressed show moderate UV sensitivity and normal UV mutability at 30 degrees C, but much more extreme UV sensitivity and drastically reduced UV mutability at 42 degrees C; and 4) that defects in excision repair or in other Uvr+-dependent processes are not responsible for most of the UV sensitivity promoted by ssb-1. We discuss our results in relation to the known properties of SSB and its possible role in the induction of DNA damage-inducible (SOS) functions.

A T7 amber mutant defective in DNA-binding protein

A T7 amber mutant, UP-2, in the gene for T7 DNA-binding protein was isolated from mutants that could not grow on sup+ ssb-1 bacteria but could grow on glnU ssb-1 and sup+ ssb+ bacteria. The mutant phage synthesized a smaller amber polypeptide (28,000 daltons) than T7 wild-type DNA-binding protein (32,000 daltons). DNA synthesis of the UP-2 mutant in sup+ ssb-1 cells was severely inhibited and the first round of replication was found to be repressed. The abilities for genetic recombination and DNA repair were also low even in permissive hosts compared with those of wild-type phage. Moreover, recombination intermediate T7 DNA molecules were not formed in UP-2 infected nonpermissive cells. The gene that codes for DNA-binding protein is referred to as gene 2.5 since the mutation was mapped between gene 2 and gene 3.

Effect of the dnaN mutation on the growth of small DNA phages

The effect of the dnaN mutation on the growth of single-stranded DNA phages was studied by burst experiments. In HC138 dnaN cells exposed to 42.5 degrees C at 5 min before infection, growth of spherical (microvirid or isometric) phages such as alpha 3, phi Kh-1 and phi X174 was partially reduced at the nonpermissive temperature. When infection was performed at 30 min after temperature shift-up, viral replication was completely inhibited at 42.5 degrees C in the dnaN strain but not in a dna+ revertant. At 41 degrees C, multiplication of filamentous (inovirid) phages M13 and fd was restricted specifically in HC138 F+ dnaN bacteria. When dnaN cells lysogenic for lambda i21 were grown at 42.5 degrees C for 60 min and then shifted down to 33 degrees C, a burst of lambda i21 occurred with concomitant cellular lysis, manifesting induction of the prophage development.

Proteins that shape DNA

During the last five years, considerable accumulation of data on nucleic acids metabolism leads to the discovery of a number of proteins designed to change the conformation of DNA and to "shape" it. Experimental results emphasize the importance of the conformation and the flexibility of DNA itself in such interactions. The mutual recognition of nucleic acids by proteins may be or not dependent on the nnucleotide sequence and in most cases is accompanied by conformational changes in the proteins involved. Among these are proteins that bind in stoichiometric amounts to DNA, proteins that promote the separation of the two strands in a duplex, and finally proteins that change the topology of DNA.

Induction of SOS functions: regulation of proteolytic activity of E. coli RecA protein by interaction with DNA and nucleoside triphosphate

Damage to cellular DNA or interruption of chromosomal DNA synthesis leads to induction of the SOS functions in E. coli. The immediate agent of induction is the RecA protein, which proteolytically cleaves and inactivates repressors, leading to induction of genes they control. RecA protein modified by tif mutations allows expression of SOS functions in the absence of inducing treatments. We show here that tif-mutant RecA protein is more efficient than wild-type RecA protein in interacting with DNA and nucleoside triphosphate. This result suggests that formation of a complex with DNA and nucleoside triphosphate is the critical event that activates RecA protein to destroy repressors after SOS-inducing treatments, and that damage to cellular DNA promotes this reaction by providing single-stranded DNA or active nucleoside triphosphate or both. Since dATP is the most effective nucleoside triphosphate in promoting repressor cleavage, we suggest that it is the natural cofactor of recA protein in vivo.

Sequences of the ssb gene and protein

We have determined the sequences of the ssb gene and protein of Escherichia coli. The coding region of ssb is 534 base pairs and is preceeded and followed by dyad symmetries of 39 base pairs and 27 base pairs, respectively. The promoter for ssb is close to that for uvrA and these two genes are transcribed in opposite directions: ssb clockwise and uvrA counterclockwise on the standard E. coli genetic map. The DNA helix-destabilizing protein encoded by the ssb gene (single-strand binding protein) contains 177 amino acids and has a calculated molecular weight of 18,873. Although there is no extensive sequence homology among the three helix-destabilizing proteins whose sequences are now known, both the E. coli and bacteriophage T4 DNA helix-destabilizing proteins do contain an acidic, alpha-helical region at their carboxy termini that may be functionally homologous. The remainder of the E. coli helix-destabilizing protein can be divided into two apparent domains on the basis of its amino acid sequence. The amino-terminal region (residues 1-105) contains 79% of the charged residues (27 out of 34 total) in the protein and is predicted to have a high degree of secondary structure (alpha helix and beta pleated sheet). In contrast, the region including residues 106-165 contains only two charged amino acids and is devoid of alpha helix or beta pleated sheet.