The uvrB gene of Escherichia coli has both lexA-repressed and lexA-independent promoters

We have found that the uvrB gene of Escherichia coli is transcribed from at least two promoters, which we call P1 and P2. Transcription from P1 begins with an ATP at +1, and transcription from P2 begins primarily with a GTP at -31. A binding site for the lexA protein (LEXA), located between the -35 sequence and Pribnow box of P2, regulates transcription from this promoter. In vitro, LEXA inhibits transcription from P2 but has no detectable effect on transcription from P1. A third promoter, P3, was also detected at -341; transcription from P3 is toward uvrB but terminates in vitro in the region of the LEXA binding site. The binding of LEXA to P2 inhibits transcription from the P3 promoter even though several hundred nucleotides separate the two promoters. The data suggest that a transcribing RNA polymerase stalls when it reaches the repressor-operator complex but remains bound to the DNA, causing a jamming of RNA polymerases between P3 and the repressor-operator complex at P2. The physiological significance of P3 is unknown.

A general approach for purifying proteins encoded by cloned genes without using a functional assay: isolation of the uvrA gene product from radiolabeled maxicells

The uvrA protein (UVRA) of E. coli has been extensively purified from a strain in which UVRA is overproduced and specifically labeled with 35S-methionine. This approximately 100-fold overproduction relative to normal strains is a result of having the uvrA gene present on a multicopy plasmid in a spr recA cell that makes defective lexA protein, the normal repressor of the uvrA gene, while the specific labeling of UVRA is done with maxicells. This approach facilitates the preparation of the protein since enzyme assays do not have to be carried out during the intermediate stages of purification. The purified UVRA binds to DNA and has ATPase activity but does not have intrinsic endonuclease activity. When added to extracts of uvrA- cells, the purified UVRA does promote the specific cutting of UV-irradiated DNA. Since this approach for working out rapid purification procedures by specifically labeling the proteins encoded by cloned genes does not require the use of a functional assay, it is a general one that can be applied to a wide variety of other gene products in addition to UVRA.

Identification of the uvrC gene product

We have constructed a multicopy plasmid that carries the uvrC gene of Escherichia coli. By inserting the transposon Tn1000 (previously designated gamma delta) into this plasmid, we obtained many derivatives that fail to complement uvrC34. The proteins synthesized by the original plasmid and the uvrC::Tn1000 derivatives were labeled in maxicells and analyzed on gels, demonstrating that a protein of Mr 70,000 encoded by the original uvrC+ plasmid was absent from the mutated noncomplementing derivatives; this protein is presumed to be the uvrC gene product. We found that this protein of Mr 70,000 binds to DNA and have partially purified the uvrC protein by DNA-cellulose chromatography. Because some of the uvrC::Tn1000 derivatives produce truncated polypeptides, the orientation of expression and the location of the promoter were determined by correlating the sizes of the truncated polypeptides with the sites of insertion of Tn1000.

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.

Impaired incision of ultraviolet-irradiated deoxyribonucleic acid in uvrC mutants of Escherichia coli

The production of single-strand breaks in the deoxyribonucleic acid of irradiated uvrC mutants of Escherichia coli K-12 was studied both in vivo and in vitro. In vivo, uvrC mutants displayed a slow accumulation of breaks after irradiation, and in this respect appeared different from uvrA mutants, in which very few breaks could be detected. The breakage observed in uvrC mutants differed from that observed in wild-type strains in both the slow rate of break accumulation and the very limited dose response. The behavior of the uvrC lig-7(Ts) double mutant was shown not to be consistent with the suggestion of ligase reversal as the explanation for the lower rate and limited dose response of break formation observed in ultraviolet-irradiated uvrC mutants in vivo. Rather, there appeared to be a real defect in incision. In toluene-treated cells, we studied the effect of the ligase inhibitor nicotinamide mononucleotide on strand incision. Whereas uvrC mutants displayed more strand breakage in the presence of this inhibitor, the same amount of breakage was seen in uvrA mutants, and as such the breakage could be judged as not due to the main excision repair pathway. Experiments using a cell-free system comprising the partially purified uvr+ gene products demonstrated clearly that there is a requirement for the uvrC+ gene product for strand incision. We suggest that in vivo in the absence of the uvrC+ gene product, a partial analog of this protein may allow some abnormal incision.

Amplification of single-strand DNA binding protein in Escherichia coli

An E. coli strain containing a recombinant plasmid carrying the E. coli ssbA+ gene has been shown to produce 12 to 15 fold increased amounts of single-strand DNA binding-protein relative to wild-type strains. In addition, a gamma transducing phage carrying the E. coli uvrA+ gene has been shown to also carry the ssbA+ gene and to be capable of producing increased amounts of binding protein.

Sequences of the recA gene and protein

We have determined the nucleotide sequence of the recA gene of Escherichia coli; this permits the formulation of the primary structure for the recA protein. This structure is consistent with the amino acid composition of the tryptic peptides obtained from the recA protein. The coding region of the recA gene has 1059 base pairs, which specify 352 amino acids. The recA protein has alanine and phenylalanine as its NH2- and COOH-terminal amino acids, respectively, and has the following amino acid composition: Cys3 Asp20 Asn15 Met9 Thr17 Ser20 Glu30 Gln13 Pro10 Gly35 Ala38 Val22 Ile27 Leu31 Tyr7 Phe10 His2Lys27 Trp2 Arg14. Of the three cysteine residues, only two can be alkylated under reducing and denaturing conditions. The molecular weight of the recA polypeptide is 37,842.

Physical map of the recA gene

We have cloned the recA gene of Echerichia coli K12 and some of its restriction fragments on the plasmid cloning vehicle pBR322. The recA gene was mapped with regard to the restriction sites of EcoRI, BamHI, Pst I, Hha I, Hae III, HinfI, and Taq I restriction endonucleases. The recA promoter was localized by the binding of RNA polymerase to restriction fragments. The initiation point of transcription of recA mRNA and the direction of transcription were determined from in vitro transcription of recA gene fragments and from analysis of the polypeptides made in maxicells that contain plasmids carrying only part of the recA gene.

Potential radiosensitizing agents. Dinitroimidazoles

New compounds of the nitroimidazole series have been synthesized as radiosensitizers which selectively sensitize hypoxic cells to the lethal effect of radiation. The reaction of 2,4(5)-dinitroimidazole (2) with chloroethanol or hydrochloric acid yielded 4(5)-nitro-5(4)-chloroimidazole (3), which upon reaction with ethylene oxide yielded the 4-nitro-5-chloroimidazole-1-ethanol (6). Reaction of 2 with ethylene oxide resulted in a mixture of two compounds, the 2,4-dinitroimidazole-1-ethanol (4) and 2,3-dihydro-5-nitroimidazo[2,1-b]oxazole (5). The structure of the new heterocyclic compound 5 was confirmed by 1H NMR, mass spectrum, and X-ray crystallography. These agents were tested for their ability to sensitize hypoxic Escherichia coli cells to killing by ionizing radiation. Compound 4 was found to be the most active agent of this series of compounds.

Simple method for identification of plasmid-coded proteins

Proteins encoded by plasmid DNA are specifically labeled in UV-irradiated cells of Escherichia coli carrying recA and uvrA mutations because extensive degradation of the chromosome DNA occurs concurrently with amplification of plasmid DNA.

Hypoxic radiosensitizers: prospects for effective compounds with fewer toxic side-effects

Several radiosensitizing chemicals, including a family of simple nitroimidazoles, were examined in E. coli and compared with misonidazole for toxic side-effects on endpoints such as mutagenesis, cell killing and inhibition of the synthesis of the inducible enzyme beta-galactosidase. While all the compounds were similar to misonidazole or better in radiosensitization, marked differences in the various side effects were found. There results show that for E. coli it is possible to find compounds that sensitize as well as misonidazole but which have decreased mutagenicity and fewer other side-effects. Of the compounds examined, KA121 (2,5-dinitroimidazole) is the most promising for future study because it combines good radiosensitization with low mutagenicity and toxicity.

Lambda bacteriophage gene produces and X-ray sensitivity of Escherichia coli: comparison of red-dependent and gam-dependent radioresistance

When gene products of lambda bacteriophage are introduced into a cell by transient induction of a lysogen, increased resistance of the cells to X rays results. This phenomenon has been called phage-induced radioresistance. Genetic studies show at least two classes of induced radioresistance. The first type depends on the products of the lambda red genes and is observed in bacteria that are mutated in the recB gene. It is thought that the lambda red products compensate for the missing RecBC nuclease in the repair of X-ray damage. An optimal effect is obtained even when the lambda red products are supplied 1 h after irradiation. The lesions that are affected by the red-dependent process are probably not deoxyribonucleic acid strand breaks because the extent of deoxyribonucleic acid strand rejoining is not altered by the red products. The second type of phage-induced radioresistance requires the gam product of lambda and is observed in wild-type and polA strains. The lambda gam+ gene produce must be present immediately after irradiation to exert its full effect. In its presence, DNA breakdown is decreased, and a greater fraction of DNA is converted back to high molecular weight. Strains carrying lex, recA, or certain other combinations of mutations do not show any detectable phage-induced radioresistance.

Biochemically aberrant Salmonella enteritidis ser. newington from human sources in Connecticut

Three isolates of a lactose-fermenting, xylose-negative variety of Salmonella enteritidis ser. newington, identical in biochemical and serological reactions and in the antibiogram, were recovered from three patients in different areas of Connecticut in January 1974. Hydrogen sulfide production was not visible in Salmonella-Shigella agar, in triple sugar iron agar, and in Kligler iron agar but was noticed in lysine iron agar and on XLD agar, among others. The amount of fermentable carbohydrates present was found to correlate with failure to show hydrogen sulfide production (pH effect). In contrast to lactose-fermenting Salmonella strains reported by other authors, we could not elicit a direct transfer of the lac(+) character at frequencies above 10(-6). An epidemiological follow-up remained unsuccessful. Recommendations for the recognition of similar strains are presented.

Recombination and postreplication repair

The available data concerning postreplication repair are summarized. In Escherichia coli, recombination is implicated in this repair because the recA+ gene is necessary and because strand exchanges occur that extend over long regions. Other experiments involving phage-induced resistance also point to an interrelation between recombination and repair. In this phenomenon, gene products of lambda bacteriophage are introduced into bacteria, resulting in an increased resistance of the cells when they are subsequently exposed to X rays.

DNA strand breaks measured within 100 milliseconds of irradiation of Escherichia coli by 4 MeV electrons

A method was developed in which E. coli cells were irradiated with four MeV electrons and transferred to alkaline detergent within a fraction of a second. This technique minimizes the amount of repair of radiation damage before analysis without the necessity of using physical or chemical treatments to inhibit repair and alter the physiological condition of the cells. The yield of DNA strans breaks formed in covalent circular superhelical lambda DNA molecules superinfecting E. coli lysogens was about 4-fold greater when the cells were irradiated in oxygen than when they were irradiated under nitrogen anoxia. The same yields were obtained in phosphate buffer at 3 degrees and 22 degrees as well as in growth medium at 37 degrees, and the yields were not altered by the polA1 mutation. When E. coli lysogenic cells superinfected with lambda were irradiated with doses sufficient to introduce at least seven breaks in the phage DNA, the chromosomal DNA and the superinfecting phage DNA sedimented similarly in alkaline sucrose gradients, indicating that both DNAs were broken to a similar extent during irradiation. However, the yield of breaks calculated for chromosomal DNA in similar experiments was greater than the yield calculated from the first break introduced into covalent circular lambda DNA molecules. These apparently contradictory results are explicable either if the initial break in a superhelical molecule occurs with an efficiency different from that for subsequent breaks, or if the pulsed electron radiation produces a high proportion of double-strand breaks.

Interaction of bacterial and lambda phage recombination systems in the x-ray sensitivity of Escherichia coli K-12

E. coli cells lysogenic for the thermoinducible prophage lambdacI857 can be transiently induced by a brief heat treatment. Although this treatment does not kill the cells, some lambda products normally formed during vegetative phage development are made that can alter the response of host cells to x-irradiation by causing an increase in radioresistance. This increased resistance is particularly striking in the recombination-deficient recB-strain, which is normally much more radiosensitive than its recB(+) parent. After pulse-heating at 42 degrees , the survival curve of E. coli recB(-) lysogenized with lambdacI857 does not differ from that of the wild-type strain. Since lambda red mutants do not increase the radioresistance of recB(-) strains, both lambda red gene products, lambda exonuclease and beta-protein, are required to compensate for the missing recB product. Furthermore, phage-induced radioresistance also occurs in recB(+) lysogens even when they carry lambda red(-), but not when the lambda prophage is gam(-). Thus, in wild-type cells, phage-induced radioresistance requires some interaction between the bacterial recB gene product (exonuclease V) and the phage lambda-protein.