Linkage map of Escherichia coli K-12, edition 6

The 19-kDal protein encoded by early region 1b of adenovirus type 12 is synthesized efficiently in Escherichia coli only as a fused protein

We have constructed recombinant plasmids that direct the synthesis of the Mr 19 000 protein encoded by the adenovirus type 12 (Ad12) E1b region as either a native protein or a protein fused to the amino-terminal portion of the elongation factor EF-TuB in Escherichia coli cells. Using these recombinants, we could synthesize a large amount of the fused protein, while only a small amount of the native Mr 19 000 protein was produced. The failure to synthesize the native Mr 19 000 protein in E. coli cells was ascribed to inefficient translation.

Nucleotide sequence of the promoter region of the citrate synthase gene (gltA) of Escherichia coli

The gltA gene, specifying the citrate synthase (EC 4.1.3.7) of Escherichia coli, has been isolated and the nucleotide sequence of a 752 basepair segment containing the gltA promoter and encoding 96 aminoterminal residues of the protein has been defined using the dideoxy/M13 method. The results confirm the location and transcriptional polarity of the gltA gene and indicate that the gltA transcript may contain a long leader sequence of 302-306 nucleotides upstream from the coding region.

The nucleotide sequence of the rho gene of E. coli K-12

We have determined the nucleotide sequence of the rho gene which encodes the E. coli K-12 transcription termination factor. The structural gene was located on a cloned 3.6 kilobase BglII-HindIII restriction fragment by the introduction of the insertion element gamma delta and analysis of the recombinant plasmids by restriction analysis and in maxicells. The coding region consists of 1260 nucleotides directing the synthesis of a polypeptide 419 amino acids in length with a calculated molecular weight of 46,094. The deduced amino acid composition, amino-terminal protein sequence and calculated molecular weight are consistent with the data from the analysis of purified rho protein (16). We have shown that the rho genes from E. coli K-12, B and C strains are located on PvuII-HindIII fragments of the same size by hybridization to the rho (K-12) coding sequences.

Trimethoprim-induced DNA polymerase I deficiency in Escherichia coli K-12

Curing of the mini-ColE1 plasmid pML21 was observed among cells of Escherichia coli K-12 strain C600(pML21) grown under subinhibitory conditions in the presence of trimethoprim, a specific inhibitor of dihydrofolate reductase. Some of the cured colonies showed (i) a reduction in frequency of transformation with pML21 compared with those of isogenic strains not treated with trimethoprim, (ii) loss of viability after acquisition of a recA mutation, and (iii) UV sensitivity greater than that of the original isogenic strain. These colonies therefore had PolA- phenotypes. Moreover, they were found to be deficient in DNA polymerase I activity in the in vitro assays, indicating the occurrence of a polA mutation in them. Many of the colonies with PolA- phenotypes were also thyA deoC mutants, and these mutations, in addition to the polA mutations, appeared to be involved in the expression of the PolA- phenotypes.

IlvHI locus of Salmonella typhimurium

In Escherichia coli K-12, the ilvHI locus codes for one of two acetohydroxy acid synthase isoenzymes. A region of the Salmonella typhimurium genome adjacent to the leucine operon was cloned on plasmid pBR322, yielding plasmids pCV47 and pCV49 (a shortened version of pCV47). This region contains DNA homologous to the E. coli ilvHI locus, as judged by hybridization experiments. Plasmid pCV47 did not confer isoleucine-valine prototrophy upon either E. coli or S. typhimurium strains lacking acetohydroxy acid synthase activity, suggesting that S. typhimurium lacks a functional ilvHI locus. However, isoleucine-valine prototrophs were readily isolated from such strains after mutagenesis with nitrosoguanidine. In one case we found that the Ilv+ phenotype resulted from an alteration in bacterial DNA on the plasmid (new plasmid designated pCV50). Furthermore, a new acetohydroxy acid synthase activity was observed in Ilv+ revertants; this enzyme was similar to E. coli acetohydroxy acid synthase III in its lack of activity at low pH. This new activity was correlated with the appearance in minicells of a new polypeptide having an approximate molecular weight of 61,000. Strains carrying either pCV49 or pCV50 produced a substantial amount of ilvHI-specific mRNA. These results, together with results from other laboratories, suggest that S. typhimurium has functional ilvB and ilvG genes and a cryptic ilvHI locus. E. coli K-12, on the other hand, has functional ilvB and ilvHI genes and a cryptic ilvG locus.

Ribonuclease BN: identification and partial characterization of a new tRNA processing enzyme

A new ribonuclease, RNase BN, has been identified and partially purified from a strain of Escherichia coli lacking RNase II and RNase D by using the artificial tRNA precursor tRNA-C-[14C]U as substrate. This enzyme is present in E. coli B but absent from the tRNA processing mutant strain BN which is unable to process extraneous 3' residues on certain phage T4-specified tRNA precursors. The properties of RNase BN clearly distinguish this enzyme from other known E. coli exoribonucleases. It is optimally active at pH 6.5 with 0.2 mM divalent cation and 0.2 M monovalent cation. It is most active against tRNA substrates containing nucleotide substitutions within the -C-C-A sequence and relatively inactive against other types of RNAs. This substrate specificity in vitro is consistent with a processing function in vivo. However, in contrast to the other processing enzymes whose function has been confirmed by mutation, RNase BN is an exoribonuclease. The presence of multiple RNases in E. coli and a strategy for their identification and separation are discussed.

In vivo cloning of Erwinia carotovora genes involved in the catabolism of hexuronates

Using the RP4::mini-Mu pULB113 plasmid, an RP4 derivative carrying a deleted Mu prophage which allows the plasmid to pick up any chromosomal DNA segment to form R' plasmids, we cloned all of the genes of Erwinia carotovora involved in the catabolism of the hexuronates and in the transport of these substrates. With the R' plasmids we isolated, we performed complementation analysis and found that, in the Erwinia carotovora strain we used, the genes involved in the catabolism of the hexuronates are clustered in four regions of the chromosome. This genetic organization is compared with that of Escherichia coli K-12.

Gene-protein index of Escherichia coli K-12

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Plasmid-controlled resistance to copper in Escherichia coli

The copper resistance of a strain of Escherichia coli isolated from the effluent of a piggery where pigs were fed a diet supplemented with copper sulfate was controlled by a conjugative 78-megadalton plasmid designated pRJ1004. Plasmid pRJ1004 exhibited surface exclusion and incompatibility with standard plasmids belonging to incompatibility groups I1 and K. Sensitive strains of E. coli K-12 were unable to form colonies on nutrient agar containing more than 4 mM copper, whereas transconjugants which harbored pRJ1004 were able to form colonies on medium containing up to 20 mM copper.

Identification of the enzymatic reactions encoded by the purG and purI genes of Escherichia coli

The chromosomal locations of the genes purG and purI on the Escherichia coli linkage map are the opposites of those of Salmonella typhimurium. By methods which permit the identification of lesions in any of the five early enzymes of the purine de novo pathway, the gene-enzyme relationships of the purG and purI loci have been reevaluated in these two organisms. The results demonstrate that the relative locations of the genes encoding the two enzymes (phosphoribosylformylglycinamidine synthetase and phosphoribosylaminoimidazole synthetase) are similar in the two organisms. The gene products have been correctly determined in S. typhimurium. The gene products currently listed for the loci in E. coli are incorrect. The E. coli purG locus is equivalent to the S. typhimurium purI locus, and the E. coli purI locus is equivalent to the S. typhimurium purG locus.

Utilization of plasmid pULB113 (RP4::mini-Mu) to construct a linkage map of Erwinia carotovora subsp. chrysanthemi

We report experimental evidence that pULB113, an RP4::mini-Mu plasmid, mediates chromosome transfer in a strain of Erwinia carotovora subsp. chrysanthemi which does not accept the F episome. This allowed us to construct a genetic map of that strain by measuring the frequencies of cotransfer of different markers (thy, leu, pro, [his, trp], thyA, rpsL, ile).

R-plasmid effects on bacterial multiplication and survival

The multiplication of Escherichia coli C containing either the plasmid R46 or its non-selftransmissible derivative was studied in the presence or absence of the isogenic R- parent strain. Neither plasmid conferred any detectable effect on the host's ability to multiply. Similarly under conditions of prolonged incubation neither plasmid conferred a disadvantage on its host when the bacteria were grown in pure culture. However, when the incubation of mixed R+/R- cultures was prolonged, the possession of either R-plasmid resulted in small but reproducible differences which favoured the R- strain.

Nucleotide sequence of the structural gene (pyrB) that encodes the catalytic polypeptide of aspartate transcarbamoylase of Escherichia coli

The deoxyribonucleotide sequence of pyrB, the cistron encoding the catalytic subunit of aspartate transcarbamoylase (carbamoylphosphate: L-aspartate carbamoyltransferase, EC 2.1.3.2), has been determined. The pyrB gene encodes a polypeptide of 311 amino acid residues initiated by an NH2-terminal methionine that is not present in the catalytically active polypeptide. The DNA sequence analysis revealed the presence of an eight-amino-acid sequence beginning at Met-219 that was not detected in previous analyses of amino acid sequence. This octapeptide sequence provides an additional component of the disordered loop in the equatorial domain of the catalytic polypeptide. It had been found previously that the catalytic polypeptide is expressed from a bicistronic operon that also produces the regulatory polypeptide encoded by pyrI. A single transcriptional control region precedes the structural gene of the catalytic polypeptide and a simple 15-base-pair region separates its COOH terminus from the structural gene of the regulatory polypeptide. The chain-terminating codon of the catalytic polypeptide may contribute to the ribosomal binding site for the regulatory polypeptide and thus assist coordinate expression of the two cistrons.

Transductional construction of a threonine-hyperproducing strain of Serratia marcescens: lack of feedback controls of three aspartokinases and two homoserine dehydrogenases

To construct a threonine-hyperproducing strain of Serratia marcescens Sr41, the six regulatory mutations for three aspartokinases and two homoserine dehydrogenases were combined in a single strain by three transductional crosses. The constructed strain, T-1026, carried the lysC1 mutation leading to lack of feedback inhibition and repression of aspartokinase III, the thrA1(1) mutation desensitizing aspartokinase I to feedback inhibition, the thrA2(1) mutation releasing feedback inhibition of homoserine dehydrogenase I, the two hnr mutations derepressing aspartokinase I and homoserine dehydrogenase I, and the etr-1 mutation derepressing aspartokinase II and homoserine dehydrogenase II. The strain produced ca. 40 mg of threonine per ml of medium containing sucrose and urea. Furthermore, the productivity of strain T-1026 was compared with those of strains devoid of more than one of the six regulatory mutations.

New mutation (mmrA1) in Escherichia coli K-12 that affects minimal medium recovery and postreplication repair after UV irradiation

After UV irradiation, Escherichia coli uvrA mutant cells show higher survival on minimal than on rich growth medium, i.e., they show minimal-medium recovery. This effect of rich growth medium on survival is not observed in a uvrA mutant carrying an mmrA1 mutation, and the uvrA mmrA strain showed the same survival rate on minimal and rich growth media as the uvrA strain did on minimal medium plates. The mmrA1 mutation was isolated as a hidden mutation from a uvrA polA mutant strain and shown to map at 84.3 min on the E. coli K-12 linkage map. In contrast to the uvrA strain, the repair of DNA daughter strand gaps was not inhibited in the uvrA mmrA strain by rich growth medium after irradiation. However, the uvrA and uvrA mmrA strains were similar in their ability to repair DNA when compared in minimal medium. These data are consistent with the idea that the mmr gene product is not involved directly in the repair of UV radiation-induced DNA damage, but rather allows rich growth medium to inhibit a portion of postreplication repair.

Genetic analysis of a pleiotropic deletion mutation (delta igf) in Bacillus subtilis

A delta igf mutation of Bacillus subtilis (formerly called fdpAl) is a large deletion causing pleiotropic defects. The mapping of the delta igf deletion by phage PBS1 transduction revealed the following map order: sacA, thiC, hsrE, delta igf, ts199, purA. To analyze the pleiotropic nature of the delta igf mutation, mutants affected in each property of the pleiotropic mutation were isolated, and the mutations were mapped. iol and gnt mutants could not grow on inositol and gluconate, respectively, and fdp mutants were affected only in fructose-bisphosphatase. The map order from sacA to purA was as follows: sacA, thiC, hsrE, iol-6, gnt-4, fdp-74, hsrB, ts199, purA. The delta igf deletion covered loci from iol-6 to hsrB.

Genetic mapping of the Escherichia coli leader (signal) peptidase gene (lep): a new approach for determining the map position of a cloned gene

The gene for leader peptidase, termed lep, was mapped to the region between purI and nadB at min 54 to 55 on the Escherichia coli chromosome. Mapping involved (i) cloning the gene into the plasmid pBR322, (ii) transforming the plasmid into a polA strain where it cannot replicate autonomously, (iii) selecting by ampicillin resistance the rare cell in which the plasmid had recombined into the chromosome, and (iv) mapping the chromosomal site of drug resistance (and thus plasmid integration) by Hfr matings and P1 transduction. The map position was confirmed by an assay of the enzyme content of cells bearing an F' factor which covered that region of the chromosome.

Isolation of conditionally lethal amber mutations affecting synthesis of the nusA protein of Escherichia coli

Amber mutants (am3 and am4) of Escherichia coli K12 defective in the synthesis of nusA protein (Friedman 1971) were isolated from a strain harboring an amber suppressor (sup-126) that is active only at low temperatures. These mutants grew at low temperature (30 degrees C) but did not grow at temperatures above 38 degrees C. Complementation experiments with plasmids carrying the nusA+ gene and its derivatives or with plasmids carrying the nusA1 or am4 mutation indicated that the mutations am3, am4 and nusA1 affected the same gene function. Analysis of proteins produced by minicells containing a plasmid demonstrated that the plasmid pYN87, which can complement the nusA1 and amber mutations, codes for three bacterial proteins, a truncated nusA gene product (61 K), argG gene product (48 K) and a 21 K dalton protein, and that the am4 mutation affects the synthesis of only NusA protein. lambda Nam7 (and lambda Nam7Nam53) phages could grow on these amber mutants at 32 degrees C but not on the parental strain. Spontaneous temperature-resistant revertants of the amber mutants simultaneously lost the ability to permit lambda Nam7 phage development, indicating that the two phenotypes are due to a single mutation. These results suggest that the nusA gene function is essential for the growth of E. coli, and that the lambda N function is dispensable for phage development if the nusA gene is defective.

A partial restriction map of the proA-purE region of the Escherichia coli K12 chromosome

EcoRI restriction mapping data for fragments larger than 0.7 kb and contained in a 350-kb region of the Escherichia coli K-12 chromosome are presented. 75% of these fragments have been located relative to proA, B, argF, lac, proC, purE, and various insertion sequence elements normally present in this region. BglII and BamHI maps for the regions near argF and purE are also provided.

Role for fadR in unsaturated fatty acid biosynthesis in Escherichia coli

Escherichia coli K-12 mutants constitutive for the synthesis of the enzymes of fatty acid degradation (fad) synthesize significantly less unsaturated fatty acid (UFA) than do wild-type (fadR+) strains. The constitutive fadR mutants synthesize less UFA than do fadR+) strains both in vivo and in vitro. The inability of fadR strains to synthesize UFAs at rates comparable to those of fadR+ strains is phenotypically asymptomatic unless the fadR strain also carries a lesion in fabA, the structural gene for beta-hydroxydecanoyl-thioester dehydrase. Unlike fadR+ fabA(Ts) mutants, fadR fabA(Ts) strains synthesize insufficient UFA to support their growth even at low temperatures and, therefore, must be supplemented with UFA at both low and high temperatures. The low levels of UFA in fadR strains are not due to the constitutive level of fatty acid-degrading enzymes in these strains. These results suggest that a functional fadR gene is required for the maximal expression of UFA biosynthesis in E. coli.

Threonine production by ethionine-resistant mutants of Serratia marcescens

Ethionine reduced both the growth rate and the final growth level of Serratia marcescens Sr41. Growth inhibition was completely reversed by methionine. Strain D-315, defective in homoserine dehydrogenase I, was more sensitive to ethionine-mediated growth inhibition than was the wild-type strain. Ethionine-resistant mutants were isolated from cultures of strain D-316, which was derived from strain D-315 as a threonine deaminase-deficient mutant. Of 60 resistant colonies, 7 excreted threonine on minimal agar plates. One threonine-excreting strain, ETr17, was highly resistant to ethionine and, moreover, insensitive to methionine-mediated growth inhibition, whereas the parent strain was sensitive. When cultured in minimal medium with or without excess methionine, strain ETr17 had a higher homoserine dehydrogenase level than did strain D-316. The homoserine dehydrogenase activity was not inhibited by threonine or methionine. Transductional analysis revealed that the ethionine-resistant (etr-1) mutation carried by strain ETr17 was located in the metBM-argE region and caused the derepressed synthesis of homoserine dehydrogenase II. Strain ETr17 had a higher aspartokinase level than did the parent strain. By transductional cross with the argE+ marker, the etr-1 mutation was transferred into strain D-562 which was derived from D-505, a strain defective in aspartokinases I and III. The constructed strain had a higher aspartokinase level than did strain D-505 in medium with or without excess methionine, indicating that the etr-1 mutation led to the derepressed synthesis of aspartokinase II. Strain ETr17 produced about 8 mg of threonine per ml of medium containing sucrose and urea.

Genetic and biochemical analyses of Escherichia coli strains having a mutation in the structural gene (poxB) for pyruvate oxidase

Mutants of Escherichia coli K-12 deficient in pyruvate oxidase were isolated from an aceEF (pyruvate dehydrogenase-deficient) strain by selection for a complete absence of growth on medium lacking acetate. Extracts of two of the mutants were shown to contain normal levels of pyruvate oxidase antigen, although the enzymatic activities of the extracts were reduced or absent. The poxB locus was mapped by using closely linked transposon insertions to min 18.7 of the E. coli linkage map between the cmlA and aroA loci, a location far removed from that of the regulatory gene, poxA.

Cloning of the nusA gene of Escherichia coli

The EcoRI restriction fragment of wild-type Escherichia coli DNA that can complement the argG mutation was cloned into the EcoRI site on pBR322. The resulting chimeric plasmid (pYN81) contains a 16.0 kilobase fragment and can complement the nusA1 (Friedman 1971) as well as argG mutations. Examination of several deletion derivatives of pYN81 revealed that the activity that complements nusA1 and argG mutations is localized within the 5.3 kilobase segment defined by SalI and BglII sites. When the nusA gene segment was recloned into lambda vector L512, the resulting transducing phages lambda nusA+-1 and lambda nusA+-2 grew normally in nusA1 cells at 40 degrees C or above, unlike the vector phage L512. Proteins encoded by the cloned DNA fragment were examined with minicells containing the chimeric plasmid or UV-irradiated cells infected by the transducing phages. At least six proteins were apparently encoded by the 16.0 kilobase DNA fragment, and genes coding for each of these proteins were localized on the respective restriction segment. One of them with a molecular weight of 64,000 was identified as the nusA gene product. The nusA gene was found to be transcribed counterclockwise with respect to the E. coli genetic map. Endonulease BglII cleaves the gene in the vicinity of the C-terminus, generating a truncated nusA gene product with a molecular weight of 61,000 that can complement the nusA1 mutation.

Cloning and orientation of the gene encoding polynucleotide phosphorylase in Escherichia coli

Mutations which affect the activity of polynucleotide phosphorylase (PNPase) map near 69 min on the bacterial chromosome. This region of the chromosome has been cloned by inserting the kanamycin-resistant transposon Tn5 near the argG and mtr loci at 68.5 min. Large SalI fragments of chromosomal DNA containing the Tn5 element were inserted into pBR322, and selection was made for kanamycin-resistant recombinant plasmids. Two of these plasmids were found to produce high levels of PNPase activity in both wild-type and host strains lacking PNPase activity. The pnp gene was further localized and subcloned on a 4.8 kilobase HindIII-EcoRI fragment. This fragment was shown to encode an 84,000-molecular weight protein which comigrated with purified PNPase during sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The orientation of the pnp gene was determined by insertion of Tn5 into the 4.8 kilobase fragment cloned in pBR322. Some of the insertions had lost the ability to elevate the level of PNPase activity in the host bacterium. Restriction mapping of the positions of the Tn5 insertions and analysis of plasmid-encoded polypeptides in UV-irradiated maxi-cells indicated that the pnp gene is oriented in the counterclockwise direction on the bacterial chromosome.

Postexcision transposition of the transposon Tn10 in Escherichia coli K12

An experimental analysis of the fate of transposon Tn10 after excision from a proA::Tn10 site localized on the plasmid F' leads to the conclusions: 1. The precise excision is a progressive process. Its probability is estimated per time unit. 2. An excised Tn10 is always integrated into a different genetic locus. 2. An excised Tn10 is always integrated into a different genetic locus. 3. The kinetics of postexcision transposition are sometimes very slow. The excised transposon is inherited in one cell line in spite of cell multiplication. 4. The processes of excision and secondary insertion have no absolute requirement for the recA+ genotype but they are strongly enhanced in recA+ cells. 5. The kinetics of postexcision transposition are strongly dependent on the genetic site from which the transposon was excised. 6. The probability of postexcision transposition is fully determined by the probability of excision and depends on the genotype of the host and many other factors.

Molecular cloning of pldA, the structural gene for outer membrane phospholipase of E. coli K12

The pldA gene of Escherichia coli K12, which is involved in the synthesis of an outer membrane (OM) phospholipase, has been cloned using a cosmid cloning system. For detection of the cloned gene a newly developed, in vivo phospholipase assay was used. Subsequent cloning of the pldA gene was performed into the multicopy plasmid vectors pBR322 and pACYC184. The gene was localised on these hybrid plasmids by the analysis of in vitro-constructed deletion plasmids and mutant plasmids generated by transposon gamma delta-insertions. Analysis of plasmid-encoded proteins in a minicell system showed that the pldA gene product is a polypeptide with apparent molecular weight of 29,000. This apparent molecular weight changes from 29,000 to 26,000 when the denaturing temperature is changed from 95 degrees C to 37 degrees C. These data are in agreement with those on purified OM phospholipase (Nishijima et al. 1977), and therefore strongly suggest that pldA is the structural gene for this phospholipase. From the minicell experiments the direction of transcription of pldA could be established relative to the metE gene, which is also cloned on the same hybrid plasmids. Strains carrying the pldA gene on these high copy vectors do not appear to be affected by the product with respect to cell growth in any way. However they do harbour increased amounts of 29 K protein in cell envelope fractions, indicating that gene expression and product translocation to the OM are proportional to the increased gene copy number. We therefore conclude that phospholipase enzymatic activity is strictly regulated at the protein level.

Escherichia coli mutants with an altered sensitivity to cecropin D

Cecropins are a family of small, basic antibacterial polypeptides which can be isolated from pupae of immunized Lepidoptera. They are active against both gram-negative and gram-positive bacteria. We studied a mutant of Escherichia coli, strain SB1004, which is more sensitive to cecropin D than is the parental strain. The mutant was selected as resistant to a host range mutant of a Serratia marcescens phage. When the protein composition of the outer membrane was examined, strain SB1004 and some other phage-resistant mutants were found to be deficient in the OmpC protein. It was concluded that the OmpC protein is the receptor of the phage. Strain SB1004 was found to differ from other ompC mutants in being especially sensitive to hydrophobic antibiotics and to cecropin D. Furthermore, strain SB1004 has a tendency for spontaneous autolysis. A genetic analysis showed the mutations in strain SB1004 and a suppressor mutant to map in the ompC region. The activity of cecropin D against different strains of E. coli was specifically enhanced when divalent cations were absent. No such effect was found with cecropins A and B, which are less hydrophobic than the D form.

Proteins induced by aerobiosis in Escherichia coli

The role of protein induction and repression in the adaptation of Escherichia coli to changes in the supply of oxygen and other electron acceptors is only poorly understood. We have studied the changes in cellular protein composition associated with this adaptation by measuring the levels of 170 individual polypeptides produced during aerobic or anaerobic growth of E. coli, with and without nitrate. Nineteen polypeptides had levels highest during aerobic growth. These proteins include the enzymes of the pyruvate dehydrogenase complex, several tricarboxylic acid cycle enzymes, superoxide dismutase, and tetrahydropteroyltriglutamate transmethylase. The other aerobiosis-induced proteins have not been identified. These polypeptides are major cellular proteins during aerobic growth and display several different patterns of regulation in response to medium composition. Induction ratios for oxygen ranged from 2.2 to 11.2, with one exceptional member, superoxide dismutase, increasing 71-fold with aeration. Most of the proteins were also induced by nitrate during anaerobic growth. The time course of induction after shifts in oxygen supply revealed similarities in response among proteins of related function or metabolic regulation class. These results are discussed in relation to previously reported information on the identified aerobiosis-induced proteins.

Inducible expression of a gene specific to the RecF pathway for recombination in Escherichia coli K12

The Mud(Aplac) operon fusion technique of Casadaban and Cohen (1979) was used to search for inducible functions specific to the RecF pathway of conjugal recombination. A fusion mutant of a recBC sbcB mutant which showed less than 1% of the normal level of recombination in Hfr crosses has been isolated and designated as rec-259. The mutation is shown to be closely linked to tyrA at approximately 57.5 min in relation to the standard genetic map, and is quite distinct from recA. Two point mutations within this gene have also been obtained. Mutation of this gene interferes specifically with the RecF pathway of recombination, and also causes increased sensitivity to mitomycin C and UV light. Expression of the lac genes in the rec-259 fusion strain is increased following damage to DNA, but not in lexA and recA derivatives. These observations demonstrate the existence of an inducible gene which is regulated by lexA and whose expression is required for RecF recombination and DNA repair.

Chromosomal location of the gene encoding phosphoribosylpyrophosphate synthetase in Escherichia coli

A mutant of Escherichia coli with a partially defective phosphoribosylpyrophosphate synthetase (ribosephosphate pyrophosphokinase) has been characterized genetically. The genetic lesion causing the altered phosphoribosylpyrophosphate synthetase, prs, was mapped at 26 min on the linkage map by conjugation. Transductional analysis of the prs region established the gene order as purB-fadR-dadR-tre-pth-prs-hemA-trp. Two additional mutations were identified in the mutant: one in gsk, the gene encoding guanosine kinase, and one in lon, conferring a mucoid colony morphology. The contribution of each mutation to the phenotype of the mutant has been evaluated.

Expression of the gene for ribosomal protein S20: effects of gene dosage

We have exploited the properties of three different plasmids which carry the gene for Escherichia coli ribosomal protein S20 (rpsT) to test the effects of gene dosage on the expression of rpsT. Over a range of total copies of rpsT of 1 to 58 per haploid genome equivalent, the rate of incorporation of uridine during a 30-s pulse into RNA annealing to either of two specific probes for S20 mRNA increased essentially in proportion to copy number. In contrast, the rate of synthesis of S20 protein increased no more than 2.1-fold at the highest copy number. We conclude, in contrast to an earlier report (D. Geyl, and A. Böck, Mol. Gen. Genet. 154:327-334, 1977), that the synthesis of S20 is regulated at a posttranscriptional step. We propose that S20 itself is the regulatory agent and that binding of S20 to its own mRNA in regions homologous in structure with 16S rRNA can account for our results.

Cytoplasmic L-asparaginase: isolation of a defective strain and mapping of ansA

An Escherichia coli mutant defective in the production of cytoplasmic l-asparaginase I has been isolated. The mutation (ansA) has been mapped between the gap and pncA loci at 39 min on the E. coli map.

Expression of the argF gene of Pseudomonas aeruginosa in Pseudomonas aeruginosa, Pseudomonas putida, and Escherichia coli

R' plasmids carrying argF genes from Pseudomonas aeruginosa strains PAO and PAC were transferred to Pseudomonas putida argF and Escherichia coli argF strains. Expression in P. putida was similar to that in P. aeruginosa and was repressed by exogenous arginine. Expression in E. coli was 2 to 4% of that in P. aeruginosa. Exogenous arginine had no effect, and there were no significant differences between argR' and argR strains of E. coli in this respect.

Molecular cloning and characterization of the genes (pbpA and rodA) responsible for the rod shape of Escherichia coli K-12: analysis of gene expression with transposon Tn5 mutagenesis and protein synthesis directed by constructed plasmids

Two cell shape-determining genes of Escherichia coli K-12, pbpA, the structural gene for penicillin-binding protein 2, and rodA, whose protein is unknown, were subcloned into plasmid vectors from the transducing phage lambda MAd lip24, which carries the lip-leuS region of the E. coli chromosome. Plasmids with restriction enzyme-created deletions or transposon Tn5 insertions were isolated, and studies of genetic complementation of these plasmids with chromosomal mutations were carried out. Thus, a physical and genetic map of the rodA-pbpA region was established. The genes rodA and pbpA lie side by side within a 4.4-kilobase-pair region. The size of the rodA gene has been shown to be between 0.86 and 1.6 kilobase pairs; such DNA would encode a protein with a molecular weight between 32,000 and 59,000. Since Tn5 mutagenesis of the rodA gene did not affect the expression of the pbpA gene and vice versa, the genes rodA and pbpA seem to have independent promoters. Analysis of the proteins synthesized from the constructed plasmids in maxicells revealed that the plasmid carrying the pbpA gene encoded penicillin-binding protein 2 and amplification of the protein occurred. The product of the rodA gene was not identified.

Conditional change of DNA replication control in an RNA polymerase mutant of Escherichia coli

A temperature-sensitive mutant of Escherichia coli with a temperature-dependent change in the control of initiation of DNA replication was isolated. The phenotype of the mutant was dependent on a mutation in the RNA polymerase gene rpoC. In vitro RNA polymerase activity was temperature sensitive. The mutant grew and synthesized DNA at 30 degrees C as did the wild type. After a shift to 39 degrees C, a temperature still permissive for growth, the mutant increased its origin concentration more than twofold. After a shift from 39 to 30 degrees C, initiation of DNA replication was inhibited until the normal origin concentration was reestablished.

Mapping of the gene for cytidine deaminase (cdd) in Escherichia coli K-12

The structural gene encoding cytidine deaminase (cdd) has been mapped in Escherichia coli K-12. It is located counterclockwise to ptsF between 46 and 47 min. The gene order in this region of the E. coli chromosome was found to be his-udk-gat-dld-cdd-ptsF.

The association of proton movement with galactose transport into subcellular membrane vesicles of Escherichia coli

1. Subcellular membrane vesicles were prepared from a strain of Escherichia coli constitutive for the GalP galactose-transport system. 2. The addition of substrates of the GalP transport system to vesicle suspensions promoted alkaline pH changes, which provided direct evidence for the coupling of sugar and proton transport. 3. Respiration-energized galactose transport was progressively inhibited at pH values above 6.0, and was abolished by agents that render the membrane permeable to protons. 4. The combined effects of valinomycin, the nigericin-like compound A217 and pH on galactose transport suggested that both delta pH and delta psi components of the protonmotive force contributed to energization of galactose transport. 5. These results substantiate the conclusion that the GalP transport system operates by a chemiosmotic mechanism.

Initiation site of deoxyribonucleotide polymerization at the replication origin of the Escherichia coli chromosome

A new round of chromosomal replication of a temperature-sensitive initiation mutant (dnaC) of Escherichia coli was initiated synchronously by a temperature shift from a nonpermissive to a permissive condition in the presence of arabinosyl cytosine. Increased amounts of nascent DNA fragments with homology for the chromosomal segment containing the replication origin (oriC) were found. The nascent DNA fragments were purified and treated with alkali to hydrolyze putative primer RNA and to expose 5'-hydroxyl DNA ends at the RNA-DNA junctions. The ends were then labeled selectively with T4 polynucleotide kinase and [gamma-32P]ATP at 0 degrees C and the terminally-labeled initiation fragments were purified by hybridization with origin probe DNAs containing one each of the constituent strands of oriC-DNA segment. The 32P-labeled initiation sites were then located at the resolution of single nucleotides in the nucleotide sequence of the oriC segment after cleavage with restriction enzymes. Two initiation sites of DNA synthesis, 37 nucleotides apart, were detected in one of the component strands of the oriC; in other words, in the strand whose 5' to 3' polynucleotide polarity lies counterclockwise on the E. coli genetic map. The results support the involvement of the primer RNA in the initiation of DNA synthesis at the origin of the E. coli genome and suggest that the first initiation event is asymmetric.

Control of arg gene expression in Salmonella typhimurium by the arginine repressor from Escherichia coli K-12

The regulation of synthesis of arg enzymes in Salmonella typhimurium by the arginine repressor of Escherichia coli K-12 has been reevaluated using a strain of S. typhimurium in which the argR gene was rendered nonfunctional by inserting the translocatable tetracycline-resistance element Tn10 into the argR gene. In contrast to previous studies, the introduction of the argR+ allelle of E. coli on an F-prime factor to the argR::Tn10 S. typhimurium strain reduced the synthesis of arg enzymes to essentially wild-type levels. The elevated levels of arg enzymes observed in other hybrid merodiploids may have been the consequence of the formation of hybrid repressor molecules. The readily scoreable phenotype of tetracycline resistance facilitated establishing linkage of cod and argR (0.6% cotransduction) by P22 phage-mediated transduction.

The use of transposon insertion zdc-235::Tn10 (min 32) to clone and delete DNA from the terminus region of Escherichia coli

Transposon zdc-235::Tn10 is inserted at min 32 on the genetic map of Escherichia coli, and we have used this transposon to clone 14 kb of DNA that flanks this insertion. The site of insertion of the transposon, and the restriction map of the cloned DNA, correspond well with the predictions of the Bouché restriction map for the terminus region (Bouché 1982). The zdc-235::Tn10 insertion, along with the zdd-230::Tn9 insertion, was used to obtain deletions of the region that has been cloned. Strains lacking a minimum of 14 kb, and more likely a minimum of 40 kb of DNA, showed no alteration of growth or cell morphology.

Recombination-induced suppression of cell division following P1-mediated generalized transduction in Klebsiella aerogenes

Klebsiella aerogenes recombinants resulting from bacteriophage P1-mediated generalized transduction failed to increase in number for approximately six generations after transduction. Nevertheless these recombinants continued to grow and became sensitive to penicillin after a transient resistance, suggesting that the cells were growing as long, non-dividing filaments. When filamentous cells were isolated from transduced cultures by gradient centrifugation, recombinants were 1000-fold more frequent among the filaments than among the normal-sized cells. The suppression of cell-division lasted for six generations whether markers near the origin (gln, ilv) or terminus (his, trp) of chromosome replication were used, despite a 50-fold difference in transduction frequencies for these markers. The suppression of cell division was a host response to recombination rather than to P1 invasion since cells lysogenized by P1 in these same experiments showed only a short (two generation) suppression of cell division. We speculate that the suppression of cell-division is an SOS response triggered by the degraded DNA not incorporated in the final recombinant. We demonstrate that both the filamentation and the transient penicillin resistance of recombinant cells can be exploited to enrich greatly for recombinants, raising transduction frequencies to as high as 10(-3).

Isolation and characterization of Tn5 insertion mutations in the lexA gene of Escherichia coli

A Mu d(Ap lac)-generated fusion of lacZ to dinD, a gene induced by DNA damage, was used to isolate Tn5 insertion mutations that affect the regulation of the SOS responses. Three mutants were obtained that contained Tn5 insertions genetically linked to the lexA gene and had properties that suggested the mutants were deficient in lexA expression. The lexA protein has been shown to function as the repressor for genes involved in the SOS responses. By Southern blotting experiments, the three Tn5 insertions were physically mapped to distinct locations within the coding region of the lexA gene. The introduction of these mutations in six strains carrying lacZ fusions to different damage-inducible genes resulted in high expression of beta-galactosidase in all but one of the strains. In the dinF fusion strain, lacZ expression was reduced below that seen in a lexA+ background. Physical mapping studies of the dinF locus gave results consistent with the notion that dinF is part of the lexA transcription unit and that a lexA::Tn5 mutation has a polar effect on dinF expression. With certain din-lac fusion strains, a correlation was seen between the amount of beta-galactosidase production and the location of the particular Tn5 insertion within the lexA gene.

Genetic analysis of regulation of the RecF pathway of recombination in Escherichia coli K-12

Genetic evidence is provided supporting the hypothesis that one or more genes of the RecF pathway of recombination other than recA are controlled by the lexA repressor. Using lexA, recA, and recA operator mutations, we also analyze the role of recA and sbcB in regulating the RecF pathway.

Multilocus genetic structure in natural populations of Escherichia coli

A survey of allozyme variation at 12 enzyme loci in 1,705 clones of the genetic species Escherichia coli (including four species of Shigella) from natural populations revealed 302 unique allele combinations (electrophoretic types). Single-locus diversity estimates fall within the range predicted by the neutral allele theory of molecular evolution, but the combination of alleles in electrophoretic types are highly nonrandom, as indicated by a test of association over all loci and by evidence of complex linkage disequilibria in several four-locus combinations. These linkage disequilibria reflect genetic differentiation of E. coli into three groups of strains. Because of restricted recombination, both the stochastic extinction of lines and selective differences between particular genetic combinations may have contributed to the evolution of subspecific structure in E. coli.

Indirect stimulation of genetic recombination

Recombination between lacZ alleles in crosses of lambdalacZ(1) (-) x lambdalacZ(2) (-) and F(-)lacZ(1) (-) x lambdalacZ(2) (-) in Escherichia coli (lambda) can be stimulated manyfold by UV irradiation of one of the lambdalacZ phages [Porter, R. D., McLaughlin, T. & Low, B. (1979) Cold Spring Harbor Symp. Quant. Biol. 43, 1043-1048]. Analogous stimulation has now been observed by coinfection of the cells by UV-irradiated lambda phage which carries no lac region. This indirect stimulation is not dependent on induction of the SOS system. The bacterial uvr system can effectively remove the damages on the lambda DNA which cause the indirect stimulation. Among a number of mutations tested, only ssb-1 was found to cause a drastic decrease in the indirect stimulation. Indirect stimulation was caused only by using phage that had a region of homology with the recombining phage. The homologous region can be separated from the recombining region by an extended nonhomologous region (>7.9 x 10(3) base pairs). This implies that damages to the DNA molecule, which stimulate recombination, can be located very far from the recombining region of the molecule.

Intragenic localization of amber and temperature-sensitive rpoD mutations affecting RNA polymerase sigma factor of Escherichia coli

A set of multi-copy plasmids carrying part or all of the rpoD gene of Escherichia coli have been used to localize several amber and temperature-sensitive mutations affecting RNA polymerase sigma factor. In contrast to the plasmid carrying a complete rpoD sequence, plasmids carrying part of rpoD could not complement any of the rpoD mutations tested. However, the mutants harboring some of the latter plasmids produced wild-type recombinants at high frequency, provided that they carry the recA+ gene. The results permitted us to localize the rpoD mutations into one of the three intragenic segments. Thus, the rpoD285(ts) mutation (Harris et al. 1978) was located on the 0.8 kilobase segment defined by the Bg/II and BamHI sites in the middle segment, and the amber mutation rpoD40 (Osawa and Yura 1980) in the N-terminal 0.8 kilobase segment. Four additional amber mutations were also identified and classified into one of the segments of rpoD. It was further revealed that plasmids carrying certain amber mutations (rpoD47 or rpoD63) in the C-terminal segment of rpoD render all rpoD mutants tested (including rpoD47 and rpoD63 mutants themselves) able to grow at the restrictive condition. It is suggested that the enhanced synthesis of incomplete sigma polypeptides encoded by rpoD47 or rpoD63 phenotypically suppresses the defects in sigma function at least partially.