Linkage map of Escherichia coli strain K-12

Identification of the enantiomeric nature of 2-keto-3-deoxy-galactonate in the catabolic pathway of 3,6-anhydro-L-galactose

A novel metabolic pathway of 3,6-anhydro-L-galactose (L-AHG), the main sugar component in red macroalgae, was first discovered in the marine bacterium Vibrio sp. EJY3. L-AHG is converted to 2-keto-3-deoxy-galactonate (KDGal) in two metabolic steps. Here, we identified the enantiomeric nature of KDGal in the L-AHG catabolic pathway via stereospecific enzymatic reactions accompanying the biosynthesis of enantiopure L-KDGal and D-KDGal. Enantiopure L-KDGal and D-KDGal were synthesized by enzymatic reactions derived from the fungal galacturonate and bacterial oxidative galactose pathways, respectively. KDGal, which is involved in the L-AHG pathway, was also prepared. The results obtained from the reactions with an L-KDGal aldolase, specifically acting on L-KDGal, showed that KDGal in the L-AHG pathway exists in an L-enantiomeric form. Notably, we demonstrated the utilization of L-KDGal by Escherichia coli for the first time. E. coli cannot utilize L-KDGal as the sole carbon source. However, when a mixture of L-KDGal and D-galacturonate was used, E. coli utilized both. Our study suggests a stereoselective method to determine the absolute configuration of a compound. In addition, our results can be used to explore the novel L-KDGal catabolic pathway in E. coli and to construct an engineered microbial platform that assimilates L-AHG or L-KDGal as substrates. KEY POINTS: • Stereospecific enzyme reactions were used to identify enantiomeric nature of KDGal • KDGal in the L-AHG catabolic pathway exists in an L-enantiomeric form • E. coli can utilize L-KDGal as a carbon source when supplied with D-galacturonate.

Overexpression of biotin synthase and biotin ligase is required for efficient generation of sulfur-35 labeled biotin in E. coli

Background

Biotin is an essential enzyme cofactor that acts as a CO₂ carrier in carboxylation and decarboxylation reactions. The E. coli genome encodes a biosynthetic pathway that produces biotin from pimeloyl-CoA in four enzymatic steps. The final step, insertion of sulfur into desthiobiotin to form biotin, is catalyzed by the biotin synthase, BioB. A dedicated biotin ligase (BirA) catalyzes the covalent attachment of biotin to biotin-dependent enzymes. Isotopic labeling has been a valuable tool for probing the details of the biosynthetic process and assaying the activity of biotin-dependent enzymes, however there is currently no established method for ³⁵S labeling of biotin.

Results

In this study, we produced [³⁵S]-biotin from Na³⁵SO₄ and desthiobiotin with a specific activity of 30.7 Ci/mmol, two orders of magnitude higher than previously published methods. The biotinylation domain (PfBCCP-79) from the Plasmodium falciparum acetyl-CoA carboxylase (ACC) was expressed in E. coli as a biotinylation substrate. We found that overexpression of the E. coli biotin synthase, BioB, and biotin ligase, BirA, increased PfBCCP-79 biotinylation 160-fold over basal levels. Biotinylated PfBCCP-79 was purified by affinity chromatography, and free biotin was liberated using acid hydrolysis. We verified that we had produced radiolabeled biologically active [D]-biotin that specifically labels biotinylated proteins through reuptake in E. coli.

Conclusions

The strategy described in our report provides a simple and effective method for the production of [³⁵S]-biotin in E. coli based on affinity chromatography.

Random mutagenesis in Corynebacterium glutamicum ATCC 13032 using an IS6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway

BACKGROUND

Corynebacterium glutamicum, a Gram-positive bacterium of the class Actinobacteria, is an industrially relevant producer of amino acids. Several methods for the targeted genetic manipulation of this organism and rational strain improvement have been developed. An efficient transposon mutagenesis system for the completely sequenced type strain ATCC 13032 would significantly advance functional genome analysis in this bacterium.

RESULTS

A comprehensive transposon mutant library comprising 10,080 independent clones was constructed by electrotransformation of the restriction-deficient derivative of strain ATCC 13032, C. glutamicum RES167, with an IS6100-containing non-replicative plasmid. Transposon mutants had stable cointegrates between the transposon vector and the chromosome. Altogether 172 transposon integration sites have been determined by sequencing of the chromosomal inserts, revealing that each integration occurred at a different locus. Statistical target site analyses revealed an apparent absence of a target site preference. From the library, auxotrophic mutants were obtained with a frequency of 2.9%. By auxanography analyses nearly two thirds of the auxotrophs were further characterized, including mutants with single, double and alternative nutritional requirements. In most cases the nutritional requirement observed could be correlated to the annotation of the mutated gene involved in the biosynthesis of an amino acid, a nucleotide or a vitamin. One notable exception was a clone mutagenized by transposition into the gene cg0910, which exhibited an auxotrophy for histidine. The protein sequence deduced from cg0910 showed high sequence similarities to inositol-1(or 4)-monophosphatases (EC 3.1.3.25). Subsequent genetic deletion of cg0910 delivered the same histidine-auxotrophic phenotype. Genetic complementation of the mutants as well as supplementation by histidinol suggests that cg0910 encodes the hitherto unknown essential L-histidinol-phosphate phosphatase (EC 3.1.3.15) in C. glutamicum. The cg0910 gene, renamed hisN, and its encoded enzyme have putative orthologs in almost all Actinobacteria, including mycobacteria and streptomycetes.

CONCLUSION

The absence of regional and sequence preferences of IS6100-transposition demonstrate that the established system is suitable for efficient genome-scale random mutagenesis in the sequenced type strain C.glutamicum ATCC 13032. The identification of the hisN gene encoding histidinol-phosphate phosphatase in C. glutamicum closed the last gap in histidine synthesis in the Actinobacteria. The system might be a valuable genetic tool also in other bacteria due to the broad host-spectrum of IS6100.

Ultraviolet light-induced mutation in UV-resistant, thermosensitive derivatives of lexA-strains of Escherichia coli K-12

It was shown previously that a major class of UV-resistant derivatives of lexA- strains of E. coli K-12 is defective in cell division at 42.5 degrees. The thermosensitive mutations, judging by genetic mapping and complementation tests, are believed to be intragenic suppressor mutations that lower the activity of the diffusible product that results in the LexA- phenotype (Mount et al., 1973). Several thermosensitive derivatives have been characterized in regard to their susceptibility to mutation induction by UV at the permissive growth temperature (30 degrees). Although the strains tested are approximately as resistant to UV as lexA+ strains, they showed a level of mutation induction that was considerably lower. By means of genetic complementation tests it was demonstrated that the low levels of UV mutagenesis in lexA- strains and their thermosensitive derivatives result from the synthesis of a diffusible product. One possible interpretation of these results is that a diffusible product in lexA- strains prevents the induction of error-prone repair. Altering the activity of this product by tsl mutations can lead to increased, but not normal, levels of error-prone repair.

Genetic and physical mapping of the mcrA (rglA) and mcrB (rglB) loci of Escherichia coli K-12

We have genetically analyzed, cloned and physically mapped the modified cytosine-specific restriction determinants mcrA (rglA) and mcrB (rglB) of Escherichia coli K-12. The independently discovered Rgl and Mcr restriction systems are shown to be identical by three criteria: 1) mutants with the RglA- or RglB- phenotypes display the corresponding McrA- or McrB- phenotypes, and vice versa; 2) the gene(s) for RglA and McrA reside together at one locus, while gene(s) for RglB and McrB are coincident at a different locus; and 3) RglA+ and RglB+ recombinant clones complement for the corresponding Mcr-deficient lesions. The mcrA (rglA) gene(s) is on the excisable element e14, just clockwise of purB at 25 min. The mcrB (rglB) gene(s), at 99 min, is in a cluster of restriction functions that includes hsd and mrr, determinants of host-specific restriction (EcoK) and methyladenine-specific restriction respectively. Gene order is mcrB-hsdS-hsdM-hsdR-mrr-serB. Possible models for the acqusition of these restriction determinants by enteric bacteria are discussed.

Methyl transferases induced during chemical adaptation of M. luteus

Three peaks of methyltransferase activity specific for MNNG alkylated DNA have been identified from extracts of chemically adapted M. luteus. They are designated as TI to TIII in order to their elution from a Sephadex G-75 column. The first one of these peaks has been purified to homogeneity. TI, is an inducible, unusually salt resistant, heat labile protein which corrects O6-methylguanine in alkylated DNA by the transfer of the O6-alkyl group to a cysteine amino acid in the TI protein. There is a stoichiometric relationship between the loss of O6-methylguanine from the DNA and the production of S-methylcysteine. Partially purified TII & TIII proteins show specificity for O4-alkylthymine and methyl phosphotriesters respectively. The mode of repair by the isolated methyltransferases is similar yet there is no competition for substrate specificity. The apparent molecular weights of TI, TII & TIII proteins are 31Kd, 22Kd, and 13Kd respectively.

Adaptive response of Micrococcus luteus to alkylating chemicals

Wild type M. luteus cells have been adapted by a step-wise treatment with sub-lethal concentrations of MNNG. The adapted cells exhibit 5.7 fold increased resistance to the killing effects of the mutagen and a simultaneous efficient removal of various base modifications present in cellular DNA. A protein extract prepared from adapted cells contains inducible repair functions which can reduce 80-90% of the alkylated DNA content of 06-MeG is effected by a transmethylase and there is no concomitant release of the modified base. However, N-3 MeG is released as a free modified base through the action of a DNA glycosylase. The release of N-3 MeA is unaffected by the induction treatment whereas that of N-7 methylpurine is slightly improved in the adapted cells.

Genetic factors affecting recovery of nonpoint mutations in the region of a gene coding for ornithine transcarbamylase: involvement of both the F factor in its chromosomal state and the recA gene

Mutants of E. coli K12 that overproduce ornithine transcarbamylase can be identified in Car- strains because they permit utilization of citrulline as a carbamyl phosphate source, due to reversal of the normal OTCase reaction; they are called Cut mutants (citrulline utilizers). Hfr strains that carry the F factor adjacent to argF (one of two duplicate genes that code for ornithine transcarbamylase in E. coli K12) yield more Cut mutants than do F+ or F- strains, or Hfr strains in which the F factor is not adjacent to argF. When Hfr strains in which the F factor is integrated adjacent to argF are made recA, they yield few Cut mutants. Many of the Cut mutants recovered from one of the Hfr strains used in the investigation (Hfr P4X) are unstable; the properties of these unstable mutations suggest that they carry aberrations in the region of the argF gene. Thus, the increased yields of Cut mutants probably result from aberrations that occur when the F factor is integrated adjacent to argF. The nature of these aberrations is not yet known. The unstable Cut mutants are to a large extent stabilized by recA; such stabilization is one of the properties of duplications. Other data indicate that the aberrations may be more complex than simple gene duplications; in particular properties of segregants and some recombinants derived from unstable Cut mutants are most easily interpreted by assuming that segregation from, and possibly formation of, the unstable mutants occurs in several stages.

Absence of acetohydroxy acid synthetase in a clinical isolate of Neisseria gonorrhoeae requiring isoleucine and valine

A clinical isolate of Neisseria gonorrhoeae with an unusual growth requirement for isoleucine and valine lacked the activity of acetohydroxy acid synthetase, one of the enzymes required for the biosynthesis of these amino acids. A spontaneous mutant which no longer required isoleucine and valine had acquired this enzymatic activity.

Isolation and characterization of Escherichia coli K-12 mutants unable to induce the adaptive response to simple alkylating agents

When Esherichia coli cells are exposed to a low level of simple alkylating agents, they induce the adaptive response which renders them more resistant to the killing and the mutagenic effects of the same or other alkylating agents. This paper describes the isolation of one strain that was deficient in mutagenic adaptation and five that were deficient in both mutagenic and killing adaptation, confirming previous suggestions that killing and mutagenic adaptation are, at least to some extent, separable. These six strains have been called Ada mutants. They were more sensitive to the killing and mutagenic effects of N-methy-N'-nitro-N-nitrosoguanidine (MNNG) than the unadapted Ada+ parent. Thus, the adaptation pathway is responsible for circumventing some alkylation-induced damage even in cells that are preinduced. The increase in mutation frequency seen in Ada cells treated with MNNG was the same whether the cells were lexA+ or lexA, showing that the extra mutations found in Ada- strains do not depend upon the SOS pathway. Ada strains accumulated more O6-methyl guanine lesions than the Ada+ parent on prolonged exposure to MNNG, and this supports the idea that O6-methyl guanine is the most important lesion for MNNG-induced mutagenesis. The ada mutations have been shown to map in the 47 to 53-min region of the E. coli chromosome.

Tryptophan-requiring parental strains yield Salmonella typhimurium x Escherichia coli hybrid recombinants with functional tryptophan operons

Crosses between an Escherichia coli Hfr trp strain and three Salmonella typhimurium F- trp strains produced some trp+ hybrids in which the tryptophan operon is composed of genes from both parental species.

Transposon-insertion mutants of Escherichia coli K12 defective in a component common to galactose and ribose chemotaxis

From a collection of 8,000 transposon-insertion mutants of Escherichia coli K12 we identified two mutations, trg-1::Tn5 and trg-2::Tn10, that simultaneously eliminate chemotactic response to ribose and galactose, two attractants recognized by independent receptors. We show that these transposon-insertions confer a Trg phenotype, indicating that this specific pattern of tactic defects is a null phenotype. The two mutation sites are cotransductionally linked to an extend consistent with placement in the same gene. The Trg phenotype of a family of deletion mutants produced by curing trg-2::Tn10 implies that trg is a single gene. Experiments with appropriate F-primes and Hfr's locate the trg locus at approximately 31 min on the linkage map, with a marker order: pyrF-rac-(P.O. 43)-trg-man. We also found one trg mutant whose Trg phenotype was not linked to a transposon-insertion but is probably the result of a mutator activity in the parent strain. Selection of transposon-insertions near, but not in trg allowed demonstration of a very close linkage between the spontaneous trg-3 and the transposon-generated trg's, indicating all three mutations are probably in the same gene. In our manipulations of transposon-insertions we found that Tn5 had a tendency to translocate from its initial site of insertion while Tn10 was relatively stable. The trg-product is probably a chemotactic signal transducer, which interacts directly with two independent receptor proteins and transmits information to the central chemotactic machinery.

Fertility factors in Pseudomonas putida: selection and properties of high-frequency transfer and chromosome donors

The octane plasmid (OCT) in Pseudomonas putida strains has been shown to be transferred at low frequency. However, bacteria which had newly received this plasmid showed a transient increase in donor ability. Using Octane+ P. putida as the donor, the transfer of most chromosomal markers was shown to be independent of OCT transfer, whereas the mobilization of the octanoate catabolism genes (octanoic and acetate) was dependent on OCT plasmid transfer. The presence of a fertility factor termed FPo has been postulated to explain these results. Strains carrying only this fertility factor have been obtained from strains carrying both OCT and FPo plasmids. Strains in which the OCT plasmid was transferred at high frequencies have also been isolated, and chromosome mobilization by OCT and FPo has been compared. A different gradient of transmission by OCT and FPo has been observed. It has also been shown that chromosome transfer by OCT was dependent on the bacterial recombination system, whereas the chromosome transfer by FPo was unaffected by the presence of a rec mutation in the donor strain.

Genetic mapping of tyramine oxidase and arylsulfatase genes and their regulation in intergeneric hybrids of enteric bacteria

The genes for arylsulfatase (atsA) and tyramine oxidase (tynA) have been mapped in Klebsiella aerogenes by P1 transduction. They are linked to gdhD and trp in the order atsA-tynA-gdhD-trp-pyrF. Complementation analysis using F' episomes from Escherichia coli suggested an analogous location of these genes in E. coli, although arylsulfatase activity was not detected in E. coli. P1 phage and F' episomes were used to create intergeneric hybrid strains of enteric bacteria by transfer of the ats and tyn genes between K. aerogenes, E. coli, and Salmonella typhimurium. Intergeneric transduction of the tynK gene from K. aerogenes to an E. coli restrictionless strain was one to two orders less frequent than that of the leuK gene. The tyramine oxidase of E. coli and S. typhimurium in regulatory activity resemble very closely the enzyme of K. aerogenes. The atsE gene from E. coli was expressed, and latent arylsulfatase protein was formed in K. aerogenes and S typhimurium. The results of tyramine oxidase and arylsulfatase synthesis in intergeneric hybrids of enteric bacteria suggest that the system for regulation of enzyme synthesis is conserved more than the structure or function of enzyme protein during evolution.

Gene expression and stability of mRNA affected by DNA-arrested synthesis in gene 59, 46, and 47 mutants of bacteriophage T4

The effect of bacteriophage T4 gene 59 mutations (DNA-arrested synthesis) on kinetics of DNA synthesis, gene expression, and stability of mRNA has been studied. When Escherichia coli B was infected by a T4 gene 59 mutant, DNA synthesis proceeded to increase linearly after initiation, but started to decrease at 8 min and was completely arrested at 12 min at 37 degrees C. At various incubation temperatures (20 to 42 degrees C), the initial rates and times of arrest of DNA synthesis were different, but the total amount of DNA synthesized was constant. This result supports the hypothesis that function of gene 59 is required for the conversion of 63S DNA molecules to other replicative intermediates (39). The abnormality in protein synthesis caused by gene 59 mutation is manifested by (i) a delayed shutoff in the expression of early proteins (gene 43, 46, 39, 52, 63, 42-45, and some unidentified proteins), (ii) a reduced rate of late gene expression (gene 34, 37, 18, 20, 23, wac, 24, 22, 38, and 19), and (iii) an absence of cleavage of certain late proteins (23, 24, IPIII and 22 to 23(*), 24(*), IPIII(*), and small fragments). It appears that there was no effect on the expression of gene 33, 55, and 32 by a mutation in gene 59. Results obtained from an addition of rifampin at the prereplicative cycle after infection indicated that mRNA from genes 43, rIIA, 46, 39, 52, and 63 are more stable in T4amC5 (gene 59) than in wild-type-infected cells. mRNA remained functional longer in mutant-infected cells, and this may explain the prolonged synthesis of certain early proteins. The gene expression of other DNA arrested mutants-those in genes 46 and 47-showed a pattern of abnormal protein synthesis similar to that found in gene 59 mutant-infected cells, except more late proteins are synthesized. The gene expression in terms of phage DNA structure is discussed.

Genetics of Rhodospirillaceae

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Effect of RNase III on efficiency of translation of bacteriophage T7 lysozyme mRNA

RNase III had no positive effect on the translation of bacteriophage T7 lysozyme mRNA in vivo or in vitro. The time of appearance and quanity of lysozyme in T7-infected E. coli BL107, an RNase III- strain, and T7-infected E. coli BL15, a nearly isogenic RNase III+ strain, were indistinguishable. Nearly identical patterns of lysozyme mRNA activity were obtained when RNA extracted at different times after infection of RNase III+ and RNase III- hosts was translated in cell-free extracts of E. coli containing or lacking RNase III. Exposure of RNA extracted from T7-infected E. coli BL107 (RNase III-) to purified RNase III did not increase the lysozyme mRNA activity of this RNA. The only result that implied that RNase III has a differential effect on the translatability of the lysozyme mRNA was the translation of fractionaed RNA from T7-infected E. coli BL107. Translation of the smallest and largest lysozyme messages, 0.33 x 10(6) and 4 x 10(6) to 5 x 10(6) daltons, was the most inefficient in RNase III- cell-free extracts as compared to RNase III+ cell-free translation. The translation of the most abundant, medium-sized lysozyme mRNA between 0.9 x 10(6) and 1.5 x 10(6) daltons was the least affected by the absence of RNase III. The existence of a lag between the appearance of lysozyme mRNA and the appearance of lysozyme in T7 infection was confirmed. In these studies a very rapid method of RNA extraction was used, eliminating the possibility of continued RNA transcription during cell collection and RNA extraction. With this method of analysis, the length of the lag period was established at about 3 min. The possibility that RNase III is the controlling element of the lag period was eliminated by these investigations.

Relationship between gene function and gene location in Escherichia coli

Genes of Escherichia coli were grouped according to the "biochemical relatedness" of the enzymes they specifiy, using two schemes to determine relatedness: similarity of reaction or similarity of reactants. The tendency of biochemically related genes as so defined to lie approximately 90 degrees or 180 degrees from one another on the circular genetic map was analyzed statistically. Of the classes analyzed, only the genes for the enzymes of glucose catabolism showed a significant departure from random distribution in this respect. The glucose catabolism genes showed a pronounced tendency to lie either 90 degrees of 180 degrees from one another (P = ca. 10(-9)), and, furthermore, most of these genes were found to lie in only four gene clusters on the E. coli genome. The significance of this observation is discussed in relation to evolutionary mechanisms and to mechanisms of gene expression.

Mutations affecting the citrate-dependent iron uptake system in Escherichia coli

Isolation of six strains of Escherichia coli K-12 carrying mutations affecting the citrate-dependent iron uptake system is described. Genetic analysis of these mutants showed that the mutation affecting the citrate system are cluster together at about min 6 on the E. coli chromosome.

Permease-specific mutations in Salmonella typhimurium and Escherichia coli that release the glycerol, maltose, melibiose, and lactose transport systems from regulation by the phosphoenolpyruvate:sugar phosphotransferase system

Several carbohydrate permease systems in Salmonella typhimurium and Escherichia coli are sensitive to regulation by the phosphoenolpyruvate:sugar phosphotransferase system. Mutant Salmonella strains were isolated in which individual transport systems had been rendered insensitive to regulation by sugar substrates of the phosphotransferase system. In one such strain, glycerol uptake was insensitive to regulation; in another, the maltose transport system was resistant to inhibition; and in a third, the regulatory mutation specifically rendered the melibiose permease insensitive to regulation. An analogous mutation in E. coli abolished inhibition of the transport of beta-galactosides via the lactose permease system. The mutations were mapped near the genes which code for the affected transport proteins. The regulatory mutations rendered utilization of the particular carbohydrates resistant to inhibition and synthesis of the corresponding catabolic enzymes partially insensitive to repressive control by sugar substrates of the phosphotransferase system. Studies of repression of beta-galactosidase synthesis in E. coli were conducted with both lactose and isopropyl beta-thiogalactoside as exogenous sources of inducer. Employing high concentrations of isopropyl beta-thiogalactoside, repression of beta-galactosidase synthesis was not altered by the lactose-specific transport regulation-resistant mutation. By contrast, the more severe repression observed with lactose as the exogenous source of inducer was partially abolished by this regulatory mutation. The results support the conclusions that several transport systems, including the lactose permease system, are subject to allosteric regulation and that inhibition of inducer uptake is a primary cause of the repression of catabolic enzyme synthesis.

Explanations accounting for transduction by bacteriophage lambda in maltose negative bacteriophage lambda resistant mutants of Escherichia coli K-12

Entry of DNA from lambda phages particles into lambdarMAl- mutants of Escherichia coli K-12 is shown to be due to two distinguishable processes. One, residual transduction, results from a low level expression of lamB. The other one, background transduction, is independent of gene lamB. Interpretations are presented for these results. It is propos that residual transduction is due to a weak promoter pB3 located within or near the distal part of the gene preceeding lamB in the same operon. It is proposed that background transduction is due to a secondary receptor structure for phage lambda. Finally a tentative hypothesis relatin pB3 to insertion sequences is presented.

dnaA acts before dnaC in the initiation of DNA replication

We constructed a double mutant of Escherichia coli K-12 carrying dnaA(Ts) and dnaC(Cs) lesions. In this mutant DNA synthesis proeceeds normally at 32 degrees C and initiation is inhibited at both 41 and 20 degrees C. By shifting this culture grown at 32 degrees C to the two restrictive temperatures in different time sequences and assaying protein and DNA synthesis of cells growing at different temperatures, we found that dnaA and dnaC genes work independently with dnaA acting before dnaC. While preparing special strains for this work, we also showed that the order of genes in the neighborhood of dnaA is dnaA-tnaA-phoS-ilv.

Genetic analysis of antibiotic resistance in Streptococcus pyogenes

The genetics of antibiotic resistance in mutant strains of Streptococcus pyrogenes was studied. Utilizing a type 6 strain (9440) primarily resistant to strepttomycin (Strr), classes of mutant strains were isolated that were resistant to one of the following antibiotics: rifampin (Rifr), erythromycin (Eryr), thiostrepton (Tstr), spiramycin (Sprr), fusidic acid (Fusr), gramicidin (Grcr), ethidium bromide (Ebrr), kanamycin (Kanr), neomycin (Neor), oleandomycin (Oler), gentamicin (Genr), and novobiocin (Novr). Transduction experiments separated antibiotic resistance markers into two distinct groups: transducible markers, including Fusr, Bacr, Ksg+, Spcr, Eryr, Sprr, Rifr, Stlr, and Tstr (Bacr, Ksgr, Spcr, and Stlr refer to resistance to bacitracin, kasugamycin, spectinomycin, and streptolydigan, respectively), and nontransducible markers, including Grcr, Ebrr, Kanr, Neor, Oler, Genr, and Novr. By means of two- and three-point crosses, transducible markers (excluding tst) were located in three separate linkage groups. spr was found to be linked with ery and spc in the order spc-ery-spr, whereas in a separate linkage group the order was determined to be str-fus-bac-ksg. The third linkage group contained the rif and stl markers.

Bioautography: a general method for the visualization of isozymes

A new method has been developed for visualization of isozymes which are difficult or impossible to detect with standard histochemical or autoradiographic methods. The principle of this method, bioautography, is the use of a microbial reagent to locate an enzyme after gel electrophoresis. When bioautography was compared to other staining procedures, the bioautographic method yielded identical results to those observed by the histochemical method for lactate dehydrogenase (LDH) or by the autoradiographic method for the adenine phosphoribosyltransferase (APRT). Using the bioautographic method, stains for enzymes which could not be visualized by any other procedure have been developed: argininosuccinate lyase and branched-chain aminotransferase. By employing appropriately genetically marked bacterial strains, it should be possible to develop new isozyme stains for a large number of unstudied isozymes.

Regulation of fatty acid synthesis during the cessation of phospholipid biosynthesis in Escherichia coli

In 1975, Cronan et al. (J. Biol. Chem. 250:5835-5840) reported that free fatty acids accumulated during glycerol starvation of an Escherichia coli glycerol auxotroph. On the basis of labeling experiments showing significant incorporation of [14C]acetate into the fatty acid fraction of glycerol-starved cells, these authors concluded that fatty acid synthesis proceeded normally in the absence of phospholipid synthesis. Since these findings might have been due to an increase in the intracellular specific activity of the [1-14C]acetyl coenzyme A pool of the glycerol-starved cells, we reexamined the effect of glycerol starvation on fatty acid synthesis. We found that (i) the incorporation of 3H2O and/or [2,3-14C]succinate into the fatty acid fraction of glycerol auxotrophs is severely reduced during starvation, (ii) the incorporation of [1-14C]acetate into the lipid fraction of an acetate-requiring glycerol auxotroph is inhibited by 95% during glycerol starvation, and (iii) the accumulation of fatty acids, as measured by microtitration, in glycerol-starved cells is less than 10% that of glycerol-supplemented cells. These results indicate that fatty acid synthesis is inhibited in the absence of phospholipid synthesis of E. coli.

On the structure of the deo operon of Escherichia coli

A characterization of a specialized transducing lambda phage for the deo operon (lambdaddeo), and some composite colE1-deo plasmids is given in this paper. This includes localization of the RSmaI, RHind/III, RBamI, and REcoRI sensitive sites. The deo genes have been localized by construction of composite colE1-deo plasmids. Using the DNA fragments, obtained by digestion with REcoRI and RHindIII, respectively, as templates in an in vitro protein synthesizing system, it has been possible to give the direction of transcription and the exact location of the deo genes, relative to the endonuclease sites. Furthermore, the cytO,P and deoO,P regions have been mapped relative to the structural genes. Supercoiled co1E1-deo DNA has been used as template in the in vitro system; this DNA gives essentially the same results as the endonuclease-fragmented DNA. The use of the different types of templates is discussed.

Terminus region of the chromosome in Escherichia coli inhibits replication forks

Induction of prophage P2sig5 at 42 degrees caused replication of the bacterial chromosome in a dnaA mutant of Escherichia coli. The P2sig5 is integrated in this strain near the metG locus, which is at min 47 on the genetic map. The regions of the chromosome replicated after prophage induction have been determined by means of DNA-DNA hybridization with various DNAs obtained from Proteus mirabilis/E. coli F' merogenotes and from lambda specialized transducing phage. The replication was initiated at the prophage site and was bidirectional. Most of the replication occurred in a counterclockwise direction on the genetic map, and the replication quickly proceeded to the aroD locus (min 37). The replication forks were retarded between aroD and rac (min 31) loci, although the rac locus was finally replicated. A more severe inhibition of replication occurred between the rac and trp (min 27) loci. It is proposed that the replication terminus is near the rac locus and that the terminus inhibits replication forks.

Restriction endonuclease mapping and mutagenesis of the F sex factor replication region

The plasmids pSC138 and pML31 each contain the EcoRI-generated f5 replicator fragment of the conjugative plasmid F in addition to an EcoRI fragment encoding antibiotic resistance: ampicillin resistance derived from Staphylococcus aureus in pSC138 and kanamycin resistance from Escherichia coli in pML31. We have mapped one HindIII and two BamHI restriction sites in the f5 region of these plasmids and one HindIII site in the antibiotic resistance region of each plasmid. The HindIII site in the Km region of pML31 occurs in the kan gene whereas the HindIII site in the Ap region of pSC138 appears to occur in an area important for the regulation of beta-lactamase production. By means of in vitro recombinant DNA manipulation of plasmids pML31 and pSC138, we have shown that approximately 1.9 X 10(6) daltons of the 6.0 X 10(6) dalton f5 fragment can be deleted without disrupting plasmid stability. In addition, we have used these same techniques to isolate a novel F-controlled Ap plasmid cloning vehicle which contains a single restriction site for each of the enzymes EcoRI, HindIII, and BamHI. This cloning vehicle has been linked via either its EcoRI or HindIII site to a ColE1 plasmid replicon to yield stable recombinants.

Mapping of the aspartate and aromatic amino acid aminotransferase genes tyrB and aspC

Co-transduction experiments using P1-mediated reciprocal and three-factor crosses have been used to map two mutations affecting the aspartate and aromatic amino acid aminotransferases of Escherichia coli. tyrB-, which inactivates the tyrosine-repressible component of these activities is co-transducible with metA and malB; the gene order is metA-malB-tyrB. aspC-, which inactivates the nonrepressible aminotransferase with high activity for aspartate, maps between and is co-transducible with serC and pyrD.

Escherichia coli mutants deficient in the aspartate and aromatic amino acid aminotransferases

Two new mutations are described which, together, eliminate essentially all the aminotransferase activity required for de novo biosynthesis of tyrosine, phenylalanine, and aspartic acid in a K-12 strain of Escherichia coli. One mutation, designated tyrB, lies at about 80 min on the E. coli map and inactivates the "tyrosine-repressible" tyrosine/phenylalanine aminotransferase. The second mutation, aspC, maps at about 20 min and inactivates a nonrespressible aspartate aminotransferase that also has activity on the aromatic amino acids. In ilvE- strains, which lack the branched-chain amino acid aminotransferase, the presence of either the tyrosine-repressible aminotransferase or the aspartate aminotransferase is sufficient for growth in the absence of exogenous tyrosine, phenylalanine, or aspartate; the tyrosine-repressible enzyme is also active in leucine biosynthesis. The ilvE gene product alone can reverse a phenylalanine requirement. Biochemical studies on extracts of strains carrying combinations of these aminotransferase mutations confirm the existence of two distinct enzymes with overlapping specificities for the alpha-keto acid analogues of tyrosine, phenylalanine, and aspartate. These enzymes can be distinguished by electrophoretic mobilities, by kinetic parameters using various substrates, and by a difference in tyrosine repressibility. In extracts of an ilvE- tyrB- aspC- triple mutant, no aminotransferase activity for the alpha-keto acids of tyrosine, phenylalanine, or aspartate could be detected.

Physiological modification of alkylating agent induced mutagenesis. II. Influence of the numbers of chromosome replicating forks and gene copies on the frequency of mutations induced in Escherichia coli

The frequency of reversions induced in Escherichia coli K-12 trpA58 by any of five different monofunctional alkylating agents increased as the growth rate of the organism was raised prior to mutagen treatment. The increase in mutation frequency did not correlate with growth rate-dependent changes in cell area or total cellular protein and DNA. After treatment of cells with N-methyl-N-nitrosourea (MNUA), no growth rate-dependent change was observed in the total DNA alkylation or percentage of O6-methylguanine present in the DNA extracted. The frequency of reversions induced by one mutagen, methyl methanesulphonate (MMS), increased in proportion to the average number of trpA gene copies per cell, whereas the frequency of reversions induced by the other compounds was dependent on the average number of chromosome replicating forks per cell. This difference was attributed to the different ratios of DNA base alkylation products observed, formed after treatment with MMS, an SN2-type reagent, or after treatment with the SN1-type reagents ethyl methanesulphonate (EMS), N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), MNUA and N-ethyl-N-nitrosourea (ENUA). Possible reasons for the dependence of mutation frequency on the number of replicating forks per cell are discussed.

Mechanism of conjugation and recombination in bacteria XVI: single-stranded regions in recipient deoxyribonucleic acid during conjugation in Escherichia coli K-12

The formation of mating pairs between F- and Hfr cells resulted in increased sensitivity of recipient deoxyribonucleic acid (DNA) to single-strand-specific S1 nuclease, from 3.6% to 23.5% after 30 min conjugation. A comparable amount of single strand regions in the DNA of mated wild type and recA mutant cells was detected. 10 min of conjugation resulted in almost the same amount of single-strand recipient DNA as 30 min of continuous transfer of donor DNA. Also the transfer of plasmid DNA from F+ recA strain led to the occurrence of single-strand recipient DNA. In similar experiments with Hfr tra mutant no such effect was observed. We conclude that alterations in the sechases of conjugation associated with the formation of mating pairs and/or initiation of transfer donor DNA.

Genetics of colicin E susceptibility in citrobacter freundii

The insensitivity of Citrobacter freundii to the E colicins is based on tolerance to colicin E1 and resistance to colicins E2 and E3. Spontaneous colicin A resistant mutants of C. freundii also lost their colicin E1 receptor function. Sensitivity to colicin E1 can be induced by F'gal+tol+ plasmids, the tol A+ gene product of which is responsible for this effect. Receptor function for colicins E2 and E3 is induced by the E. coli F'14 bfe+ plasmid, which is also able to enhance notably the receptor capacity for colicin E1. The bfe+ gene product of E. coli, which is responsible for these phenomena, also restores the receptor function for colicin A and E1 in colicin A resistant mutants of C. freundii. All results show that there is a remarkable difference between the E. coli bfe+ gene product and the bfe+ gene product of C. freundii and also between the tol A+ gene products of these strains. The sensitivity to phage BF23 parallels the sensitivity to colicins E2 and E3 and is also induced by the F'14 bfe+ plasmid.

Interaction between mutations of ribosomes and RNA polymerase: a pair of strA and rif mutants individually temperature-insensitive but temperature-sensitive in combination

A temperature-sensitive lethal mutant of Escherichia coli has been constructed by combining two temperature-insensitive mutations: a rif180 mutation that modifies RNA polymerase (RNA nucleotidyltransferase; nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6) and a strA24 mutation that modifies the ribosomal protein S12. The temperature sensitivity is a property of the combination of these two particular alleles; replacement of either of the alleles relieves the temperature sensitivity. An isogenic strain containing a different strA mutation (i.e., rif180 strA11) is not temperature sensitive. Evidently ribosomes modified by the particular strA24 polymerase altered by the rif180 mutation, which suggests that in vivo there may exist some interaction between structures of ribosomes and the RNA polymerase.

[Gratuitous induction of beta-glucuronidase of Escherichia coli K 12 and the double repression mechanism]

Using natural inducers of beta-glucuronidase, methyl-glucuronide and fructuronate, under gratuitous conditions (without metabolic conversion of these two compounds), we corroborate the fact that both molecules are required simultaneously in order to derepress the enzyme synthesis to a maximum level. Structurally related analogs of the natural inducers, thiophenyl-glucuronide and mannonic amide respectively, were assayed in the wild type and suitable mutant strains of E. coli. The results are in agreement with the model where the dual negative regulation of the enzyme synthesis is exerted by two regulatory genes uidR and uxuR. The concerted action of mannonic amide and thiophenyl-glucuronide, which alone fail to induce significantly beta-glucuronidase synthesis, reveals that a cooperative effect of the two repressor molecules responsible for the complete blocking of the enzyme synthesis is occuring.

Plasmid replication and Hfr formation in strains of Escherichia coli carrying seg mutations

Several conditional-lethal mutantions that do not permit the replication of F-factors of Escherichia coli K-12 are located at a site called seg. This gene is located on the E. coli chromosome between ser B and thr. It is unrelated to other known genes involved in DNA replication. Strains carrying seg mutations were unable to replicate F'-lac+, several F'-gal+s, F'-his+ and bacteriophage gamma at 42 degrees. However, neither phage T4, ColE1, nor any of the R factors tested were prevented from replicating at 42 degrees C. When the kinetics of the loss of F-primes is studied in seg strains, it is found that the rate of curing depends on the size of the plasmid, larger F factors curing faster than smaller ones, and that Hfrs are formed at high frequencies. The Hfrs showed both F-genote enlargement and normal transfer of chromosomal markers. The F-genotes are unstable and segregate chromosomal markers at high frequencies. Some orthodox Hfrs were examined, and two that were known to revert to the F+ condition relatively frequently were found to generate enlarged F-genotes on mating, whereas two strains that were very stable with respect to the F+ state did not show F-genote formation. F-genote formation from seg Hfr stains is dependent on a functional recA gene, as F-genote formation was not seen with a seg-2, recA-1 Hfr. This is in contrast to F-genote enlargement shown by both orthodox Hfrs and an Hfr strain constructed by integration of a temperature-sensitive F'-gal+, whose F-genote enlargement is Rec-independent. Thus there may be more than one mechanism for the formation of enlarged F-genotes.

Interaction of cytoplasmic membrane and ribosomes in Escherichia coli: spectinomycin-induced disappearance of membrane protein I-19

Incubation of Escherichia coli with spectinomycin caused the disappearance of a major protein from the cytoplasmic membrane. This protein, called "I-19", was not a ribosomal protein. Its disappearance was not a result of the direct action of spectinomycin on the cytoplasmic membrane, but a result of its action on ribosomes. The disappearance was specifically induced by spectinomycin, and other antibiotics such as neomycin, erythromycin, and chloramphenicol had no effect. Although growth was not required for spectinomycin-induced disappearance of protein I-19 from the cytoplasmic membrane, the disappearance was not observed under conditions where protein synthesis was inhibited completely either by the addition of chloramphenicol or by cooling in ice. It is suggested that at least some ribosomes interact with the cytoplasmic membrane and that a modification of the mode of interaction through the action of spectinomycin on ribosomes caused the deletion of membrane protein I-19.

L-Glyceraldehude 3-phosphate, a bactericidal agent

At a concentration of 2.5 mM, dl-glyceraldehyde 3-phosphate has a bactericidal effect upon Escherichia coli. The glycerol 3-phosphate transport system is required for the entry of the biologically active l-enantiomer. l-Glyceraldehyde must be phosphorylated by the cell to exert its full effect upon growth. The addition of dl-glyceraldehyde 3-phosphate to a culture of E. coli caused no preferential inhibition of the accumulation of deoxyribonucleic acid, ribonucleic acid, or phosphoglycerides, although protein accumulation was less affected. Studies with mutant strains ruled out catabolic glycerol 3-phosphate dehydrogenase, anabolic nicotinamide adenine dinucleotide (phosphate):sn-glycerol 3-phosphate oxidoreductase, and fructose 1,6-diphosphate aldolase as the primary sites of action. l-Glyceraldehyde 3-phosphate is a competitive inhibitor of sn-glycerol 3-phosphate in the reactions catalyzed by acyl coenzyme A:sn-glycerol 3-phosphate acyltransferase (K(i) of 1.8 mM) and cytidine 5'-diphosphate-diglyceride:sn-glycerol 3-phosphate phosphatidyltransferase (K(i) of 2.7 mM). A K(m) mutant for the former enzyme was susceptible to the inhibitor. l-Glyceraldehyde 3-phosphate does not affect acyl coenzyme A:lysophosphatidate acyltransferase activity. In vivo, phosphatidylethanolamine and phosphatidylglycerol accumulation are inhibited to the same extent by the addition of dl-glyceraldehyde 3-phosphate to a culture of E. coli.

Thymidine-requiring mutants of Salmonella typhimurium that are defective in deoxyuridine 5'-phosphate synthesis

In a Salmonella typhimurium strain made diploid for the thy region by introduction of the Escherichia coli episome, F'15, mutants resistant to trimethoprim in the presence of thymidine were selected. One was shown to be defective in deoxyuridine 5'-phosphate (dUMP) synthesis; it requires deoxyuridine or thymidine for growth and is sensitive to trimethoprim in the presence of deoxyuridine. Genetic studies showed that the mutant is mutated in two genes, dcd and dum, located at 70 and 18 min, respectively, on the Salmonella linkage map. The dcd gene cotransduces 95% with udk, the structural gene for uridine kinase. Both mutations are necessary to create a deoxyuridine requirement, providing evidence for the existence of two independent pathways for dUMP synthesis. Pool studies showed that a dum mutation by itself causes a small decrease in the deoxythymidine 5'-triphosphate (dTTP) pool of the cells, whereas a dcd mutation results in a much more marked decrease. The double mutant dcd dum, when incubated in the absence of deoxyuridine, contains barely detectable levels of dTTP. Enzyme analysis revealed that dcd encodes deoxycytidine 5'-triphosphate deaminase. The gene product of the dum gene has not yet been identified; it does not encode either subunit of ribonucleoside diphosphate reductase or deoxyuridine 5'-triphosphate pyrophosphatase. Mutants deleted for the dcd-udk region of the S. typhimurium chromosome were isolated.

Genetic studies of the ribosomal proteins in Escherichia coli. X. Mapping of the ribosomal proteins, L21 and S15, by intergeneric mating experiments between Serratia marcescens and Escherichia coli K12

Episomes of E. coli, which cover argG but not the str region, were transferred to Serratia marcescens. Ribosomal proteins from these hybrid strains were analyzed with phospho-cellulose or carboxy-methyl-cellulose column chromatography. Two E. coli ribosomal proteins, L21 and S15, could be detected in the ribosome from the hybrid strains in addition to the ribosomal proteins of S. marcescens.