Isolation of transducing bacteriophages for the histidine and isoleucine-valine operons in Escherichia coli K-12

Cloning and expression of the distal portion of the histidine operon of Escherichia coli K-12

The operator-distal genes hisBHAFI(E) of the Escherichia coli K-12 histidine operon were mapped on a DNA fragment 4,500 base pairs long. This fragment, originally present in a lambda transducing phage, was cloned in the vector plasmid pBR313. A restriction map was determined, allowing identification of the orientation of the genes in the fragment. The cloned genes were expressed in appropriate hosts, independent of the orientation of the DNA fragment, as shown by transformation tests and by enzyme assays of one of the gene products, hisB, histidinol phosphatase. An internal transcription initiation site was identified by isolation of the cellular RNA, hybridization to specific DNA probes, and mapping by S1 nuclease.

Nucleotide sequence of ilvGEDA operon attenuator region of Escherichia coli

The nucleotide sequence of the DNA thought to contain the control region for the ilvGEDA operon in Escherichia coli has been determined by the Maxam-Gilbert procedure. The sequence includes a region that, upon transcription, would yield a leader transcript specifying a peptide 32 residues long. This putative peptide would contain four leucine, five isoleucine, and six valine residues. A model is proposed that correlates the multivalent control of the ilvGEDA operon with the extent to which this leader transcript is translated. In vitro transcription experiments yielded a transcript of about 183 nucelotides, compatible with the predictions of the model.

Structural and physiological studies of the Escherichia coli histidine operon inserted into plasmid vectors

A fragment of deoxyribonucleic acid 5,300 base paris long and containing the promoter-proximal portion of the histidine operon of Escherichia coli K-12, has been cloned in plasmid pBR313 (plasmids pCB2 and pCB3). Restriction mapping, partial nucleotide sequencing, and studies on functional expression in vivo and on protein synthesis in minicells have shown that the fragment contains the regulatory region of the operon, the hisG, hisD genes, and part of the hisC gene. Another plasmid (pCB5) contained the hisG gene and part of the hisD gene. Expression of the hisG gene in the latter plasmid was under control of the tetracycline promoter of the pBR313 plasmid. The in vivo expression of the two groups of plasmids described above, as well as their effect on the expression of the histidine genes not carried by the plasmids but present on the host chromosome, has been studied. The presence of multiple copies of pCB2 or pCB3, but not of pCB5, prevented derepression of the chromosomal histidine operon. Possible interpretations of this phenomenon are discussed.

Physical characterization of ilv-lac fusions

Electron microscopic heteroduplex analysis and comparative restriction digests have been used to characterize lambda p123(209), the complementary pair of phages used in the Casadaban technique of gene fusion. Derivatives of lambda 1(209) constructed to carry fusions of the lac genes to the control regions of the ilvC and ilvEDA operons were also analyzed. These physical maps have provided confirmation of the genetic models for these constructions and physical specifications important in interpreting the behavior of these ilv-lac fusions.

Threonine deaminase: autogenous regulator of the ilv genes in Escherichia coli K-12

In this paper we analyze the effect of mutations in three genes, ilvO, ilvA and rho, on the expression of the ilvEJGDA gene cluster of Escherichia coli K-12. The ilvO603 mutation causes a cis-dominant derepression of the ilvEJGDA genes. In particular, the ilvG gene, not expressed in the wild type, becomes expressed in the ilvO603 strain. We have introduced ilvA mutations (ilvA454 or ilvA628) in the ilvO603 strain and we show that ilvG expression requires the presence in cis of both an ilvO603 mutation and of an ilvA+ allele. The ilvG gene is not expressed when in trans is present an ilvO+, ilvA+ genotype. However, it is expressed when the chromosome in trans is ilvO603, ilvA+ (ilvG-). We suggest that ilvO603 is part of ilvA, the structural gene for threonine deaminase, and that threonine deaminase from the ilvO603 mutant binds the ilvO603 site and not the ilvO+ site. Therefore, the ilvA gene product would be a cis-acting protein. Mutations in the rho gene cause derepression of the ilvEJGDA gene cluster without a concomitant expression of the ilvG gene. We show that introduction of either a rho-218 or a rho-115 mutation into the ilvO603, ilvA454 double mutant causes expression of ilvG. We therefore suggest that the ilvA gene product, threonine deaminase, is involved in termination of transcription as an antagonist of the rho gene product. Introduction of ilvA454 into an ilvO603 strain causes also a decrease in expression of the ilvE, ilvJ and ilvD genes. This effect is maximum in the case of the ilvD gene and we studied it in detail in isogenic strains containing also the rho-218 mutation.

Mutations affecting the formation of acetohydroxy acid synthase II in Escherichia coli K-12

Genetic mapping experiments have established that two recently isolated valine-resistant mutants of the K-12 strain of Escherichia coli have lesions lying between ilvE and rbs. These lesions allowed expression of the ilvG gene, specifying the valine-insensitive acetohydroxy acid synthase (synthase II) and an increased expression of the ilvEDA operon. In this respect, they resembled an earlier described ilvO lesion that was reported to lie between ilvA and ilvC. All three lesions were cis-dominant in cis-trans tests. Reexamination of the earlier studied ilvO lesion revealed that it, too, lies between ilvE and rbs. Valine-sensitive derivatives with lesions presumed to be in ilvG were selected from each of the valine-resistant strains. In two of the valine-resistant strains, the ilvG mutations were on the rbs side of ilvO, indicating a gene order rbs-ilvG-ilvO-ilvE-ilvD-ilvA-ilvC. In one of the recently isolated valine-resistant stocks, however, the apparent ilvG mutation was found to be between ilvE and the aline resistance marker. This finding suggests that either ilvO and ilvG mutations are interspersed or there is another locus, ilvR, that behaves phenotypically like ilvO and which lies between ilvG and rbs.

Effects of the rex gene of phage lambda on lysogeny

Mutations in therexgene of phage λ affect lysogeny. λrex−phages have an increased probability of forming abortive lysogens instead of stable lysogens. In addition, established lysogens produce elevated levels of cured cells during anaerobic but not aerobic growth. It is suggested that the function of therexgene is related to excision or repressor function.

Dual autogenous regulatory role of threonine deaminase in Escherichia coli K-12

We describe the regulatory properties of two strains carrying either the ilvA624 or the ilvA625 mutations, located in the structural gene for threonine deaminase. Crude extracts of both these strains possess a threonine deaminase activity migrating on polyacrylamide gels, differently from the wild type enzyme. Growth studies demonstrate that these mutations do not cause a limitation of isoleucine biosynthesis, suggesting normal catalytic activity of deaminase. A regulatory consequence of the ilvA624 allele is a derepression of the isoleucine-valine biosynthetic enzymes, which is recessive to an ilvA+ allele. The ilvA625 mutation causes a derepression which is dominant in an ilvA625/ILVA+ diploid. We interpret these data assuming that threonine deaminase, previously shown to be an autogenous regulator of the ilv genes, lacks a repressor function in the ilvA624 mutant, while in the ilvA625 mutant it is a better activator than wild type threonine deaminase. The data are discussed in terms of a model requiring that threonine deaminase, or a precursor of it, is in equilibrium between two forms, one being an activator of gene expression and the other being a repressor.

Physical organization of the ilvEDAC genes of Escherichia coli strain K-12

We have determined the physical location of the ilvEDAC genes on the restriction cleavage map of the ilv region of Escherichia coli K-12 by two methods: (i) heteroduplex and endonuclease cleavage analysis of hybrid phages carrying genetically defined parts of the ilv cluster and (ii) complementation analysis and enzyme assays to determine ilv gene expression from hybrid plasmids containing DNA restriction fragments of the transducing phage lambdah80dilv. The ilvEDA and ilvC operons occupy 2.4 and 0.9 megadalton sequences of DNA, respectively, and are separated by a region of 0.6-0.75 megadalton. The ilvD region, specifying dihydroxy acid dehydrase, has a maximum coding capacity of about 55,000 daltons of polypeptide. Our results confirm that ilvC is transcribed clockwise on the E. coli K-12 map, in the same direction as ilaEDA. A secondary lambda attachment site within ilvC has been located on a small (0.45 megadalton) EcoRI fragment. Our results are compared to other physical studies of ilv DNA.

In vitro synthesis of beta-galactosidase with ilv-lac fusion deoxyribonucleic acid as template

An in vitro protein-synthesizing system has been developed to study the mechanism of induction of ilvC gene in Escherichia coli strain K-12. Deoxyribonucleic acid (DNA) from a lambda phage carrying an ilvC-lac fusion was employed as a template for the in vitro synthesis of beta-galactosidase under the control of the ilvC promoter. The use of this template allowed an investigation of the components required for induction of the ilvC gene and the kinetics of the induction. The in vitro synthesis of beta-galactosidase under the control of the ilvC promoter was found to be DNA, acetohydroxy acid, and guanosine-3'-diphosphate-5'-diphosphate dependent, and sensitive to rifampin, actinomycin D, and chloramphenicol. Uncoupling experiments indicate that the inducer, acetohydroxybutyrate, acts at the transcriptional level. Investigation of a proposed noninducible ilvC regulatory mutant has shown normal induction in vitro. It was also observed that an intact ilvA gene is not required for the induction of the ilvC gene.

Biochemical and regulatory properties of Escherichia coli K-12 hisT mutants

Escherichia coli K-12 hisT mutants were isolated, and their properties were studied. These mutants are derepressed for the histidine operon, map close to the purF locus at about 49.5 min on the E. coli linkage map, and lack pseudouridylate synthetase activity. The defect in this enzyme leads to the absence of pseudouridines in the anticodon loop of several transfer ribonucleic acid species, as evidenced by the altered elution profile on reversed-phase chromatography and resistance to amino acid analogues. Finally, the hisT mutants studied have a reduced growth rate that appears to be linked to hisT, although it is not known whether it is due to the same mutation. The normal generation time can be restored by supplementing the medium with adenine, uracil, and isoleucine.

Detection of messenger RNA from the isoleucine--valine operons of Salmonella typhimurium by heterologous DNA-RNA hybridization: involvement of transfer RNA in transcriptional repression

A hybridization assay using Escherichia coli K-12 DNA isolated from the specialized transducing bacteriophage gammaCI857St68h80 dilv was used to examine the rate of synthesis of the messenger RNA's (mRNA) derived from the isoleucine-valine (ilv) gene cluster of Salmonella typhimurium. In all cases examined, changes in ilv enzyme levels could be correlated with changes in the rate of synthesis of ilv mRNA. Several well characterized regulatory mutants of S. typhimurium had rates of synthesis of ilv mRNA 3 to 8-fold higher than the repressed wild-type strain. The increased rates of ilv mRNA synthesis found in a hisT strain as well as in isoleucyl-and leucyl-tRNA SYNTHETASE MUTANTS, STRONGLY SUGGESTS A ROLE FOR BRANCHED-CHAIN AMINOACYL-TRNA's in transcriptional control.

Fusion of two F-prime factors in Escherichia coli studied by electron microscope heteroduplex analysis

A fused F prime factor was obtained from a mating of a recA donor carrying an F'- factor containing the genes metBJF, ppc and argECBH (KLF5) with a recA recipient carrying an F' factor containing att80, trp and lac (f155). lysogenization of this fused F-prime factor with gammacI857hphi80 phage followed by thermoinduction produced the transducing phages phi80 dmetBJF and phi80 dppcargECBH. This kind of fusion provides a general procedure for the construction of transducing phages carrying genes from different regions of the E. coli genome. To understand the mechanism of this fusion, the parental F prime factors (F155 and KLF5) were analyzed by the electron microscope heteroduplex technique. F155 has a length of 176 +/- 3 kilobases including two substitutions. The F sequence 0 F-2.8 F has been substituted by 53 kb of chromosomal DNA including the lac operon and the F sequences 8.5 F-16.3 F has been substituted by 27 kb of a chromosome sequence including att80 and the trp operon KLF5 contains 221 +/- 4 kilobases of DNA (molecular weight, 148 megadaltons). It contains complete F and the segment of the E. coli chromosome from polA to rif. The F sequence 2.8 F-8.5 F known to be involved in F specific recombination in recA+ and recA backgrounds occurs twice on KLF5, once at each of the junctions of F DNA with chromosomal DNA. The population of closed circular plasmid molecules extracted from KLF5-containing strains is heterogeneous. It is proposed that this heterogeneity is due to intramolecular recombination events occurring in KLF5 between the duplicated 2.8 F-8.5 F sequences. Such recombination can account for the genetic instability of KLF5 observed in both recA+ and recA hosts. The F sequence 2.8 F-8.5 (also called gammadelta) is one of the characterized integration sequences on F. A model for the fusion of the parental F prime factors is proposed in which recombination between gammadelta sequences brings att80 close to the metBJF genes. This is followed by a deletion of an F' lac factor. The resulting fused F' factor still carries two gammadelta sequences and is therefore expected to be unstable. The closed circular molecules isolated from the fused F' containing strains show two different sizes of molecules. Genetic and physical analyses of these molecules are in agreement with the predicted instability of the fused F' factor and the existance of the gammadelta sequence in the phi80 dmet phages isolated from fused F' and previously analyzed by the electron microscope heteroduplex technique.

Genetic characterization of a phi80 transducing bacteriophage carrying the histidine operon of Salmonella typhimurium

A phi 80 transducing phage, phi 80imm lambdadhis, carrying the Salmonella his-gnd region, was characterized by immunity studies, tonB deletion analysis, and marker rescue analysis. Phi 80imm lambdadhis retains the phage immunity region of the phi 80-lambda hybrid phage from which it was derived. Bacterial genes replace most late phage genes. Deletion analysis shows the prophage gene order to be immlambda-his-gnd and indicates the orientation of the his operon to be hisOGDCBHAFIE-gnd. The structure of phi 80imm lambdadhis is remarkably similar to two independently isolated phi 80 phages that carry the his-gnd region of Escherichia coli and that, like phi80imm lambdahis, were derived by directed gene transposition to the tonB locus. A derivative of phi 80imm lambdadhis that is phi 80 immune is also reported.

Expression of a valine-resistant acetolactate synthase activity mediated by the ilv O and ilv G genes of Escherichia coli K-12

A strain carrying the ilv0603 mutation has been isolated in E. coli K-12 and its characteristics were found to be very similar to those previously reported by Ramakrishnan and Adelberg (1965a) for other ilv0 mutants. The strain carrying the ilv0603 mutation is resistant to valine inhibition (Valr) and we show that this resistance depends on the expression of a newly recognized gene, ilvG, which is located at min 75, between ilvE and ilvD on the E. coli K-12 map. The ilvG gene causes the expression of a Valr acetolactate synthase, which is detectable only when the ilv0603 mutation is also present in cis on the same chromosome. Under these conditions the Valr acetolactate synthase activity is eluted, on a hydroxylapatite column, at an ionic strength slightly lower than that required for elution of the remaining acetolactate synthase activity (sensitive to valine inhibition). The Valr peak is missing in a strain carrying an ilvG (amber) mutation.

Significance of autogenously regulated and constitutive synthesis of regulatory proteins in repressible biosynthetic systems

The functional implications of the different modes of regulation have been examined systematically. The results lead to certain predictions. The regulatory protein in repressor-controlled systems is constitutively synthesised. In activator-controlled systems synthesis of the regulatory protein is autogenously regulated. There is favourable agreement between these predictions and published experimental evidence.

Transcriptional control of the isoleucine-valine messenger RNA's in E. coli K-12

Hybridization of messenger ribonucleic acid (mRNA) isolated from Escherichia Coli K-12 to deoxyribonucleic acid (DNA) from lambdaCI857st68h80dilv was used to detect isoleucine-valine (ilv) specific mRNA. A number of strains partially constitutive for the isoleucine-valine enzymes had levels of ilv mRNA 2 to 3-fold higher than the parent strain. Starvation for any of the branched-chain amino acids resulted in a 20 to 23-fold increase in ilv mRNA as compared to repressed levels. These differences were not due to altered growth rates or to changes in the stability of ilv mRNA. These data indicate that regulation of the isoleucine-valine enzymes by multivalent repression occurs mainly at the level of transcription. Kinetics of elongation of ilv mRNA after repression are consistent with the assumption that the mechanism of multivalent repression involves the prevention of further initiations by RNA polymerase.

Deoxyribonucleic acid-directed in vitro synthesis of ilv-specific messenger ribonucleic acid by extracts of Escherichia coli K-12

The synthesis of ilv-specific messenger ribonucleic acid (mRNA) by extracts of Escherichia coli K-12 has been demonstrated in a deoxyribonucleic acid (DNA)-dependent, coupled transcription-translation system. ilv-Specific mRNA was determined by hybridization either to double-stranded lambdacI857St68h80dilv DNA (lambdah80dilv DNA) immobilized on nitrocellulose filters or to its separate l and r strands in liquid. During conditions optimal for protein synthesis, slightly more than 6% of the total [(3)H]RNA synthesized by S-30 extracts of the threonine deaminase-negative strain CU5136 was ilv-specific. Of this RNA, nearly 30% was complementary to the l (correct) strand. Total ilv-specific mRNA synthesis in vitro was not affected by omission of valine or all 20 amino acids from the reaction mixture. Hybridization of ilv-specific mRNA made in vitro to the l strand of lambdah80dilv DNA was effectively reduced in the presence of unlabeled RNA extracted from an ilv derepressed strain but not from an ilv deletion strain. In a purified transcription system, employing commercial RNA polymerase, twofold more ilv-specific mRNA was synthesized than in the coupled system, but this increase was entirely due to greater transcription of the r (incorrect) strand. An S-30 extract prepared from a strain isogenic to strain CU5136 but derepressed for ilvA gene expression synthesized twofold more ilv-specific mRNA in the coupled system. The significance of these findings is discussed.

Isoleucine and valine metabolism in Escherichia coli K-12: detection and measurement of ilv-specific messenger ribonucleic acid

Ribonucleic acid-deoxyribonucleic acid (RNA-DNA) hybridization was employed for the determination of messenger RNA transcribed from the ilv gene cluster of Escherichia coli K-12. Strains with derepressed levels of the isoleucine and valine biosynthetic enzymes owing to linked or unlinked genetic lesions were found to exhibit ilv messenger RNA levels from 1.5- to 4-fold higher than did their isogenic parents. When grown under conditions that specifically repressed the synthesis of isoleucine- and valine-forming enzymes, most strains exhibited drastically reduced ilv messenger RNA levels. Hybridization performed with the separated strands of ilv DNA showed that all the ilv genes are transcribed from the same strand, the "l strand" of lambdaphi80CI857St68dilv DNA. Sucrose gradient analyses of RNA extracted from cells starved for isoleucine, valine, or leucine resulted in the detection of at least two distinct types of ilv messenger RNA.

Complementation between different mutations in the ilvA gene of Escherichia coli K-12

An ilvA mutation carried by a ø80i(lambda)dilv transducing phage complemented some ilvA mutations and did not complement others. Complementation was accompanied by appearance of threonine deaminase activity in vivo. These results divided the ilvA mutations into two sets which formerly appeared to define two cistrons.

Autogenous regulation of gene expression

A new term, autogenous regulation, is used to describe a phenomenon that is not a new discovery but rather is newly appreciated as a mechanism common to a number of systems in both prokaryotic and eukaryotic organisms. In this mechanism the product of a structural gene regulates expression of the operon in which that structural gene resides. In many (perhaps all) cases, the regulatory gene product has several functions, since it may act not only as a regulatory protein but also as an enzyme, structural protein, or antibody, for example. In a few cases, this protein is the multimeric allosteric enzyme that catalyzes the first step of a metabolic pathway, gearing together the two most important mechanisms for controlling the biosynthesis of metabolites in bacterial cells-feedback inhibition and repression. Autogenous regulation may provide a mechanism for amplification of gene expression (84); for severe and prolonged inactivation of gene expression (85); for buffering the response of structural genes to changes in the environment (45, 52); and for maintaining a constant intracellular concentration of a protein, independent of cell size or growth rate (86). Thus, autogenous regulation provides the cell with means for accomplishing a number of different regulatory tasks, each suited to better satisfying the needs of the organism for its survival.

Isolation of specialized transducing bacteriophages for gluconate 6-phosphate dehydrogenase (gnd) of Escherichia coli

Specialized transducing phages for gluconate 6-phosphate dehydrogenase (gnd), a constitutive enzyme in Escherichia coli, have been isolated using a method previously described for other genes. The gnd-his region, carried on an F' episome, was first transposed to tonB. Rare phages carrying gnd were selected, by transduction, from phi80 lysogens of these strains; one phage also carried his (phi80gndhis). From the transductants, high-frequency transducing lysates were obtained; low multiplicity of infection then yielded defective lysogens. tonB deletion analysis of the phi80dgndhis lysogen shows the order of genes in the prophage to be imm80...hisOGD...gnd; according to a marker rescue experiment most phage late genes have been replaced by bacterial deoxyribonucleic acid. A heat-inducible, lysis-defective lambda-phi80 hybrid derivative of phi80dgndhis has been prepared.

Deletion mapping and orientation of the histidine operon of Escherichia coli on a transducing bacteriophage

The defective prophage phi80ilambdac(I)857dhis has been mapped through both marker rescue and deletion analysis. Deletions have been isolated which put residual his genes close to trp genes. Analysis of these deletions shows that the histidine operon on the prophage is oriented clockwise as on the bacterial chromosome, thus opposite to the orientation of the trp operon. The presence of the his promoter-operator region is inferred by the ability of the prophage-carrying strain to derepress sequentially under conditions in which the histidine concentration is limiting. In addition to his, the gnd gene is also present on the prophage and is located between his and trp operons. The bacterial genes are inserted in the right arm of the prophage and substitute for all of the late function genes, except for the first three. These data indicate that the "sense" strand for transcription of the his operon in vivo must be the "R" strand.

Inhibition of transcription of the histidine operon in vitro by the first enzyme of the histidine pathway

An in vitro system was developed for transcription of the histidine operon of Esherichia coli carried in the genome of a defective varphi80 transducing phage. The messenger RNA (mRNA) of the histidine operon synthesized in the in vitro system was detected by hybridization to single strands of both varphi80 and varphi80dhis DNA, and by competition of this hybridization with unlabeled histidine mRNA that had been synthesized in vivo (RNA extracted from cells in which the histidine operon had been derepressed). Under the conditions used, RNA complementary to the histidine operon was about 15% of the total RNA that was synthesized in vitro from the varphi80dhis DNA template. The RNA complementary to the histidine operon was synthesized on the "sense" strand (the R strand) of varphi80dhis in the form of a polycistronic message with a sedimentation coefficient (about 38 S) very close to that observed for the histidine mRNA synthesized in vivo. Synthesis of the histidine operon RNA appears to be subject to control in vitro. Addition of the first enzyme of the pathway for histidine biosynthesis blocked transcription of the histidine operon specifically, strongly suggesting that this enzyme acts as a regulatory protein for the histidine operon.