Control of the argECBH cluster in Escherichia coli

Biosynthesis of Arginine and Polyamines

Early investigations on arginine biosynthesis brought to light basic features of metabolic regulation. The most significant advances of the last 10 to 15 years concern the arginine repressor, its structure and mode of action in both E. coli and Salmonella typhimurium, the sequence analysis of all arg structural genes in E. coli and Salmonella typhimurium, the resulting evolutionary inferences, and the dual regulation of the carAB operon. This review provides an overall picture of the pathways, their interconnections, the regulatory circuits involved, and the resulting interferences between arginine and polyamine biosynthesis. Carbamoylphosphate is a precursor common to arginine and the pyrimidines. In both Escherichia coli and Salmonella enterica serovar Typhimurium, it is produced by a single synthetase, carbamoylphosphate synthetase (CPSase), with glutamine as the physiological amino group donor. This situation contrasts with the existence of separate enzymes specific for arginine and pyrimidine biosynthesis in Bacillus subtilis and fungi. Polyamine biosynthesis has been particularly well studied in E. coli, and the cognate genes have been identified in the Salmonella genome as well, including those involved in transport functions. The review summarizes what is known about the enzymes involved in the arginine pathway of E. coli and S. enterica serovar Typhimurium; homologous genes were identified in both organisms, except argF (encoding a supplementary OTCase), which is lacking in Salmonella. Several examples of putative enzyme recruitment (homologous enzymes performing analogous functions) are also presented.

Evolution of arginine biosynthesis in the bacterial domain: novel gene-enzyme relationships from psychrophilic Moritella strains (Vibrionaceae) and evolutionary significance of N-alpha-acetyl ornithinase

In the arginine biosynthetic pathway of the vast majority of prokaryotes, the formation of ornithine is catalyzed by an enzyme transferring the acetyl group of N-alpha-acetylornithine to glutamate (ornithine acetyltransferase [OATase]) (argJ encoded). Only two exceptions had been reported-the Enterobacteriaceae and Myxococcus xanthus (members of the gamma and delta groups of the class Proteobacteria, respectively)-in which ornithine is produced from N-alpha-acetylornithine by a deacylase, acetylornithinase (AOase) (argE encoded). We have investigated the gene-enzyme relationship in the arginine regulons of two psychrophilic Moritella strains belonging to the Vibrionaceae, a family phylogenetically related to the Enterobacteriaceae. Most of the arg genes were found to be clustered in one continuous sequence divergently transcribed in two wings, argE and argCBFGH(A) ["H(A)" indicates that the argininosuccinase gene consists of a part homologous to known argH sequences and of a 3' extension able to complement an Escherichia coli mutant deficient in the argA gene, encoding N-alpha-acetylglutamate synthetase, the first enzyme committed to the pathway]. Phylogenetic evidence suggests that this new clustering pattern arose in an ancestor common to Vibrionaceae and Enterobacteriaceae, where OATase was lost and replaced by a deacylase. The AOase and ornithine carbamoyltransferase of these psychrophilic strains both display distinctly cold-adapted activity profiles, providing the first cold-active examples of such enzymes.

Arginine regulon of Escherichia coli K-12. A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression

The 12 genes which in E. coli K-12 constitute the arginine regulon are organized in nine transcriptional units all of which contain in their 5' non-coding region two 18 bp partially conserved imperfect palindromes (ARG boxes) which are the target sites for binding of the repressor, a hexameric protein. In vitro binding experiments with purified repressor (a gift from W. K. Maas) were performed on the operator sites of four genes, argA, argD, argF, argG, and of two operons, carAb and the bipolar argECBH cluster. A compilation of results obtained by DNase I and hydroxyl radical footprinting clearly indicates that in each case the repressor binds symmetrically to four helical turns covering adjacent pairs of boxes separated by 3 bp, but to one face of the DNA only. Methylation protection experiments bring to light major base contacts with four highly conserved G residues symmetrically distributed in four consecutive major grooves. Symmetrical contacts in the minor groove with A residues have also been identified. Stoichiometry experiments suggest that a single hexameric repressor molecule binds to a pair of adjacent ARG boxes. Although the wild-type operator consists of a pair of adjacent ARG boxes separated by 3 bp (except argR where there are only 2 bp), repressor can bind to a single box but with a greatly reduced affinity. Therefore, adjacent boxes behave co-operatively with respect to the Arg repressor binding, in the sense that the presence of one box largely stimulates the binding of the properly located second box. The optimal distance separating two boxes is 3 bp, but one bp more or less does not abolish this stimulation effect. However, it is completely abolished by the introduction of two or more additional bp unless a full helical turn is introduced. Large variations in the in vivo repression response between individual arginine genes or a wild-type gene and cognate Oc type mutants are not reflected by similar differences in the in vitro binding results where only small differences are observed. The significance of this lack of correlation is discussed.

Regulation and coupling of argECBH mRNA and enzyme synthesis in cell extracts of Escherichia coli

Cell extracts from Escherichia coli were used to study both transcription and coupled translation of the argECBH gene cluster. Argininosuccinase (the argH enzyme) and N-acetylornithinase (the argE enzyme) were synthesized for 90 to 120 min, and hybridizable argECBH mRNA was synthesized for 60 min after the addition of a lambda or phi 80 dargECBH DNA template. L-Arginine (2.5 mM) repressed synthesis by argR+ extracts of argECBH mRNA 2-, to 3-fold, argE enzyme 5- to 8-fold, and argH enzyme 20- to 60-fold. Repression was specific for L-arginine, and argR extracts were insensitive to added L-arginine. The argECBH mRNA made under conditions of restricted protein synthesis had reduced ability to function in the formation of the argE and argH enzymes and was found to be predominantly 6 to 8S in sucrose density gradients. When protein synthesis was allowed, the mRNA formed was functional, and large amounts of 14 to 23S argECBH mRNA appeared on sucrose gradients. An S-100 supernatant freed of ribosomes was capable of producing hybridizable arg mRNA, but significant functional message was only produced when ribosomes were present. When purified RNA polymerase was used, the formation of short 6 to 8S argECBH mRNA was dependent upon added rho protein. The data suggest that rho-dependent sites in the argECBH operon allow early termination of mRNA synthesis when transcription is not coupled to active enzyme synthesis.

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 regulatory region of the divergent argECBH operon in Escherichia coli K-12

The nucleotide sequence of the control region of the divergent argECBH operon has been established in the wild type and in mutants affecting expression of these genes. The argE and argCBH promoters face each other and overlap with an operator region containing two domains which may act as distinct repressor binding sites. A long leader sequence - not involved in attenuation - precedes argCBH. Overlapping of the argCBH promoter and the region involved in ribosome mobilization for argE translation explains the dual effect of some mutations. Mutations causing semi-constitutive expression of argE improve putative promoter sequences within argC. Implications of these results regarding control mechanisms in amino acid biosynthesis and their evolution are discussed.

Promoter mapping and selection of operator mutants by using insertion of bacteriophage Mu in the argECBH divergent operon of Escherichia coli K-12

The analysis of a large number of Arg mutants obtained by inserting phage Mu in the argECBH cluster of genes confirmed the "facing" arrangement proposed earlier for the promoters of argE (argEp) and argCBH (argCBHp) and clarified remaining ambiguities regarding the localization of argEp. Casadaban and Cohen's Mu d lac phages (M. Casadaban and S. N. Cohen, Proc. Natl. Acad. Sci. U.S.A. 76:4530-4533, 1979) were used to construct strains where either an intact or a truncated lacZ gene was fused to argC or argB. Several operator-constitutive mutations could be selected for in such strains; the mutations affected both arms of the cluster, thereby defining one common operator region for both directions of transcription.

Determination of the transcription direction of the exuT gene in Escherichia coli K-12: divergent transcription of the exuT-uxaCA operons

The exuT gene of Escherichia coli, coding for the hexuronate transport system, was fused to lac genes by the use of Mu d(Apr lac) insertions (M. J. Casadaban and S. Cohen, Proc. Natl. Acad. Sci. U.S.A. 76:4530-4533, 1979). The method of chromosome mobilization with F' lac::Mu episomes (J. B. Zeldis, A. I. Bukhari, and D. Zipser, Virology 55:289-294, 1974) made it possible to determine the transcription direction of the exuT gene from the orientation of the Mu d(Apr lac) insertion in the fusion strains. Our results for a exuT-lac fusion strain suggest that the direction of transcription of other single gene operon exuT is clockwise on the standard E. coli map and confirm that the direction of transcription of uxaC is counterclockwise. The two close operons exuT and uxaCA are thus transcribed in opposite directions.

Nucleotide sequence of the argF regulatory region of Escherichia coli K-12

The deoxyribonucleotide sequence has been determined for the regulatory region of the arginine F gene (argF) of Escherichia coli K-12. The location of the argF coding region was deduced by comparison of the DNA sequence to the sequence predicted from the primary structure of the N-terminus of the argF gene product, the subunit of the "F" isoenzyme of ornithine transcarbamylase. Transcription of the argF gene was found to initiate at a position approx. 40 bp preceding the N-terminal codon for OTCase. Comparison of the region surrounding the origin of transcription with a computer-generated "model promoter sequence" revealed structural similarities between the two sequences, in particular, the promoter-associated stretches known as the "Pribnow box" and "minus 35 contact site". Another feature noted for the argF promoter region was its extreme abundance of A : T nucleotide pairs. In the region preceding the start site for argF translation, a sequence was observed to be complementary to the 3' end of the 16S RNA component of the E. coli ribosome. Both the length and the nucleotide sequence of the argF leader region indicate that the argF gene does not contain an attenuator proposed to exist in other operons concerned with amino acid biosynthesis.

Immunological and genetic properties of Escherichia coli K12 argE mutants

CRM+ nonsense mutations, as described for E. coli K12 lacZ, in theory permit determination of the direction of transcription of an isolated gene. In the hope of utilising this approach to confirm that the E gene of the E. coli K12 argECBH cluster is transcribed in the opposite direction from the CBH unit, 30 argE mutations were investigated immunologically and genetically. Only three, E1, E25 and E26 (which map close together towards the left-hand end of the gene), were found to be CRM+. Co-suppression of each argE mutation with known strongly polar lacZ amber, ochre and UGA mutations was looked for to distinguish missfense from nonsense argE's, Arg+ revertants being screened for Lac+ and Mel+ phenotypes. Of 16 mutations not hitherto characterised as nonsense, frameshift or large deletions, only three, E1, E25 and E26, appeared to be missense. Three of the nonsense mutations were also streptomycin suppressible. It appears, therefore, that among argE mutants so far studied the correlation between CRM+ and missense is complete, so that the projected method for determining the direction of transcription of argE could not be applied.

Tandem and inverted repeats of arginine genes in Escherichia coli: structural and evolutionary considerations

Duplications of arg genes produced in the Rec+ and in the recA genetic backgrounds are shown by heteroduplex analysis to be strictly tandem at the level of resolution of this technique. The formation of these particular rearrangements therefore does not require the inclusion of transposons or other sequences of an appreciable size in their final structure. Duplications of short segments (about 2,000 nucleotides) appear unexpectedly stable when compared with duplications of longer segments (about 10,000 nucleotides). One of the structures analyzed displays two inversely repeated argE genes rearranged into an artificial divergent operon. The bearing of this observation on the origin of bipolar operons, of "mirror-image" map symmetries and on the production of inverted repeats in general, is discussed.

Expression of Escherichia coli K-12 arginine genes in Pseudomonas fluorescens

Escherichia coli argE and argH gene products were detected in Pseudomonas fluorescens argH122 carrying the E. coli F110 plasmid.

Coordinated regulation of octopine degradation and conjugative transfer of Ti plasmids in Agrobacterium tumefaciens: evidence for a common regulatory gene and separate operons

By using the analog noroctopine, mutants of agrobacterium tumefaciens were isolated with altered regulation patterns for the Ti plasmid-borne octopine utilization genes. These could be divided into three classes: (i) strains with a constitutive level of octopine enzymes and a high degree of spontaneous Ti transfer; (ii) one strain with constitutive octopine enzymes but no spontaneous Ti transfer; and (iii) strains with an altered inducibility in which, contrary to the wild-type Ti plasmid, conjugation and octopine utilization were induced by noroctopine. These results are best explained by the activity of a common regulatory gene. In a second step, using homo-octopine, mutants were isolated with lesions preventing the utilization of octopine. All mutations were plasmid borne and did not prevent the induction of tumors. Plasmids of two isolates were characterized by large deletions resulting in a decreased virulence and the absence of octopine in the tumor. With a plasmid carrying an inserted transposon Tn1, a significant number of strains were isolated which were unable both utilize octopine and to transfer the Ti plasmid. This suggests that there may be another common factor--presumably positive--between these traits. Transfer-negative mutants were still virulent. This seems to exclude a role for the conjugative transfer during the process of plant tumor induction. A way to test octopine oxidase by the use of permeable cells is described.

Studies on the control region of the bipolar argECBH operon of Escherichia coli. I. Effect of regulatory mutations and IS2 insertions

Several mutations affecting the control or the potential of gene expression in the argECBH bipolar operon have been characterized by enzyme assays, genetic mapping, dominance tests and pulse labelled RNA determinations. None of the mutations involves DNA rearrangements detectable by heteroduplex analysis (Charlier et al., 1978). Partially constitutive transcription of both argE and argCBH has been observed in mutant L10 while constitutive argE transcription and normal argCBH control characterize mutants L9, LL13 and LL2. The control region thus appears to contain two overlapping operators, as suggested previously (Elseviers et al., 1972). Two mutants (L2, LL1) and strain 6-8 from Bretscher and Baumberg (1976) display an increase in acetylornithinase specific activity (argE product) without concommittant increased argE transcription. In addition, they exhibit a decreased argCBH transcription. It is suggested that in these organisms, argE translation and argCBH transcription may be affected by the same genetic event; this explanation is compatible with present working hypothesis for the structure of the control region. An interpretation in terms of messenger attenuation also appears possible. From the properties of two strains harbouring an IS2 insertion in the control region (Charlier et al., 1978) the following conclusion may be drawn: 1. When inserted in orientation I close to the proximal end of a silent gene IS2 appears to promote a low but detectable transcription readthrough into that gene. 2. Insertion of an IS2 element in orientation II close to a neighbouring gene is not a sufficient condition to express that gene at a high rate. The properties of the two insertions appear compatible with the structure proposed for the control region.

Ribitol and D-arabitol catabolism in Escherichia coli

In Escherichia coli C, the catabolism of the pentitols ribitol and D-arabitol proceeds through separate, inducible operons, each consisting of a dehydrogenase and a kinase. The ribitol operon is induced in response to ribulose, and the D-arabitol operon is induced in response to D-arabitol. Each operon is under negative control. The genes of the ribitol and D-arabitol operons are very closely linked and lie in a mirror image arrangement, rtlB-rtlA-rtlC-atlC-atlA-atlB, between metG and his on the E. coli chromosome.

Cluster of genes controlling proline degradation in Salmonella typhimurium

A cluster of genes essential for degradation of proline to glutamate (put) is located between the pyrC and pyrD loci at min 22 of the Salmonella chromosome. A series of 25 deletion mutants of this region have been isolated and used to construct a fine-structure map of the put genes. The map includes mutations affecting the proline degradative activities, proline oxidase and pyrroline-5-carboxylic dehydrogenase. Also included are mutations affecting the major proline permease and a regulatory mutation that affects both enzyme and permease production. The two enzymatic activities appear to be encoded by a single gene (putA). The regulatory mutation maps between the putA gene and the proline permease gene (putP).

Synthesis of the Escherichia coli K12 isoenzymes of ornithine transcarbamylase, performed in vitro

The in vitro synthesis of enzymatically-active ornithine transcarbamylase (OTCase) directed by each of the E. coli K-12 OTCase genes (argF and argI) is described. The E. coli OTCase isoenzyme subunits are not identical, whether synthesized in vivo or in vitro, the argF-coded product being about 5% smaller. The OTCase protomers are enzymatically inactive but associate in vitro to an enzymatically active multimer. The rates of subunit association of argF and argI isoenzymes are considerably different. Utilizing the facile assay protocol presented, the regulation of in vitro OTCase synthesis by the specific holorepressor of the arginine regulon is demonstrated. Calculations based upon data presented indicate that there are about 65 molecules of argR gene product per bacterium, a substantially lower estimate than previously reported.

Regulation of argA operon expression in Escherichia coli K-12: cell-free synthesis of beta-galactosidase under argA control

Regulation of argA operon expression in Escherichia coli K-12 was studied in a cell-free, deoxyribonucleic acid-dependent, enzyme-synthesizing system. lambdaAZ-7 deoxyribonucleic acid, which carries a fusion of the lacZ structural gene to the argA operon so that beta-galactosidase synthesis is under argA regulation, was used as the template. To eliminate extraneous readthrough from lambda promoters, lambda repressor was introduced into the synthesis mixtures by preparing the S-30 component from a strain (514X5a-12-29) that carries a multicopy hybrid plasmid (pKB252) containing the lambdacI gene. Under these conditions beta-galactosidase synthesis was repressed 90% by the arginine repressor when a sufficient concentration of L-arginine was present. This repression could be overcome by escape synthesis when the lambdaAZ-7 deoxyribonucleic acid concentration in the synthesis mixtures was increased. Guanosine 3'-diphosphate-5'-diphosphate stimulated beta-galactosidase synthesis from this template.

Transcription of the argF and argI genes of the arginine biosynthetic regulon of Escherichia coli K12, performed in vitro

The cell-free transcription of the argF and argI genes of the arginine biosynthetic regions is described using an S-30 system capable of coupled in vitro transcription-translation. Template DNA isolated from two independently isolated arginine transducing phages was used in this work. Steady state mRNA synthesis was observed which was attributed to RNAase degradation. Regulation of argF mRNA synthesis, directed by the argF gene carried on the specialized transducing phage phi80dargF is effected to the extent of at least 95% by the arginine holorepressor at the transcriptional stage and at least 80% of the regulation of the expression of the argI gene is mediated at the transcriptional stage. Evidence is presented which indicates that the arginine holorepressor prevents RNA polymerase from binding to the arginine promoter and suggests that the operator and promoter sites may overlap.

Metabolism of arginine-specific messenger ribonucleic acid in Escherichia coli K-12

Ribonucleic acid-deoxyribonucleic acid (RNA-DNA) hybridization was employed for the determination of the level of messenger RNA (mRNA) transcribed from seven of the nine genes of the arginine regulon of Escherichia coli K-12. The quantity of RNA complexing with each of the separated DNA strands of the argA, argF, argE, and argCBH operons carried on specialized transducing phages was measured. The derepressed:repressed ratio of mRNA formed in vivo was found to vary between about 3 and 4 when measured by hybridization to DNA isolated from specialized transducing phages carrying the argA, argE, argCBH, argF, and argI operons.

In vitro transcription of the Escherichia coli K-12 argA, argE, and argCBH operons

Deoxyribonucleic acid isolated from argA and argECBH transducing phages was utilized to study the in vitro synthesis of argA, argE, and argCBH messenger ribonucleic acid. The specific regulation of these operons by the arginine holorepressor was demonstrated, providing evidence that the majority, if not all, of the control of these operons is exercised at the transcriptional level. Data are presented which indicate that the arginine holorepressor functions by binding to the operator region and concomitantly prevents the binding of ribonucleic acid polymerase to the corresponding promoter region.

EcoRI cleavage sites in the argECBH region of the Escherichia coli chromosome

The EcoRI cleavage of deoxyribonucleic acids (DNAs) from lambdadarg phages, carrying argECBH, has been examined. The phages are derived from the heat-inducible, lysis-defective strain lambda y199, and their bacterial DNA, including argECBH, is derived from Escherichia coli K-12. Such cleavage of the phage DNAs, in each case, produces the D, E, and F segments of lambda. Additionally, these DNAs yield segments, ordered from left to right, of length (in kilobases [kb]) determined by electron microscopy and 0.7% agarose slab gel electrophoresis as follows: lambdadarg13 (ppc argECBH bfe), 13.9, 2.8, 1.5, and 5.6; lambdadarg14 (ppc argECBH), 3.0, 2.0, 17.3, and 6.2; and lambdadarg23 (argECBH), 18.4 and 6.2. For lambdadarg13 sup102 DNA, the segment analogous to the 13.9-kb segment measures 12.2 kb. The direction from left to right corresponds to the clockwise orientation of the E. coli genetic map. The EcoRI segments define five cleavage sites near the arg region of the E. coli chromosome. For each of the DNAs, the arg genes occur on the largest segment produced. The 17.3-kb segment, being entirely bacterial, represents the argECBH-bearing EcoRI segment of the E. coli chromosome. The location of the arg genes was demonstrated electron microscopically in heteroduplex experiments.

Regulation of enzyme synthesis in the tryptophan pathway of Acinetobacter calcoaceticus

In Acinetobacter calcoaceticus the seven genes coding for the enzymes responsible for tryptophan synthesis map at three chromosomal locations. Two three-gene clusters, one (trpGDC) specifying the small subunit of anthranilate synthase, phosphoribosyl transferase, and indoleglycerol phosphate synthase and the other (trpFBA) specifying phosphoribosyl anthranilate isomerase and both tryptophan synthase subunits, are not linked to each other or to the trpE gene specifying the large anthranilate synthase subunit. When regulation of trp gene expression is studied in the wild type, only the level of the trpF gene product decreases upon addition of tryptophan to the medium. Tryptophan starvation of tryptophan auxotrophs, however, results in increased levels of all the tryptophan enzymes; this and additional evidence suggests that the expression of all the trp genes is subject to repression. The trpGDC genes are coordinately controlled, and the trpE gene is regulated in parallel with them. The trpFBA genes are controlled neither coordinately nor in parallel with the other trp genes, but respond proportionally when compared with each other. So far, two types of constitutive mutants have been found. The first class of mutants apparently occurs in the structural gene for a repressor protein; this repressor locus is unlinked to any of the biosynthetic trp genes and affects only the expression of trpE and the trpGDC cluster. The second class contains mutants closely linked to the trpGDC region; they overproduce only the gene products of this cluster.

Effect of arginine on the stability and size of argECBH messenger ribonucleic acid in Escherichia coli

The chemical stability of argECBH messenger ribonucleic acid (mRNA) produced by Escherichia coli was found to be unaltered during steady-state repression by arginine. During extreme arginine deprivation, the increase in argECBH mRNA stability was related to general effects of amino acid starvation on mRNA stability. Thus a mechanism whereby argECBH gene expression is regulated by altering the decay rate of this mRNA is not consistent with our data. Sucrose gradient analysis followed by hybridization revealed that both heavy (14S) and light (8S) components of argECBH mRNA were produced by cells of E. coli K-12 grown without arginine, whereas predominantly light (8S) mRNA was produced by cells grown with arginine. A functional argR gene and the EC portion of the argECBH cluster were found essential for the arginine restriction of heavy-mRNA production. Experiments suggest that light argECBH mRNA did not arise from heavy message, and 8u% of both light and heavy mRNA was found bound to ribosomes. The data appear most consistent with the notion that a second site of control by arginine regulates the amounts of light and heavy arginine mRNA in the cell either by early termination of transcription or by endonucleolytic processing. Consideration of these data in conjunction with those of the accompanying report (Krzyzek and Rogers, 1976) permits the tentative conclusion that light argECBH mRNA is not translated into active enzymes and is thus responsible for the discrepancy between the high content of hybridizable mRNA and low rates of enzyme synthesis found during arginine repression.

Dual regulation by arginine of the expression of the Escherichia coli argECBH operon

The correlation between the level of messenger ribonucleic acid (mRNA) specific for the argECBH gene cluster (argECBH mRNA) measured by ribonucleic acid-deoxyribonucleic acid (RNA-DNA) hybridization and the rates of synthesis of N-acetylornithine deacetylase (argE enzyme) and of argininosuccinate lyase (argH enzyme) of Escherichia coli strain K-12 were determined for steady-state growth with and without added L-arginine and during the transition periods between these two states. During the transient period after arginine removal (transient derepression), the synthesis of enzymes argE and argH was initially three to five times greater than the steady-state derepressed rate finally reached 50 min later. The level of argECHB mRNA correlated well both quantitatively and temporally with the rates of enzyme synthesis during this transition. The level of in vivo charged arginyl-transfer RNA (tRNAarg), monitored simultaneously, was initially only 5 to 10% and gradually increased to a final level of 80% after 45 min. During the transient period after arginine addition (transient repression), the rates of synthesis of enzymes argE and argH decreased to almost zero and gradually reached steady-state repressed rates after about 180 min. The argECBH mRNA level remained constant at the steady-state repressed level throughout transient repression, revealing a discontinuity between the level of this mRNA and rates of enzyme synthesis. A similar discrepancy was noted during the transition after ornithine addition. In vivo charged tRNAarg remained constant at 80% during this transition. After removal of arginine, the zero-level transient enzyme synthesis developed after only 7.5 min of arginine deprivation and was maximum after 30 min. The results suggest an accumulation of a molecule regulated by arginine that plays a role in transient repression. Our data indicate that arginyl-tRNA synthetase is not this molecule since its synthesis was unaffected by arginine. The ratios of steady-state argE and argH enzyme synthesis without arginine to that with arginine were 12 and 20, respectively, whereas the similar ratio for argECBH mRNA was 2 to 3. The repressed level of argECBH mRNA was not affected by attempts to repress or derepress the ppc+ gene (carried on the DNA used for hybridization), and the repressed level of argECBH mRNA was lowered about 50% in cells carrying an internal argBH deletion. These data taken together indicate the presence of an excess of untranslated argECBH mRNA during both transient and steady-state repression by arginine. Thus, a second regulatory mechanism, not yet defined, appears to play an important role in arginine regulation of enzyme synthesis.

In vitro synthesis and repression of argininosuccinase in Escherichia coli K12; partial purification of the arginine repressor

Phi80dargECBH DNA has been used to direct cell-free synthesis of argininosuccinase, the argH gene product in Escherichia coli K12. In vitro enzyme synthesis is sensitive to repression by partially purified preparations from an argR+ strain but not by corresponding preparations from an argR- strain. Using DNA-cellulose chromatography, approximately seventyfold purification of repressor has been obtained. The partially purified preparation represses argininosuccinase synthesis but has no effect on beta-galactosidase synthesis.

Isolation and characterization of lambdadargECBH transducing phages and heteroduplex analysis of the argECBH cluster

Transducing lambda bacteriophages have been isolated which carry the divergently transcribed argECBH operon of E. coli K12 and various portions of the adjacent ppc and bfe chromosomal regions. They were recovered from lysates prepared by the procedure of Schrenk and Weisberg using a Ppc+ Arg+ Bfe+ strain carrying a deletion of the usual attachment site of lambda. Heteroduplex DNA mapping of these lumbdadarg and of the phi 80 darg isolated by B. Konrad indicates that the two kinds of phages carry the arg cluster in opposite orientations, a situation favorable for the isolation of argECBH DNA. A physical map of the ppc argECBH bfe region including 2 unusual attachment sites of lambda has been constructed. The localization of the end points of certain arg deletions provides a useful reference framework for the currently pursued mapping of mutations affecting the control of divergent transcription and for the location of restriction enzyme cleavage sites in the arg region.

Parameters of gene expression in the bipolar argECBH operon of E. coli K12. The question of translational control

The pattern of divergent transcription of the argEC BH cluster of genes previously demonstrated by the hybridization of RNA to the separated strand of a phi 80 darg transducing phage, is confirmed with the DNA of a set of different lambdadarg phages. The accurate determination of argE and argCBH m-RNA levels in different steady states of expression of the arg regulon supports the following conclusions: 1. The ratio between maximal (derepressed) and minimal (repressed) rates of expression is lower when it is expressed in terms of % hybridizable RNA than in terms of expression is lower when it is expressed in terms of % hybridizable RNA than in terms of enzyme specific activities. The discrepancy is about 3 fold. Thus in conditions of repression, the cell produces relatively more unused m-RNA than in derepression. Different interpretations of this phenomenon appear possible: a) the messenger RNA molecules synthesized in repressed cells could be degraded more rapidly or translated less efficiently than in derepressed cells. b) an untranslated segment of the RNA could account for a larger part of the RNA detected in repression than in derepression. These interpretations are not mutually exclusive. 2. The discrepancy observed between the amplitudes of variation of argE and argC BH expression, expressed in terms of enzyme specific activities, is, in fact, determined at the level of DNA transcription. This provides direct evidence for the occurrence of differential transcription effectiveness in a regulon exhibiting a correlative but not strictly coordinated pattern of enzyme synthesis. This also supports our earlier suggestion regarding the possible complexity of the internal operator region situated between argE and C.

Accumulation of arginine precursors in Escherichia coli: effects on growth, enzyme repression, and application to the forward selection of arginine auxotrophs

The accumulation or ornithine, citrulline, and possibly acetylornithine by Escherichia coli K-12 arginineless mutants provided with acetylarginine as source of arginine causes severe growth inhibition. This occurs under conditions where comparable derivatives of E. coli W (Bollon and Vogel, 1973) show little or no growth inhibition. The same conditions, which have been reported to cause noncorrelative synthesis of acetylornithinase and argininosuccinase in E. coli W (Bollon and Vogel, 1973), do not alter the correlative pattern of enzyme synthesis observed in E. coli K-12. Moreover, previously reported effects of ornithine and citrulline on repression of the arginine regulon in E. coli W are not observed in the K-12 strains examined. The bearing of these observations on possible differences between the mechanism of enzyme repression operating in the two types of strains cannot yet be fully evaluated; it is, however, clear that considerable care should be exercised before extrapolating the results obtained with one type of strain to the other one. The particularly strong inhibition of acetylarginine utilization exerted by ornithine in E. coli K-12 allows the forward selection of several classes of arginine auxotrophs from strains deficient in carbamoylphosphate biosynthesis and thus capable of ornithine accumulation. Possible applications of this technique to the genetic analysis of the bipolar argECBH operon are discussed.

Resolution of the DNA strands of the specialized transducing bacteriophage lambda-h80C 1-857 dargF

The DNA strands of lambdoid phages with deletions or substitutions of the guanine plus cytosine-rich region in the left arm are not resolvable by complexing with poly UG followed by centrifugation in CsCl. This work describes a completely general procedure for the strand resolution of these phages by hybridization with fragments of separated strands of the parent phage. In particular, resolution of the DNA strands of the specialized transducing phage lambda-h80C1-857dargF is described, and evidence is presented which indicates that argF is transcribed from the r strand.

A gene cluster in Aspergillus nidulans with an internally located cis-acting regulatory region

Work reported here on the fungus Aspergillus nidulans has provided the first definitive demonstration of operon-type organisation in an eukaryote genome. It has been shown that the prnA and prnB genes concerned with proline metabolism form a gene cluster with the regulatory region lying between the two putative structural genes prnA and prnB. Regulatory mutations (prnd) probably leading to relief of carbon catabolite repression, map in between prnA and prnB and are cis-dominant with respect to both. The properties of these regulatory mutations and other findings suggest that carbon catabolite repression may be mediated by a negative control system in A. nidulans. This gene cluster is particularly interesting in view of its divergent orientation (with the regulatory region located in the centre of the operon) and for the fact that unlike the divergent operons known in prokaryotes, the divergent orientation is related to the way in which this particular operon may be regulated.

Genetic analysis of thymidine-resistant and low-thymine-requiring mutants of Escherichia coli K-12 induced by bacteriophage Mu-1

Four genes, dra, tpp, drm, and pup, that specify enzymes involved in the catabolism of nucleosides and deoxynucleosides in Escherichia coli are known to be very closely linked in the order dra-tpp-drm-pup. By infecting cells with the phage Mu-1 and isolating low-thymine-requiring derivatives of a strain lacking thymidylate synthetase and also thymidine-resistant mutants of a dra-strain, it has been possible to select for strains in which Mu-1 is inserted in this gene cluster. Making use of the polar effect of Mu-induced mutations on more distal genes in the same transcriptional unit, evidence is presented that dra and tpp are co-transcribed from a promoter to the left of dra, and drm and pup are co-transcribed from a promotor located between tpp and drm. Residual levels of purine nucleoside phosphorylase in drm- mutants induced by phage Mu seem to indicate that a weak promotor lies between drm and pup. From a strain in which Mu-1 is inserted in drm, a mutant has been isolated that has a deletion extending into tpp. Since this strain lacks thymidylate synthetase, it is unable to grow on minimal medium containing thymine. Mutants isolated from this strain that can grow on minimal medium containing thymine have been shown to have increased levels of the enzyme uridine phosphorylase.

Divergent orientation of transcription from the arginine gene ECBH cluster of Escherichia coli

Ribonucleic acid (RNA) isolated from Escherichia coli W3350 (F(-), argE(+)C(+)B(+)H(+)), in the absence of l-arginine, hybridizes with the separated leftward (l) and rightward (r) transcribing strands of the arginine transducing phage hphi80dargE(+)C(+)B(+)H(+)ppc(+)imm(lambdacI857) deoxyribonucleic acid (DNA) with a ratio of 30:70, respectively. In the presence of l-arginine and its intermediates, l-ornithine and l-citrulline, RNA transcriptions from both the strands of the argECBH cluster were repressed. The derepressed RNA, when hybridized with the separated strands of hphi80dargEC-I imm(lambda) phage DNA (the arginine genes are inversely inserted in this phage), which has a deletion in gene E and extends to gene C of the argECBH cluster, showed no leftward transcription, whereas the rightward transcription was reduced to about 40% of that when the DNA carrying the entire ECBH cluster was used for hybridization. The hybridization results thus demonstrate that (i) the regulation of the argECBH gene cluster in E. coli is under transcriptional control, (ii) the orientation of transcription is divergent, (iii) E gene transcribes anticlockwise, whereas the rest of the genes, C, B, and H, transcribe clockwise, and (iv) the position of the promoter(s) and operator(s) is located between the E and C genes of the argECBH cluster.

Regulation of argE-argH expression with arginine derivatives in Escherichia coli: extreme non-uniformity of repression and conditional repressive action

In regulatory studies of the arginine biosynthetic system of Escherichia coli, alpha-N-acetyl-l-arginine (AcA) is a useful restrictive arginine source. In strain 39A-23R3 (argA(-)), at 25 mug/ml, AcA gives suboptimal growth rates and is fully derepressive for acetylornithinase (specified by argE) and approximately 50% derepressive for argininosuccinase (specified by argH). At 10 mug/ml, the growth rate decreases, whereas the extent of derepression is unchanged; at 500 mug/ml, full repression results. In strain 3670 (argB(-)argG(-)), AcA (25 mug/ml) leads to partial derepression of acetylornithinase but full repression of argininosuccinase. Thus, the repression patterns for both strains, although not identical, are nonuniform. AcA utilization is antagonized by alpha-N-acetyl-l-ornithine (AcO). In strain 3670 (blocked before and after acetylornithinase), the growth rate on AcA (25 mug/ml) is lowered by AcO (500 mug/ml); acetylornithinase is completely derepressed, whereas argininosuccinase is fully repressed. This difference in regulatory behavior represents extreme nonuniform repression. Unexpectedly, the effect of AcO is attributable to the conversion of AcO to citrulline (Cit). In strain 3670, mixtures of AcA (25 mug/ml) and Cit (300 mug/ml) permit complete derepression of acetylornithinase; there is evidence that Cit enters the cell. In contrast, in the arginine-limited chemostat, Cit represses acetylornithinase. These opposite regulatory effects of Cit appear to stem from the difference in arginine restriction. AcA enters the cell via AcO permease and is deacylated by acetylornithinase (K(m), 5.0 mM). AcA competitively inhibits AcO cleavage (K(i), 2.4 mM), but Cit is not inhibitory. The antagonism of AcA utilization by AcO or Cit is thought to be exerted at the AcO permease.