On the functional organization of the arg ECBH cluster of genes in Escherichia coli K-12

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.

Increased transcription rates correlate with increased reversion rates in leuB and argH Escherichia coli auxotrophs

Escherichia coli auxotrophs of leuB and argH were examined to determine if higher rates of transcription in derepressed genes were correlated with increased reversion rates. Rates of leuB and argH mRNA synthesis were determined using half-lives and concentrations, during exponential growth and at several time points during 30 min of amino acid starvation. Changes in mRNA concentration were primarily due to increased mRNA synthesis and not to increased stability. Four strains of E. coli amino acid auxotrophs, isogenic except for relA and argR, were examined. In both the leuB and argH genes, rates of transcription and mutation were compared. In general, strains able to activate transcription with guanosine tetraphosphate (ppGpp) had higher rates of mRNA synthesis and mutation than those lacking ppGpp (relA2 mutants). argR knockout strains were constructed in relA(+) and relA mutant strains, and rates of both argH reversion and mRNA synthesis were significantly higher in the argR knockouts than in the regulated strains. A statistically significant linear correlation between increased rates of transcription and mutation was found for data from both genes. In general, changes in mRNA half-lives were less than threefold, whereas changes in rates of mRNA synthesis were often two orders of magnitude. The results suggest that specific starvation conditions target the biosynthetic genes for derepression and increased rates of transcription and mutation.

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.

Molecular basis for modulated regulation of gene expression in the arginine regulon of Escherichia coli K-12

We compare the nucleotide sequences of the regulatory regions of five genes or groups of genes of the arginine regulon of Escherichia coli K-12: argF, argI, argR, the bipolar argECBH operon and the carAB operon. All these regions harbour one or two copies of a conserved 18 bp sequence which appears to constitute the basic arginine operator sequence (ARG box). We discuss the influence of ARG box copy number, degree of dyad symmetry, base composition, and position relative to the cognate promoter site on the derepression-repression ratios of the genes of the regulon. A novel hypothesis, based on structural considerations, is also put forward to account for the absence ot attenuation control.

Internal promoters of the his operon in Salmonella typhimurium

Two internal promoters in the his operon of Salmonella typhimurium have been precisely mapped genetically. The internal promoters are found in, or very close to, gene border regions in the his operon. The his operon was examined for the presence of additional internal promoters whose transcripts were sensitive to rho-mediated transcription termination and therefore had escaped detection. No new internal promoters were found. It is argued that the internal promoters described here are not likely to be fortuitous message start sites, but may play a physiologically important role in operon expression.

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.

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.

Inversion induced by temperature bacteriophage mu-1 in the chromosome of Escherichia coli K-12

Induction of the Mu prophage of a lysogenic HfrP4X strongly stimulates the early transfer of the purE gene, which is located far from the origin of transfer. By using a rec- Mu cts62 X lysogenic donor, it was established that this process reflects the inversion of the origin of transfer in part of the Hfr population. Hfr's with inverted polarity of gene transfer were isolated; their analysis suggests that two Mu genomes in opposite orientation surround the inverted DNA fragment. Due to the presence of the Mu genome of the invertible G segment, homologous regions in the same orientation can appear in Mu genomes in opposite orientation. In a Rec+ background, Hfr's with inverted polarity (i) return to their original polarity of transfer by recomination between the two inverted Mu and (ii) produce new F' strains by recombination between the two similarly oriented G segments.

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.

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.

Pyrimidine biosynthesis in Serratia marcescens: a possible role for nonsequential enzyme interactions in mimicking coordinate gene expression

The coordinate expression of four sequential enzymes in the de novo pyrimidine pathway may result from the interaction of the various polypeptides of the pathway in Serratia marcescens rather than represent some unit of transcriptional regulation. These interactions were defined by examining the polypeptide association observed in extracts of parental and mutant strains in a series of pleiotropic pyrimidine auxotrophs. Extracts of pyrE auxotrophs [processing dihydroorotate (DHOase) activity but no orotidine-5'-monophosphate pyrophosphorylase (OMPppase) activity] stimulate OMPppase activity in extracts of pyrC auxotrophs (posessing reduced OMPppase activity but no DHOase activity). Separation by molecular weight on Sephadex G200 has suggested an aggregation between the final two enzymes, OMPppase and OMPdecarboxylase (OMPdecase), and the earlier enzyme, DHOase. The reduction of OMPppase activity in pyrC auxotrophs (encoding either a defective polypeptide or reduced levels) is explained by the lack of adequate levels of DHOase for aggregate formation. Such polypeptide interactions appear to mimic the coordinate formation of polypeptides which are controlled as a unit of regulation. The measurable levels of enzymatic activity vary in a quantitatively identical manner, but the variation does not result directly from the regulation of polypeptide formation.

Arginyl-tRNA synthetase from Escherichia coli. Influence of arginine biosynthetic precursors on the charging of arginine-acceptor tRNA with [14C]arginine

The behaviour of arginyl-tRNA synthetase (EC 6.1.1.19) in the presence of the arginine biosynthetic precursors, argininosuccinate, ornithine and citrulline, was studied in several Escherichia coli K12 strains and in E. coli W. The results of kinetic measurements with partially purified extracts indicate that the arginyl-tRNA synthetase of E. coli is not inhibited by the arginine precursors. The apparent affinity constant Km for arginine of the K12 enzyme is about 3.4 muM in the absence and in the presence of these precursors, whereas the W enzyme an apparently slightly lowered Km and a decreased [14C]arginyl-tRNA equilibrium level in the presence of argininosuccinate. This however was shown to be due to isotopic dilution of [14C]arginine by non-radioactive amino acid formed from argininosuccinate by argininosuccinate lyase (EC 4.3.2.1) contaminating the synthetase preparation. This finding emphasizes the necessity of using pure arginyl-tRNA synthetase in order to study the possible regulatory involvement of this enzyme in the control of the arginine regulon in vitro.

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.

Arginine control of transcription of argECBH messenger ribonucleic acid in Escherichia coli

The level of messenger ribonucleic acid specific for the argECBH gene cluster (arg-mRNA) of Escherichia coli was measured by deoxyribonucleic acid-ribonucleic acid hybridization in a number of strains. During the first 10 min after removal of arginine (derepression), the rate of arg-mRNA accumulation was six to ten times greater than that found in arginine-repressed argR(+) cells. In the absence of arginine, l-canavanine (200 mug/ml) repressed arg-mRNA synthesis to a level only 20 to 30% lower than that found after arginine deprivation. High levels of arg-mRNA were produced by argR(-) strains with or without added arginine. Within about 2 min after arginine addition to argR(+) cells, the rate of synthesis of arg-mRNA reached the repressed level. Likewise, 2.5 min after rifampin addition, all transcription of arg-mRNA was completed. These data are consistent with the view that arginine signals repression by inhibiting the initiation of transcription of arg-mRNA mediated in some way by the argR gene. The kinetics of arg-mRNA accumulation and the kinetics of completion of transcription together with the profile of hybridizable arg-mRNA in sucrose density gradients (major component 16S) suggest that the argECBH gene cluster is transcribed in short pieces rather than as a single unit.

Mapping the gene determining ornithine transcarbamylase and its operator in Escherichia coli B

The gene determining ornithine transcarbamylase in Escherichia coli B is argI, not argF. The argI gene has been located at 84 min on the linkage map, close to the gene for aspartate transcarbamylase, with neighboring markers in clockwise order fdp pyrB argI valS. A mutation in its operator locus, argO(I), has been mapped between argI and valS, so that this gene, unlike the argCBH portion of the argECBH cluster, appears to be oriented in the same direction as most of the other known E. coli operons.

Isolation of transducing particles of phi-80 bacteriophage that carry different regions of the Escherichia coli genome

It has been possible to mate two strains harboring F-prime (F') factors and to isolate from such matings rare recombinants that behave as though the two episomes had fused. Thus, two genes not previously linked may be brought into close proximity. An F' factor carrying the attachment site for varphi80 was fused with one carrying the met-ppc-arg region of the chromosome. Lysogenization of such a strain, followed by induction, led to the isolation of varphi80arg(+) and varphi80met(+) transducing phages. This technique may be utilized as a general method for joining diverse bacterial genes to the genome of phage varphi80.