In vitro repression of n- -acetyl-L-ornithinase synthesis 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.

The arginine repressor of Escherichia coli

This review tells the story of the arginine repressor of Escherichia coli from the time of its discovery in the 1950s until the present. It describes how the research progressed through physiological, genetic, and biochemical phases and how the nature of the repressor and its interaction with its target sites were unraveled. The studies of the repression of arginine biosynthesis revealed unique features at every level of the investigations. In the early phase of the work they showed that the genes controlled by the arginine repressor were scattered over the linkage map and were not united, as in other cases, in a single operon. This led to the concept of the regulon as a physiological unit of regulation. It was also shown that different alleles of the arginine repressor could result in either inhibition of enzyme formation, as in E. coli K-12, or in stimulation of enzyme formation, as in E. coli B. Later it was shown that the arginine repressor is a hexamer, whereas other repressors of biosynthetic pathways are dimers. As a consequence the arginine repressor binds to two palindromic sites rather than to one. It was found that the arginine repressor not only acts in the repression of enzyme synthesis but also is required for the resolution of plasmid multimers to monomers, a completely unrelated function. Finally, the arginine repressor does not possess characteristic structural features seen in other prokaryotic repressors, such as a helix-turn-helix motif or an antiparallel beta-sheet motif. The unique features have sustained continuous interest in the arginine repressor and have made it a challenging subject of investigation.

Prokaryotic gene expression in vitro: transcription-translation coupled systems

Transcription-translation coupled systems have been developed to study prokaryotic gene expression. Several types of expression system have been described. The original system consists of a crude unfractionated Escherichia coli extract, which supports protein synthesis directed by a template DNA. Control of gene expression at the transcriptional stage has been studied using this unfractionated system. In this respect, two examples of particular interest, lactose and tryptophan operons, are described. Other systems are either partially reconstituted or highly defined, containing up to 30 purified factors necessary for transcription (RNA polymerase) and translation (aminoacyl-tRNA synthetases, initiation, elongation and release factors). Additional differences between the various systems relate to the analysis of the gene products. Whereas most methods involve analysis of the totally synthesized protein, a particular system implies the formation of only the N-terminal di- or tripeptide of the gene product. Reconstituted systems have proved useful in studies on transcriptional, e.g., discovery and role of L factor, as well as translational regulation of gene expression, e.g., autogenous control of ribosomal protein synthesis.

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.

In vitro synthesis of Escherichia coli carbamoylphosphate synthase: evidence for participation of the arginine repressor in cumulative repression

A deoxyribonucleic acid-directed in vitro system for the synthesis of Escherichia coli carbamoylphosphate synthase has been developed, and its properties have been studied. The system uses the deoxyribonucleic acid of a lambda phage carrying the car genes (lambdadcarAB) as template and mediates the synthesis of both subunits of the enzyme. This newly synthesized enzyme exhibits the properties of native carbamoylphosphate synthase. A study of the in vitro synthetic capacities of S-30 extracts from strains containing either a mutated or the wild-type allele of gene argR supports earlier suggestions, based on in vivo evidence, that the argR product is involved in cumulative repression of carbamoylphosphate synthase by arginine and the pyrimidines. Repression in vitro is as efficient as in vivo. In keeping with such observation it is shown that in vitro synthesis of carbamoylphosphate synthase is repressed by partially purified arginine repressor. Evidence was obtained which indicates that arginine repression of carbamoylphosphate synthase mainly operates at the level of transcription. This was based on the design of an in vitro transcription system for gene carA, the structural gene for the light subunit of carbamoylphosphate synthase. This system also allowed us to demonstrate that free arginine is the corepressor involved in carbamoylphosphate synthase repression. The present in vitro approaches, in addition to the information they have already provided, open new possibilities for further investigations on the mechanism of cumulative repression and, in particular, on the participation of pyrimidine end products in this regulatory mechanism.

Evidence for translational repression of arginine biosynthetic enzymes in Escherichia coli: altered regulation in a streptomycin-resistant mutant

The formation and repressibility of the arginine biosyntietic enzymes acetylornithine delta-aminotransferase (EC 2.6.1.11), acetylornithine deacetylase (EC 3.5.1.16), ornithine carbamoyltransferase (EC 2.1.3.3), and argininosuccinate lyase (EC 4.3.2.1) were studied in an Escherichia coli W derivative (strain 250-10) that carries (a) a mutant allele of the argR regulatory gene causing a diminished repression-derepression range and (b) a streptomycin resistance mutation. In comparison with the streptomycin-sensitive parent 250, all four enzymes (a) are formed as smaller proportions of the total protein (overall range, 12% to 71%), whether the conditions are repressive (arginine excess) or derepressive (arginine restriction), and (b) show increased repressibility ratios, the carbamoyltransferase giving the largest increase (from 5.7 to 25.0). These effects appear to depend on the concurrent expression of the regulatory-gene and streptomycin resistance mutations, as indicated by analogous experiments with canavanine-resistant mutants of 250-10 that have partial argR- character. The results provide evidence for translational repression in the arginine system, and are interpreted in terms of a functional interaction of a mutant arginine repressor with a mutant S12 ribosomal protein. The locale of translational repression may be near the site of S12, and this mode of regulation may involve initiational selectivity of groupwise recognizable arginine messenger RNA's.

In vitro synthesis and and regulation of the biotin enzymes of Escherichia coli K-12

The synthesis and regulation of two of the enzymes of the biotin operon of Escherichia coli, 7,8-diaminopelargonic acid aminotransferase and dethiobiotin synthetase, were studied in vitro in a coupled transcription-translation system. These enzymes are encoded by genes located on opposite strands of the divergently transcribed operon (A. Guha, Y. Saturen, and W. Szybalski, J. Mol. Biol. 56:53-62, 1971). The kinetics of synthesis of both the enzymes were determined and the efficiency of the system was 0.3 to 0.4% that of the in vivo rate of synthesis in derepressed cells. Guanosine 3'-diphosphate 5'-diphosphate at 0.2 mM concentration stimulated the synthesis of 7,8-diaminopelargonic acid aminotransferase two- to threefold but had no effect on dethiobiotin synthetase synthesis. Biotin, which was most effective as the corepressor in vivo, also functioned in vitro at physiological concentrations in conjunction with a crude repressor protein isolated from a lysogen carrying the bioR gene. However, the two strands showed differential repression. At a repressor concentration where 7,8-diaminopelargonic acid aminotransferase synthesis was completely repressed, the repression of dethiobiotin synthetase was only 20% and did not exceed 50% with increasing repressor concentrations. Although the exact reason for the partial repression remains to be resolved, our data clearly suggest that the biotin operon is regulated from two separate operators.

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.

E. coli phosphofructokinase synthesized in vitro from a ColE1 hybrid plasmid

A hybrid plasmid, pLC 16-4, from the ColE1-DNA (E. coli) bank of Clarke and Carbon (1976) carrying pfkA was used to program an in vitro protein synthesis system from E. coli. Phosphofructokinase was the main product, as determined by enzyme assay, immunoprecipitation and gel electrophoresis. The enzyme was synthesized in vitro without added cAMP at a rate (enzyme/genome/h) ca. 30% the in vivo value, a higher efficiency than usually found in cell free systems. The plasmic molecular weight is ca. 16.10(6) daltons.

Arginine-sensitive phenotype of mutations in pyrA of Salmonella typhimurium: role of ornithine carbamyltransferase in the assembly of mutant carbamylphosphate synthetase

The phenotype of certain mutations in pyrA, the gene encoding carbamylphosphate synthetase (CPSase), is expressed only in the presence od exogenous arginine. In unsupplemented media, synthesis of carbamylphosphate and growth was almost normal; in arginine-containing media, synthesis of carbamylphosphate stopped, as did growth, as a consequence of starvation for pyrimidine. Genetic and biochemical evidence suggests that arginine exerts this inhibition by repressing the synthesis of ornithine carbamyltransferase (OTCase), the intracellular presence of which is required for assembly of the unequal subunits and proper functioning of the mutant CPSase. After the addition of arginine to a culture of the mutant, CPSase activity (glutamine dependent) characteristic of the intact holoenzyme progressively decreased, whereas activity (ammonia dependent) characteristic of the free large (alpha) subunit increased. Extracts of mutant cells contain free small (beta) subunits, as demonstrated directly by in vitro complementation using purified alpha subunits from wild type. The mutant enzyme from cultures grown in the presence of arginine had a markedly decreased affinity for adenosine 5'-triphosphate. Mutations in argR that cause depressed synthesis of OTCase suppressed the phenotype, and a certain mutation in argI, the gene encoding OTCase, enhanced it. In vitro experiments using purified enzyme confirm the stimulatory effect of OTCase on the activity of mutant CPSase.

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.

Expression of the argA gene carried by a defective lambda bacteriophage of Escherichia coli

Evidence is presented that the increase in specific activity of N-acetylglutamate synthase observed upon heat induction of Escherichia coli (lambdadargA) is primarily due to a gene dosage effect.

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.

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.

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.

Derepression of uridine diphosphate-glucose pyrophosphorylase (galU) in capR(lon), capS, and capT mutants and studies on the galU repressor

Mutation of the capR(lon), capS, or capT genes in Escherichia coli K-12 causes overproduction of capsular polysaccharide leading to a mucoid phenotype. Several of the enzymes involved in capsular polysaccharide synthesis are derepressed in cap mutants. Previously it was shown that uridine diphosphate-glucose (UDPG) pyrophosphorylase, an enzyme involved in the synthesis of three of the nucleotide sugar precursors of the capsule, is derepressed in capR mutants. The control of galU, the gene which codes for UDPG pyrophosphorylase, is described in this study. In addition, it has been found that the enzyme is also derepressed in capS and capT mutants. The effect of galU gene dosage in cap mutants and the wild-type strain (all lysogenic for phi80) was studied by infecting them with the purified transducing phage phi80dgalU. The level of UDPG pyrophosphorylase increased in proportion to the number of galU copies added. The rate of enzyme synthesis in the mutants was about sixfold higher than in the wild type per galU gene added for multiplicities of infection from one to twenty. Thus, all the galU copies added to the wild-type lysogen were repressed. We obtain greater than 20 galU copies per cell by infecting the nonlysogenic strain which allows multiplication of phi80dgalU. With some number of galU copies greater than 20, the rate of UDPG pyrophosphorylase synthesis in the wild type approaches the mutant rate of synthesis. The results suggest that there may indeed be a galU repressor pool in the cell which can be completely titrated. This pool must be composed of more than 20 galU repressor molecules. Since the capR, capS, and capT gene products or combinations thereof are known to control other widely separated operons of the cell besides the galU gene, it is postulated that the galU repressor may be capable of binding other operators. This would account for the relatively large pool of galU repressors per cell.