In vivo role of the relA+ gene in regulation of the lac operon

Unexpected coregulator range for the global regulator Lrp of Escherichia coli and Proteus mirabilis

The Lrp/AsnC family of transcription factors links gene regulation to metabolism in bacteria and archaea. Members of this family, collectively, respond to a wide range of amino acids as coregulators. In Escherichia coli, Lrp regulates over 200 genes directly and is well known to respond to leucine and, to a somewhat lesser extent, alanine. We focused on Lrp from Proteus mirabilis and E. coli, orthologs with 98% identity overall and identical helix-turn-helix motifs, for which a previous study nevertheless found functional differences. Sequence differences between these orthologs, within and adjacent to the amino acid-responsive RAM domain, led us to test for differential sensitivity to coregulatory amino acids. In the course of this investigation, we found, via in vivo reporter fusion assays and in vitro electrophoretic mobility shift experiments, that E. coli Lrp itself responded to a broader range of amino acids than was previously appreciated. In particular, for both the E. coli and P. mirabilis orthologs, Lrp responsiveness to methionine was similar in magnitude to that to leucine. Both Lrp orthologs are also fairly sensitive to Ile, His, and Thr. These observations suggest that Lrp ties gene expression in the Enterobacteriaceae rather extensively to physiological status, as reflected in amino acid pools. These findings also have substantial implications for attempts to model regulatory architecture from transcriptome measurements or to infer such architecture from genome sequences, and they suggest that even well-studied regulators deserve ongoing exploration.

Influence of amino acids on low-density Escherichia coli responses to nutrient downshifts

A vast bibliography on nutrient effects on high-density cultures exists, while it has been overlooked that low densities of starving cells are often the rule in natural environments. By means of a novel sensitive beta-galactosidase assay, we examined Escherichia coli transitions to minimal media when the cell concentration was 100 to 10,000 cells per ml. As in high-density cultures, the enzyme activity depended on amino acid availability and was subject to catabolite repression and stringent control. In all conditions tested, despite the presence of other nutrient sources, the relationship between beta-galactosidase activity and the l-amino acid pool was hyperbolic. The affinity constant when the amino acid pool was the only nutrient source averaged 14 muM after 90 min and increased up to 222 muM after 4.5 h. While investigating the transition from lag phase to exponential phase, we observed that the cells did not enter into starvation mode in the presence of amino acids, even when the nutrient amount was insufficient to support full survival. Based on these premises, the switch from starvation to hunger was investigated in relation to the amino acid pools. A critical range of concentrations at which E. coli linearly synthesized beta-galactosidase despite, at the same time, suffering a large decrease in cell viability was then recognized. Since both beta-galactosidase production and the dilution rate were reduced by more than half in the absence of leucine, we examined the contribution of leucine to cell recovery capabilities.

Guanosine 3',5'-bispyrophosphate coordinates global gene expression during glucose-lactose diauxie in Escherichia coli

Guanosine 3',5'-bispyrophosphate (ppGpp), also known as "magic spot," has been shown to bind prokaryotic RNA polymerase to down-regulate ribosome production and increase transcription of amino acid biosynthesis genes during the stringent response to amino acid starvation. Because many environmental growth perturbations cause ppGpp to accumulate, we hypothesize ppGpp to have an overarching role in regulating the genetic program that coordinates transitions between logarithmic growth (feast) and growth arrest (famine). We used the classic glucose-lactose diauxie as an experimental system to investigate the temporal changes in transcription that accompany growth arrest and recovery in wild-type Escherichia coli and in mutants that lack RelA (ppGpp synthetase) and other global regulators, i.e., RpoS and Crp. In particular, diauxie was delayed in the relA mutant and was accompanied by a 15% decrease in the number of carbon sources used and a 3-fold overall decrease in the induction of RpoS and Crp regulon genes. Thus the data significantly expand the previously known role of ppGpp and support a model wherein the ppGpp-dependent redistribution of RNA polymerase across the genome is the driving force behind control of the stringent response, general stress response, and starvation-induced carbon scavenging. Our conceptual model of diauxie describes these global control circuits as dynamic, interconnected, and dependent upon ppGpp for the efficient temporal coordination of gene expression that programs the cell for transitions between feast and famine.

In vivo and in vitro effects of (p)ppGpp on the sigma(54) promoter Pu of the TOL plasmid of Pseudomonas putida

The connection between the physiological control of the sigma(54)-dependent Pu promoter of the TOL plasmid pWW0 of Pseudomonas putida and the stringent response mediated by the alarmone (p)ppGpp has been examined in vivo an in vitro. To this end, the key regulatory elements of the system were faithfully reproduced in an Escherichia coli strain and assayed as lacZ fusions in various genetic backgrounds lacking (p)ppGpp or overexpressing relA. Neither the responsiveness of Pu to 3-methyl benzylalcohol mediated by its cognate activator XylR nor the down-regulation of the promoter by rapid growth were affected in relA/spoT strains to an extent which could account for the known physiological control that governs this promoter. Overexpression of the relA gene [predicted to increase intracellullar (p)ppGpp levels] did, however, cause a significant gain in Pu activity. Since such a gain might be the result of indirect effects, we resorted to an in vitro transcription system to assay directly the effect of ppGpp on the transcriptional machinery. Although we did observe a significant increase in Pu performance through a range of sigma(54)-RNAP concentrations, such an increase never exceeded twofold. The difference between these results and the behavior of the related Po promoter of the phenol degradation plasmid pVI150 could be traced to the different promoter sequences, which may dictate the type of metabolic signals recruited for the physiological control of sigma(54)-systems.

Ribosomes can slide over and beyond "hungry" codons, resuming protein chain elongation many nucleotides downstream

In cells subjected to moderate aminoacyl-tRNA limitation, the peptidyl-tRNA-ribosome complex stalled at the "hungry" codon can slide well beyond it on the messenger RNA and resume translation further downstream. This behavior is proved by unequivocal amino acid sequence data, showing a protein that lacks the bypassed sequence encoded between the hungry codon and specific landing sites. The landing sites are codons cognate to the anticodon of the peptidyl-tRNA. The efficiency of this behavior can be as high as 10-20% but declines with the length of the slide. Interposition of "trap" sites (nonproductive landing sites) in the bypassed region reduces the frequency of successful slides, confirming that the ribosome-peptidyl-tRNA complex passes through the untranslated region of the message. This behavior appears to be quite general: it can occur at the two kinds of hungry codons tested, AUA and AAG; the sliding peptidyl-tRNA can be any of three species tested, phenylalanine, tyrosine, or leucine tRNA; the peptidyl component can be either of two very different peptide sequences; and translation can resume at any of the three codons tested.

Analysis of the effect of ppGpp on the ftsQAZ operon in Escherichia coli

Escherichia coli loses its rod shape by inactivation of PBP2 (penicillin-binding protein 2), target of the beta-lactam mecillinam. Under these conditions, cell division is blocked in rich medium. Division in the absence of PBP2 activity is restored (and resistance to mecillinam is conferred) when the three cell division proteins FtsQ, FtsA and FtsZ are overproduced, but not when only one or two of them are overproduced. Division in the absence of PBP2 activity is also restored by a doubling in the ppGpp pool, as in the argS201 mutant. However, the nucleotide ppGpp, a transcriptional regulator of many operons, does not govern any of the five promoters of the ftsQAZoperon, as shown by S1 mapping of ftsQAZ mRNA 5' ends in exponentially growing wild-type cells in the mecillinam-resistant argS201 mutant (intermediate ppGpp level) or during the stringent response elicited by isoleucine starvation (high ppGpp level). Furthermore, the concentration of FtsZ protein is not increased in exponentially growing mecillinam-resistant argS201 cells. These results show that the ftsQAZ operon is not the ppGpp target responsible for mecillinam resistance. We are currently trying to identify those targets that, at intermediate ppGpp levels, allow cells to divide as spheres in the absence of PBP2.

The RNA chain elongation rate of the lambda late mRNA is unaffected by high levels of ppGpp in the absence of amino acid starvation

In this study, the effects of high levels of guanosine tetraphosphate (ppGpp) on the decay and RNA chain elongation kinetics of the bacteriophage lambda late transcript in Escherichia coli were examined in the absence of amino acid starvation. The accumulation, mRNA decay kinetics, and RNA chain elongation rate of the lambda late mRNA were determined after heat induction of lambdacI857 lysogens in the presence of high levels of ppGpp induced from a RelAalpha fragment-overproducing plasmid. The accumulation kinetics and elongation rate determinations of the late mRNA were made at long times after induction to allow a new steady state of transcriptional activities under conditions of elevated intracellular levels of ppGpp. The results indicate no prolonged or significant effect on either mRNA decay or the RNA chain elongation rate of the late mRNA as a result of elevated ppGpp levels. Surprisingly, the RNA chain elongation rate determinations indicate an RNA polymerase processivity of approximately 90-100 nucleotides/s for the lambda late transcript despite the presence of high levels of ppGpp. The results are discussed in terms of various models for regulation of stable and messenger RNA synthesis in E. coli.

The function of a ribosomal frameshifting signal from human immunodeficiency virus-1 in Escherichia coli

A 15-17 nucleotide sequence from the gag-pol ribosome frameshift site of HIV-1 directs analogous ribosomal frameshifting in Escherichia coli. Limitation for leucine, which is encoded precisely at the frameshift site, dramatically increased the frequency of leftward frameshifting. Limitation for phenylalanine or arginine, which are encoded just before and just after the frameshift, did not significantly affect frameshifting. Protein sequence analysis demonstrated the occurrence of two closely related frameshift mechanisms. In the first, ribosomes appear to bind leucyl-tRNA at the frameshift site and then slip leftward. This is the 'simultaneous slippage' mechanism. In the second, ribosomes appear to slip before binding aminoacyl-tRNA, and then bind phenylalanyl-tRNA, which is encoded in the left-shifted reading frame. This mechanism is identical to the 'overlapping reading' we have demonstrated at other bacterial frameshift sites. The HIV-1 sequence is prone to frame-shifting by both mechanisms in E. coli.

The gene encoding dihydrolipoyl transacetylase from Azotobacter vinelandii. Expression in Escherichia coli and activation and isolation of the protein

The gene encoding the dihydrolipoyl transacetylase (E2) component from Azotobacter vinelandii has been cloned in Escherichia coli. High expression of the gene was found when the cells were grown for more than 14 h. The E2 produced was partially active, varying 10 and 90% in different experiments. By limited proteolysis of the protein it was shown that the catalytic domain was incorrectly folded, caused by formation of intermolecular or intramolecular S-S bridges. The enzyme was fully activated after unfolding in 2.5 M guanidine hydrochloride containing 2 mM dithiothreitol, followed by refolding by dialysis. Active E2 was isolated in a simple three-step procedure. It possessed a specific activity in the same order as that found after isolation of E2 from purified pyruvate dehydrogenase complex from A. vinelandii. Active E2 comprises about 7% of the total soluble cellular protein in the E. coli clone. By genetic manipulation, deletion mutants of E2 were created, one encoding the lipoyl domain and the N-terminal half of the pyruvate-dehydrogenase (E1)- and lipoamide-dehydrogenase (E3)-binding domain, the other encoding the catalytic domain and the C-terminal half of the E1- and E3-binding domain. In E. coli expression of both mutants was observed.

Correlation between histidine operon expression and guanosine 5'-diphosphate-3'-diphosphate levels during amino acid downshift in stringent and relaxed strains of Salmonella typhimurium

We have analyzed the correlation of attenuator-independent expression of the Salmonella typhimurium histidine operon in vivo with levels of the "alarmone" guanosine 5'-diphosphate 3'-diphosphate. Amino acid downshift caused by serine hydroxamate addition increased his expression in a relA+ strain and decreased his expression in a relA mutant, whereas levels of guanosine 5'-diphosphate-3'-diphosphate varied in parallel with the changes in his expression in the two strains. In several experiments, overall variations in his expression ranged from 20- to 60-fold after downshift. The mild downshift allowed growth of the cultures to continue at near-preshift rates. Serine hydroxamate addition was also used to analyze the effect of amino acid downshift on induced expression of wild-type and mutant lac promoters. There was a 12-fold difference in lac expression when a relA+-relA1 pair was subjected to mild starvation but only a 3-fold difference when the strains carried the lacZpL8UV5 promoter mutation. These results suggest that guanosine 5'-diphosphate-3'-diphosphate stimulates gene expression in vivo at the level of transcription initiation.

Expression of arg genes of Escherichia coli during arginine limitation dependent upon stringent control of translation

The transcription and translation of operons for arginine biosynthetic enzymes after arginine removal (arginine down shift) were studied in relA and relA+ strains of Escherichia coli. After arginine down shift, derepression of synthesis of the arginine biosynthetic enzymes ornithine carbamoyltransferase (argF) and argininosuccinate lyase (argH) began at about 15 min in relA+ cells but was delayed in relA cells for more than 2 h. However, both relA+ and relA cells accumulated high levels of argCBH mRNA, as shown by dot blot hybridization, after arginine down shift. After 15 min of arginine limitation, the proportion of ribosome-bound argCBH mRNA was equivalent in both relA+ and relA cells. During the 15 min after the arginine down shift, relA+ cells produced a significant burst of argF and argH enzyme synthesis when arginine was added back to the culture, whereas relA cells did not produce this burst of enzyme synthesis. The relA cells regained the ability to produce a burst of argF and argH enzyme synthesis when alpha-methylglucose-induced glucose starvation was combined with arginine limitation. Significant guanosine 5'-diphosphate 3'-diphosphate accumulated in relA cells under this condition. Our results support the view that during periods of severe amino acid limitation guanosine 5'-diphosphate 3'-diphosphate acts in some way to ensure the translation of argCBH mRNA.

Promoter domain mediates guanosine tetraphosphate activation of the histidine operon

We have analyzed the effects of the "alarmone" guanosine 5'-diphosphate 3'-diphosphate (ppGpp) on regulation of the Salmonella typhimurium histidine operon in vitro. Expression of the wild-type promoter, measured in a DNA-dependent transcription-translation system, was strongly dependent on ppGpp; addition of ppGpp stimulated his expression 22-fold with plasmid DNA templates. Oligonucleotide-directed, site-specific mutations that increase the homology of the -10 hexamer to the consensus sequence of the E sigma 70 promoters dramatically increased his expression in the absence of ppGpp and reduced the stimulation to less than a factor of 2. A deletion mutation that alters the sequence between the -10 hexamer and the start point of transcription, generated by BAL-31 nuclease, affected ppGpp regulation in a similar manner. We propose that the -10 hexamer sequence and the adjacent downstream region are both important in regulating transcription by ppGpp. Mechanisms to account for activation and repression of transcription by ppGpp are discussed.

Independence of cyclic AMP and relA gene stimulation of glycogen synthesis in intact Escherichia coli cells

Previous studies from our laboratory established that in Escherichia coli, glycogen synthesis is regulated by both the relA gene, which mediates the stringent response, and by cyclic AMP. However, those studies raised the question of whether this dual regulatory system functions in an independent or a dependent manner. We show here that this regulation is independent, i.e., each regulatory process can express its action in the absence of the other. Triggering the stringent response by amino acid starvation increased glycogen synthesis even in mutants lacking the ability to synthesize cyclic AMP or lacking cyclic AMP receptor protein; and cyclic AMP addition stimulated glycogen synthesis in relA mutant strains. We also show that physiological concentrations of GTP inhibit ADP-glucose synthetase (glucose-1-phosphate adenylyltransferase, EC 2.7.7.27), the rate-limiting enzyme of bacterial glycogen synthesis, in vitro. Because the stringent response is known to cause an abrupt decrease in the cellular level of GTP, modulation of ADP-glucose synthetase activity by this nucleotide could account for a substantial portion of the step-up in the cellular rate of glycogen synthesis observed when the stringent response is triggered.

Negative control of ornithine decarboxylase and arginine decarboxylase by adenosine-3':5'-cyclic monophosphate in Escherichia coli

The polyamine biosynthetic enzymes, ornithine decarboxylase (EC 4.1.1.17) (ODC) and arginine decarboxylase (EC 4.1.1.19) (ADC), are negatively controlled by cAMP in Escherichia coli. The specific activities of ODC and ADC were determined in crude extracts prepared from E. coli strains carrying a mutation in the adenylate cyclase (EC 4.6.1.1) structural gene (cya) and wildtype strains. These strains were cultured on various carbon sources in the presence and absence of cAMP. In wild-type strains, ODC and ADC activities were diminished in cells grown on glycerol compared to these strains cultured on glucose. When cya strains were grown on glucose or glycerol, ODC and ADC activities were the same. Addition of 1 mM cAMP to glucose-based medium repressed ODC and ADC activities in both the wild-type and cya strains. Furthermore, cAMP exerts its negative control through the cAMP receptor protein, since strains carrying a mutation in the crp structural gene fail to repress ODC and ADC activities in response to increased cAMP obtained by carbon source manipulation or cAMP supplementation of the growth medium. This evidence suggests that negative control of ODC and ADC by cAMP occurs at the level of transcription.

lac Transcription in Escherichia coli cells treated with chloramphenicol

When protein synthesis was blocked by chloramphenicol in vivo, transcription initiation of lac mRNA was severely inhibited. In a promoter mutant (L8-UV5) or in wild-type cells supplemented with adenosine 3',5'-phosphate (greater than or equal to 5 mM), nearly normal initiation could be achieved, and when the mRNA chains formed were extracted, they coded for the 5'-terminal alpha-peptide of the lacZ gene in vitro. However, even under such conditions, only a fraction of RNA polymerases proceeded to the end of the Z gene in the presence of chloramphenicol; as a consequence, a wide range of sizes of mRNA was produced, and very few transcripts were formed all the way to the natural termination site of the operon. In other words, premature transcription termination occurred in chloramphenicol-treated cells, as current models predict, but terminations occurred to variable extents at several intragenic sites and apparently at least one intergenic site. Termination at intragenic sites occurred far less in cells bearing a mutation in the transcription termination factor rho.

Nonsense suppression in aminoacyl-t-RNA limited cells

A number of nonsense alleles of lacZ exhibit phenotypic suppression (as much as a sixteen-fold increase in leakiness) during partial limitation for certain aminoacyl-tRNA species in relA mutant cells. Each responsive allele has its individual pattern of response to limitation for one or more amino acids or aminoacyl-tRNA's. The phenotypic suppression occurs only during limitation, and ceases once limitation is reversed. Suppression is much reduced by the presence of the relA+ allele or an allele of rpsL which restricts ribosomal ambiguity. In one case, the suppressed product has been identified by radioimmune assay and gel electrophoresis, and is a full-length lacZ protomer. Mechanisms are discussed whereby aberrations of translation at codons calling for an aminoacyl-tRNA species in short supply might lead to readthrough of a nearby nonsense codon.

Positive involvement of ppGpp in derepression of the nif operon in Klebsiella pneumoniae

The kinetics of derepression of the enzyme nitrogenase were investigated, after exhaustion of a limiting amount of ammonium from the culture medium, in a prototrophic stringent-relaxed pair of Klebsiella pneumoniae strains and in their F relA+-F relA derivatives. The results indicate that ppGpp (guanosine 3'-5' diphosphate) increases the nitrogen fixation capability of K. pneumoniae by at least three different mechanisms. (1) It prevents exhaustion of the ATP pool when nitrogen starvation is imposed. (2) The translational defects in relaxed mutants are suppressed by ppGpp during nif derepression. (3) The synthesis of nitrogenase components is at least five times higher in the presence of ppGpp than in its absence. This latter conclusion was based on experimental results obtained when following the incorporation of (35S)-methionine into nitrogenase components after pulse labelling at various time intervals during nif derepression. The nitrogenase components were separated by solid phase radioimmunoassay as well as by two-dimensional gel electrophoresis.

Mechanism of the rel defect in beta-galactosidase synthesis

Relaxed (relA) mutants of Escherichia coli are defective in beta-galactosidase synthesis during amino acid limitation. We show here that this defect comprises both a transcriptional component and a translational component.