Trp repressor protein is capable of intruding into other amino acid biosynthetic systems

MetJ repressor interactions with DNA probed by in-cell NMR

Atomic level characterization of proteins and other macromolecules in the living cell is challenging. Recent advances in NMR instrumentation and methods, however, have enabled in-cell studies with prospects for multidimensional spectral characterization of individual macromolecular components. We present NMR data on the in-cell behavior of the MetJ repressor from Escherichia coli, a protein that regulates the expression of genes involved in methionine biosynthesis. NMR studies of whole cells along with corresponding studies in cell lysates and in vitro preparations of the pure protein give clear evidence for extensive nonspecific interactions with genomic DNA. These interactions can provide an efficient mechanism for searching out target sequences by reducing the dependence on 3-dimensional diffusion through the crowded cellular environment. DNA provides the track for MetJ to negotiate the obstacles inherent in cells and facilitates locating and binding specific repression sites, allowing for timely control of methionine biosynthesis.

Transcriptome analysis of a shikimic acid producing strain of Escherichia coli W3110 grown under carbon- and phosphate-limited conditions

Shikimic acid, which is produced in the aromatic amino acid pathway in plants and microorganisms, is an industrially interesting chiral starting material for the synthesis of many chemical substances, e.g. the influenza medicine Tamiflu. When produced by genetically modified Escherichia coli it has previously been found that carbon-rich conditions (e.g. phosphate-limitation) favors production of shikimic acid over shikimate pathway by-products, whereas the situation is the opposite at carbon-(glucose-) limited conditions. In the present study, gene expression patterns of the shikimate producing strain W3110.shik1 (W3110 with aroL deletion and plasmid-overexpressed aroF) and the wild type strain W3110 grown under carbon- and phosphate-limited (carbon-rich) chemostat conditions (D=0.23h(-1)) were analyzed. The study suggests that the by-product formation under carbon-limitation is explained by a set of upregulated genes coupled to the shikimate pathway. The genes, ydiB, aroD and ydiN, were strongly induced only in carbon-limited W3110.shik1. Compared to W3110 the lg(2)-fold changes were: 6.25 (ydiB); 3.93 (aroD) and 8.18 (ydiN). In addition, the transcriptome analysis revealed a large change in the gene expression when comparing phosphate- to carbon-limitation, which to a large part could be explained by anabolic-catabolic uncoupling, which is present under phosphate-limitation but not under carbon-limitation. Interestingly, there was also a larger difference between the two strains under carbon-limitation than under phosphate-limitation. The reason for this difference is interpreted in terms of starvation for aromatic amino acids under carbon-limitation which is relieved under phosphate-limitation due to an upregulation of aroK and aroA.

Biochemical pathways and mechanisms nitrogen, amino acid, and carbon metabolism

For both nitrogen and carbon metabolism there exist specific regulatory mechanisms to enable cells to assimilate a wide variety of nitrogen and carbon sources. Superimposed are regulatory circuits, the so called nitrogen and carbon catabolite regulation, to allow for selective use of "rich" sources first and "poor" sources later. Evidence points to the importance of specific regulatory mechanisms for short term adaptations, while generalized control circuits are used for long term modulation of nitrogen and carbon metabolism. Similarly a variety of regulatory mechanisms operate in amino acid metabolism. Modulation of enzyme activity and modulation of enzyme levels are the outstanding regulatory mechanisms. In prokaryotes, attenuation and repressor/operator control are predominant, besides a so called "metabolic control" which integrates amino acid metabolism into the overall nutritional status of the cells. In eukaryotic cells compartmentation of amino acid metabolites as well as of part of the pathways becomes an additional regulatory factor; pathway specific controls seem to be rare, but a complex regulatory network, the "general control of amino acid biosynthesis", coordinates the synthesis of enzymes of a number of amino acid biosynthetic pathways.

The activator of GntII genes for gluconate metabolism, GntH, exerts negative control of GntR-regulated GntI genes in Escherichia coli

Gluconate is one of the preferred carbon sources of Escherichia coli, and two sets of gnt genes (encoding the GntI and GntII systems) are involved in its transport and metabolism. GntR represses the GntI genes gntKU and gntT, whereas GntH was previously suggested to be an activator for the GntII genes gntV and idnDO-gntWH. The helix-turn-helix residues of the two regulators GntR and GntH exhibit extensive homologies. The similarity between the two regulators prompted analysis of the cross-regulation of the GntI genes by GntH. Repression of gntKU and gntT by GntH, as well as GntR, was indeed observed using transcriptional fusions and RNA analysis. High GntH expression, from cloned gntH or induced through 5-ketogluconate, was required to observe repression of GntI genes. Two GntR-binding elements were identified in the promoter-operator region of gntKU and were also shown to be the target sites of GntH by mutational analysis. However, the GntI genes were not induced by gluconate in the presence of enhanced amounts of GntH, whereas repression by GntR was relieved by gluconate. The repression of GntI genes by GntH is thus unusual in that it is not relieved by the availability of substrate. These results led us to propose that GntH activates GntII and represses the GntI genes in the presence of metabolites derived from gluconate, allowing the organism to switch from the GntI to the GntII system. This cross-regulation may explain the progressive changes in gnt gene expression along with phases of cell growth in the presence of gluconate.

Maintenance of repression control of the ilvGMEDA operon in a temperature-sensitive leucyl-transfer RNA synthetase mutant of Escherichia coli K-12 at a restrictive temperature

The mechanism of L-leucine regulation of ilvGMEDA is thought to be by ribosome-mediated attenuation that is dependent upon the concentration of Leu-tRNA(Leu) which results from leucyl-tRNA synthetase (LeuRS) activity. The requirement for LeuRS activity in attenuation control was tested in an Escherichia coli K-12 strain containing a temperature-sensitive LeuRS and the ilvGMEDA operon with an active ilvGM. Growth of this strain at 30 degrees C followed by a shift to 37 degrees C to inactivate the LeuRS revealed that ilvGM expression decreased at the restrictive temperature whereas the downstream gene expression was slightly elevated. We suggest that ilvGM does not respond to a deattenuation signal, and that, possibly, a secondary repression/derepression mechanism exists.

Effects of the flrA regulatory locus on biosynthesis and excretion of amino acids in Escherichia coli B/r

We have partially characterized phenotypic effects of an unusual amino acid regulatory locus, flrA, in E. coli B/r that alters the expression of the ilv and leu operons [Kline, E.L (1972) J. Bacteriol. 110:1127-1134]. This study demonstrated that a primary effect of the flrA7 mutation in haploid strains was overproduction of valine. In diploid strains (FflrA+/flrA7) this mutation resulted in excretion of valine, isoleucine, leucine, aspartate, threonine, glutamate, histidine and lysine. Increased excretion of amino acids by mutant strains might be explained by a membrane alteration or by flrA encoding a positive regulatory factor that affects the ilv operon and has pleiotropic effects on other amino acid operons.

Gene expression from multicopy T7 promoter vectors proceeds at single copy rates in the absence of T7 RNA polymerase

Three different genes (trpR+, tyrR+ and phi (trpR-lacZ)) were inserted into pET3a, a multicopy transcription-translation vector designed by Rosenberg et al. (1) for the T7 RNA polymerase-driven overexpression of proteins in Escherichia coli. Gene orientation was in the anticlockwise ("silent") direction. Gene expression in the absence of T7 RNA polymerase was evaluated either directly using lacZ reporter systems or indirectly by observing the susceptibility of plasmid-bearing tester strains to inhibition by an aromatic amino acid analog. The production of repressor proteins and of a Trp repressor-LacZ chimera was readily detected, at levels comparable to those of haploid trpR+ or tyrR+ E. coli strains. Such T7 vector constructs thus have two especially useful properties: first, they provide a means for the high-level production of various proteins in E. coli; second, they offer a technically advantageous point of departure for structure-function studies of genes whose overexpression from multicopy plasmids would normally be cytotoxic.

A procedure for amino acid sequencing in internal regions of proteins

We describe a novel procedure for determining the amino acid (aa) sequence of the internal regions of proteins. This procedure has been implemented by directly determining the sequence of aa 65-75 of the product of the trpR gene of Escherichia coli, the trp repressor. This method is based on the insertion of the cleavage site of a specific protease (factor Xa) into the protein immediately before the region to be sequenced by Edman degradation. The simplicity of the procedure makes it appealing for studies of protein structure-function relationships, and of the expression of genetic information. The method is particularly useful when there is ambiguity concerning the co-linearity of the aa and nucleotide sequences.

Shared operator recognition specificity between Trp repressor and the repressors of bacteriophage 434

Trp repressor is the only DNA-binding regulatory protein having a helix-turn-helix motif that has been reported to engage its operator target by a mechanism termed indirect readout: the Trp repressor-DNA interface is replete with hydrogen bonds between amino acid residues and non-esterified oxygen atoms of the sugar-phosphate backbone, and contains numerous specifically positioned water molecules. In Escherichia coli mutants deleted for trpR, the immunity repressor of phage 434 led to an eightfold reduction in trp promoter utilization. The Cro434 repressor also inhibited transcription from the trp promoter. The 434 repressors, considered to interact directly with operator targets, carry recognition helices positioned near the N terminus of each protein. The DNA-recognizing elements of Trp repressor lie toward the C terminus. The trp operator thus appears to possess significant plasticity in terms of its ability to assume conformational states that allow complex formation with more than one class of regulatory protein.

High level production and rapid purification of the E. coli trp repressor

Two small, multicopy, expression plasmids were constructed that permit convenient insertion of trpR, the structural gene for the trp repressor of Escherichia coli, with its natural ribosome binding site or adjacent to the ribosome binding site for the trp leader peptide. In these plasmids trpR is positioned between the strong regulated tac promoter and the rpoC transcription terminator. IPTG induction of lacIq strains bearing these plasmids results in the production of 25-50% of the soluble cell protein as trp repressor. Mutant and wild type repressors overproduced in this manner have been purified by simple procedures.

Regulation of in vivo transcription of the Escherichia coli K-12 metJBLF gene cluster

We subcloned DNA of the intercistronic region between the divergently transcribed metJ and metB genes of Escherichia coli into the transcription-fusion vector pK01 and localized the metJ promoters by deletion analysis. The plasmid-borne promoters of both genes were repressed by chromosomal metJ. In addition, S1 nuclease mapping of chromosomally derived mRNA from a derepressed strain revealed the start sites of transcription for metBL, metF, and metJ. The metBL and metF genes each had a single transcript which was repressed by metJ, while the metJ gene had three transcripts, of which the first was strongly repressed by metJ, the second was less strongly repressed, and the third was not repressed.

New regulatory genes involved in the control of transcription initiation at the thr and ilv promoters of Escherichia coli K-12

The gene ileR+, considered to encode a transacting protein involved in the regulation of the thr and ilv operons of Escherichia coli, has been cloned and localized to a 1.2 Kb BglII-SalI fragment of DNA. In strains harboring attenuation-defective fusions of lacZ to the promoter regions of the thr and ilv operons, ileR mutations lead to beta-galactosidase levels higher than those of the deattenuated parental strains. Reduced utilization of the thr and ilv promoters was observed in ileR cells harboring either ilvR+ plasmids or plasmids leading to the hyperproduction of Trp repressor. These results support the idea that ileR+ encodes a repressor protein that negatively affects the expression of the thr and ilv operons. Two additional trans-acting positive regulatory elements that act at the thr and ilv promoters have been identified by an analysis of deletion mutants. It thus appears that there exist positive as well as negative controlling elements that can act independently of attenuation to modulate the ilv and thr operons.

Trp holorepressor-trp operator interaction studied by protein distribution analysis

Trp repressor protein of Escherichia coli (Mr 24,700) undergoes a conformational change upon interaction with L-tryptophan that enables the resulting binary complex to bind with high specificity to several operator targets in double-stranded DNA. By protein distribution analysis it was shown that a significant fraction of Trp repressor is inert in operator binding. The equilibrium dissociation constant for Trp holorepressor-Trp operator interaction is 6.7 nM at 20 degrees in 0.05M NaCl, pH 7.4. The Trp holorepressor-trp operator complex consists of one molecule of each of the participating species, even at high molar ratios of protein to DNA.

Transcription of the trpR gene of Escherichia coli: an autogeneously regulated system studied by direct measurements of mRNA levels in vivo

The expression of the trpR gene of Escherichia coli was investigated by measuring trpR messenger RNA levels in vivo under various physiological conditions. Trp repressor, when present, led to significant decreases in the amount of trpR message produced; this effect was enhanced by providing excess L-tryptophan to the system. In the absence of Trp repressor, no changes in trpR message levels were observed under any of the conditions employed. Sedimentation profiles of trpR mRNA revealed a single species under all circumstances. These results suggest that autogenous repression alone acts to regulate transcription of the trpR gene. The activity of the trpR promoter in vivo was evaluated using a trpR-lacZ operon fusion. Very good agreement was found between relative promoter activity and trpR message levels under all experimental conditions.

Analysis in vivo of factors affecting the control of transcription initiation at promoters containing target sites for trp repressor

An investigation of repression in the trp system of Escherichia coli was undertaken using operon fusions and plasmids constructed via recombinant DNA technology. The promoters of the trp operon and the trpR gene were fused to lacZ, enabling the activity of these promoters to be evaluated under various conditions through measurements of beta-galactosidase production. In confirmation of earlier studies, the trpR gene was shown to be regulated autogenously. This control feature of the trp system was found to maintain intracellular Trp repressor protein at essentially invariant levels under most conditions studied. Increasing the trpR+ gene dosage did not significantly elevate Trp repressor protein levels, nor did the introduction of additional operator "sinks" result in significantly decreased levels of Trp repressor protein. Definite alterations in intracellular Trp repressor protein levels were achieved only by subverting the normal trpR regulatory elements. The placement of the lacUV5 or the lambda PL promoters upstream of the trpR gene resulted in significant increases in repression of the trp system. Substituting the primary trp promoter/operator for the native trpR promoter/operator resulted in an altered regulatory response of the trp system to tryptophan limitation or excess. The regulation of the trpR gene effectively imparts a broad range of expression to the trp operon in a manner finely attuned to fluctuations in intracellular tryptophan levels.

Studies on the interaction of Trp holorepressor with several operators. Evidence that the target need not be palindromic

The interaction of Trp repressor protein with partial trp operators was studied in vitro and in vivo. At high ratios of protein to DNA, Trp holorepressor formed stable complexes with DNA molecules containing half operators. When plasmids conferring the capacity to hyperproduce Trp repressor were present in trpOc strains of Escherichia coli, repression of downstream tryptophan synthase occurred. Palindromicity of the trp operator may facilitate stable interaction with Trp repressor, but this attribute need not be regarded as a critically essential structural feature. Sufficient information for the recognition by Trp repressor protein of an appropriate target resides within a DNA sequence of approximately ten base-pairs.