The tyrosine repressor negatively regulates aroH expression in Escherichia coli

Biosynthesis of the Aromatic Amino Acids

This chapter describes in detail the genes and proteins of Escherichia coli involved in the biosynthesis and transport of the three aromatic amino acids tyrosine, phenylalanine, and tryptophan. It provides a historical perspective on the elaboration of the various reactions of the common pathway converting erythrose-4-phosphate and phosphoenolpyruvate to chorismate and those of the three terminal pathways converting chorismate to phenylalanine, tyrosine, and tryptophan. The regulation of key reactions by feedback inhibition, attenuation, repression, and activation are also discussed. Two regulatory proteins, TrpR (108 amino acids) and TyrR (513 amino acids), play a major role in transcriptional regulation. The TrpR protein functions only as a dimer which, in the presence of tryptophan, represses the expression of trp operon plus four other genes (the TrpR regulon). The TyrR protein, which can function both as a dimer and as a hexamer, regulates the expression of nine genes constituting the TyrR regulon. TyrR can bind each of the three aromatic amino acids and ATP and under their influence can act as a repressor or activator of gene expression. The various domains of this protein involved in binding the aromatic amino acids and ATP, recognizing DNA binding sites, interacting with the alpha subunit of RNA polymerase, and changing from a monomer to a dimer or a hexamer are all described. There is also an analysis of the various strategies which allow TyrR in conjunction with particular amino acids to differentially affect the expression of individual genes of the TyrR regulon.

THE SHIKIMATE PATHWAY

The shikimate pathway links metabolism of carbohydrates to biosynthesis of aromatic compounds. In a sequence of seven metabolic steps, phosphoenolpyruvate and erythrose 4-phosphate are converted to chorismate, the precursor of the aromatic amino acids and many aromatic secondary metabolites. All pathway intermediates can also be considered branch point compounds that may serve as substrates for other metabolic pathways. The shikimate pathway is found only in microorganisms and plants, never in animals. All enzymes of this pathway have been obtained in pure form from prokaryotic and eukaryotic sources and their respective DNAs have been characterized from several organisms. The cDNAs of higher plants encode proteins with amino terminal signal sequences for plastid import, suggesting that plastids are the exclusive locale for chorismate biosynthesis. In microorganisms, the shikimate pathway is regulated by feedback inhibition and by repression of the first enzyme. In higher plants, no physiological feedback inhibitor has been identified, suggesting that pathway regulation may occur exclusively at the genetic level. This difference between microorganisms and plants is reflected in the unusually large variation in the primary structures of the respective first enzymes. Several of the pathway enzymes occur in isoenzymic forms whose expression varies with changing environmental conditions and, within the plant, from organ to organ. The penultimate enzyme of the pathway is the sole target for the herbicide glyphosate. Glyphosate-tolerant transgenic plants are at the core of novel weed control systems for several crop plants.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Expression, purification, and functional analysis of the TyrR protein of Haemophilus influenzae

The gene that was inferred to encode the TyrR protein of Haemophilus influenzae Rd was synthesized by polymerase chain reaction and inserted into a T7-based expression vector. Methods were developed to overexpress the TyrR protein of H. influenzae in Escherichia coli and to purify the protein on a large scale. Both in vitro and in vivo functional comparisons of the H. influenzae and E. coli TyrR proteins were carried out. The TyrR protein of H. influenzae was able to bind in vitro to an operator target upstream of the aroF-tyrA gene of E. coli. In the presence of [gamma-S]ATP, the DNA binding ability of the H. influenzae TyrR protein was drastically reduced. Despite the much shorter peptide chain length (318 amino acid residues vs 513), the TyrR protein of H. influenzae was as active in repressing the aroF promoter as the TyrR protein of E. coli. Repression by both proteins was enhanced in the presence of tyrosine; however, the transcriptional activation function associated with the TyrR protein of E. coli could not be detected when the H. influenzae TyrR protein was expressed in E. coli. By computer analysis, at least five operator targets for TyrR were identified within the genomic DNA of H. influenzae. These observations show that the assignment of function to the tyrR gene of H. influenzae was correctly made. Further studies of the H. influenzae TyrR protein in comparison to its E. coli counterpart should provide valuable mechanistic information on transcriptional regulation in this system.

Impaired Wound Induction of 3-Deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) Synthase and Altered Stem Development in Transgenic Potato Plants Expressing a DAHP Synthase Antisense Construct

Potato (Solanum tuberosum L.) cells were transformed with an antisense DNA construct encoding part of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase (EC 4.1.2.15), the first enzyme of the shikimate pathway, to examine the role(s) of this protein in plant growth and development. Chimeric DNA constructs contained the transcript start site, the first exon, and part of the first intron of the shkA gene in antisense or sense orientations under the control of the cauliflower mosaic virus 35S promoter. Some, but not all, of the transgenic plants expressing antisense DAHP synthase RNA showed reduced levels of wound-induced DAHP synthase enzyme activity, polypeptide, and mRNA 12 and 24 h after wounding. No alteration in the wound induction of DAHP synthase gene expression was observed in transgenic potato tubers containing the chimeric sense construct. Reduced steady-state levels of DAHP synthase mRNA were observed in stem and shoot tip tissue. Some plants with the chimeric antisense construct had reduced stem length, stem diameter, and reduced stem lignification.

Aromatic amino acid biosynthesis in Buchnera aphidicola (endosymbiont of aphids): cloning and sequencing of a DNA fragment containing aroH-thrS-infC-rpmI-rplT

A 4.5-kilobase DNA fragment from Buchnera aphidicola, the endosymbiont of the aphid Schizaphis graminum, was cloned and sequenced. On the basis of homology to Escherichia coli, the following genes were found in the order listed: aroH-thrS-infC-rpmI-rplT. AroH corresponds to the E. coli tryptophan-inhibited 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase. Evidence was presented indicating that this is the sole gene for DAHP synthase in the B. aphidicola genome. This enzyme initiates the complex branched pathway leading to aromatic amino acid biosynthesis. The presence of aroH is consistent with past observations indicating that aphid endosymbionts are able to synthesize tryptophan for the aphid host. thrS, infC, rpmI, and rplT correspond to genes for threonine tRNA synthase, initiation factor-3, and large ribosome subunit proteins L35 and L20, respectively. Sequence comparisons indicate some differences and similarities between E. coli and B. aphidicola with respect to the possible regulation of synthesis of these proteins.

Mutations in the tyrR gene of Escherichia coli which affect TyrR-mediated activation but not TyrR-mediated repression

Site-directed mutagenesis has been used to further characterize amino acid residues necessary for the activation of gene expression by the TyrR protein. Amino acid substitutions have been made at positions 2, 4, 5, 6, 7, 8, 9, 10, and 16. TyrR mutants with amino acid substitutions V-5-->P (VP5), VF5, CS7, CR7, DR9, RI10, RS10, and ER16 show no or very little activation of expression of either mtr or tyrP. In each case, however, the ability to repress aroF is unaltered. Amino acid substitutions at positions 4, 6, and 8 have no effect on activation. Small internal deletions of residues 10 to 19, 20 to 29, or 30 to 39 also destroy phenylalanine- or tyrosine-mediated activation of mtr and tyrP. In these mutants repression of aroF is also unaltered. In activation-defective tyrR mutants, expression of mtr is repressed in the presence of tyrosine. This tyrosine-mediated repression is trpR dependent and implies an interaction between TrpR and TyrR proteins in the presence of tyrosine.

A mutational analysis of the structural basis for transcriptional activation and monomer-monomer interaction in the TyrR system of Escherichia coli K-12

In response to the binding of tyrosine or phenylalanine, the TyrR protein (513 amino acids) activates certain promoters and represses others. In a previous study (J. Cui and R. L. Somerville, J. Bacteriol. 175:303-306, 1993), it was shown that promoter activation was selectively abolished in mutant proteins lacking amino acid residues 2 to 9. An additional series of constructs that encoded mutant TyrR proteins having deletions or point mutations near the N terminus were analyzed. Residues Arg-2 and Leu-3 were shown to be critical for the activation of the mtr promoter. In confirmation of previous findings, none of the activation-defective mutant TyrR proteins had lost significant repression function. The TyrR protein was shown by chemical cross-linking to be dimeric. The polypeptide segments critical for dimer formation in vivo were identified by evaluating the negative dominance phenotypes of a series of mutant proteins, all defective in DNA binding, lacking progressively greater numbers of amino acid residues from either the N terminus or the C terminus. Amino acid residues 194 to 438 were found to contain all of the essential dimerization determinants.

Cloning of the trp gene cluster from a tryptophan-hyperproducing strain of Corynebacterium glutamicum: identification of a mutation in the trp leader sequence

Corynebacterium glutamicum ATCC 21850 produces up to 5 g of extracellular L-tryptophan per liter in broth culture and displays resistance to several synthetic analogs of aromatic amino acids. Here we report the cloning of the tryptophan biosynthesis (trp) gene cluster of this strain on a 14.5-kb BamHI fragment. Subcloning and complementation of Escherichia coli trp auxotrophs revealed that as in Brevibacterium lactofermentum, the C. glutamicum trp genes are clustered in an operon in the order trpE, trpD, trpC, trpB, trpA. The cloned fragment also confers increased resistance to the analogs 5-methyltryptophan and 6-fluorotryptophan on E. coli. The sequence of the ATCC 21850 trpE gene revealed no significant changes when compared to the trpE sequence of a wild-type strain reported previously. However, analysis of the promoter-regulatory region revealed a nonsense (TGG-to-TGA) mutation in the third of three tandem Trp codons present within a trp leader gene. Polymerase chain reaction amplification and sequencing of the corresponding region confirmed the absence of this mutation in the wild-type strain. RNA secondary-structure predictions and sequence similarities to the E. coli trp attenuator suggest that this mutation results in a constitutive antitermination response.

Mutational uncoupling of the transcriptional activation function of the TyrR protein of Escherichia coli K-12 from the repression function

The tyrosine repressor (TyrR) protein of Escherichia coli can function either as a transcriptional enhancer or as a repressor. The structural basis for these opposite effects was analyzed in specific tyrR deletion mutants constructed in vitro. The functional behavior of the mutant TyrR proteins was evaluated in vivo by using single-copy lacZ reporter systems based on the mtr promoter (10-fold activation by wild-type TyrR protein, mediated by phenylalanine or tyrosine) or the aroF promoter (over 20-fold repression by wild-type TyrR protein, mediated by tyrosine). A mutant TyrR protein lacking amino acids 2 to 9 was completely devoid of transcriptional activation function. Five additional mutant TyrR proteins lacking progressively greater numbers of N-terminal amino acids were likewise activation defective. The mutant TyrR proteins lacking amino acid residues 2 to 9 or 2 to 19 were essentially identical to the wild-type TyrR protein in their ability to repress the aroF promoter. Three other TyrR mutant proteins, lacking up to 143 amino acid residues from the N-terminal end of the protein, retained the ability to repress the aroF promoter, to different extents, in a tyrosine-dependent manner.

Synergism between the Trp repressor and Tyr repressor in repression of the aroL promoter of Escherichia coli K-12

Computer analysis identified a potential Trp repressor operator 56 nucleotides downstream of the transcriptional start point of aroL, the gene that encodes shikimate kinase II. Tryptophan-dependent interaction of Trp repressor with this operator was demonstrated in vitro by means of a restriction endonuclease protection assay. Regulation of expression from the aroL promoter was evaluated with several genetically marked Escherichia coli strains by using a single-copy aroL-lacZ transcriptional-translational reporter system. The expression of aroL was repressed 6.9-fold by the Tyr repressor alone and 29-fold when both Tyr and Trp repressors were present. The Trp repressor had no effect on expression from the aroL promoter in the absence of the Tyr repressor. Possible mechanisms for Trp repressor-mediated repression, including cooperative interactions with the Tyr repressor, are discussed.

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.