Nucleotide sequence of the promoter--operator region of the tryptophan operon of Salmonella typhimurium

The tryptophan repressor sequence is highly conserved among the Enterobacteriaceae

Tryptophan biosynthesis in Escherichia coli is regulated by the product of the trpR gene, the tryptophan (Trp) repressor. Trp aporepressor binds the corepressor, L-tryptophan, to form a holorepressor complex, which binds trp operator DNA tightly, and inhibits transcription of the tryptophan biosynthetic operon. The conservation of trp operator sequences among enteric Gram-negative bacteria suggests that trpR genes from other bacterial species can be cloned by complementation in E. coli. To clone trpR homologues, a deletion of the E. coli trpR gene, delta trpR504, was made on a plasmid by site-directed mutagenesis, then crossed onto the E. coli genome. Plasmid clones of the trpR genes of Enterobacter aerogenes and Enterobacter cloacae were isolated by complementation of the delta trpR504 allele, scored as the ability to repress beta-galactosidase synthesis from a prophage-borne trpE-lacZ gene fusion. The predicted amino acid sequences of four enteric TrpR proteins show differences, clustered on the backside of the folded repressor, opposite the DNA-binding helix-turn-helix substructures. These differences are predicted to have little effect on the interactions of the aporepressor with tryptophan, holorepressor with operator DNA, or tandemly bound holorepressor dimers with one another. Although there is some variation observed at the dimer interface, interactions predicted to stabilize the interface are conserved. The phylogenetic relationships revealed by the TrpR amino acid sequence alignment agree with the results of others.

Nucleotide sequence of the Salmonella typhimurium trpR gene

The sequence of the Salmonella typhimurium trpR gene and flanking DNA was determined on both strands. The DNA sequence predicts a polypeptide product of 108 amino acids with a molecular weight of 12,274 daltons. The TrpR protein of S. typhimurium differs by three amino acid residues from that of E. coli. The promoter/operator region of trpR is completely conserved between E. coli and S. typhimurium. The nucleotide sequence of the trpR sector of the S. typhimurium genome was 87.4% identical to the corresponding region of the E. coli genome. Within the protein coding segments of the two organisms, 94.4% of the amino acid residues were identical. In S. typhimurium, as in E. coli, there is a Palindromic Unit element (PU) between the translation termination triplet of trpR and that of a divergently oriented unidentified reading frame (URF-143). However, the PU segment of S. typhimurium is 85 nucleotides shorter than its E. coli counterpart.

Conformational properties of the -35 region of the trp promoter in solution: comparison of the wild-type sequence with an AT transversion

The majority of the 1H NMR resonances of the protons in a tetradecamer containing the -35 region of the trp promoter d(GCTGTTGACAATTA): d(TAATTGTCAACAGC) and in the TA transversion have been assigned. The conformational properties of the nucleotides have been determined and compared in the two duplexes. Analysis of spin-spin coupling and NOEs shows that all sugar puckers are in the south domain (i.e. near C2' endo) and the glycosidic torsion angles are anti (chi approximately 110 degrees). The NMR data are consistent with the duplex being in the B family of conformations. Significant differences in chemical shifts between the two molecules were observed only for nearest neighbours to the transversion site, suggesting the absence of long range conformational effects. This was confirmed by the similarity of coupling constants and NOEs. Other properties are also not greatly affected at positions more than two base pairs from the mutation site. These results are consistent with the hypothesis that unconstrained oligonucleotides are highly flexible, and can readily accommodate significant perturbations of the local structure, such as a transversion.

Development of a trpE promoter-strength measuring system and its use in comparison of the trpEDCBA, trpR and aroH promoters

An expression system was developed for measuring in vivo promoter strength at the single copy level and this system was used to compare the trp, aroH and trpR promoters. This system employs trpE enzyme activity as a measure of promoter strength and lacZ expression for internal copy number reference. Promoter-containing fragments are inserted into a cloning vector and subsequently recombined on to phage lambda by genetic exchange. Single lysogens are then prepared and used in promoter-strength analyses. The strength of several promoters was determined using this system. Among the promoters tested, the Escherichia coli trpEDCBA promoter was the strongest; it was four times more active than the lacUV5 promoter and about ten times stronger than the trpR and aroH promoters. To validate measurement of trpE enzyme activity as an indicator of promoter strength, trpE enzyme activity was compared with the level of trpE mRNA. There was excellent correspondence between the two, suggesting that with this system trpE enzyme activity accurately reflects promoter strength. We also examined a homologous promoter-strength measuring system in which the promoter-cloning plasmid lacked a 104 base-pair DNA spacer that was present immediately downstream from the promoter-cloning site in our preferred system. We found that the spacer was essential; the transcribed region accompanying a cloned promoter apparently affected trpE translational efficiency and/or trpE mRNA stability.

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.

Nuclear magnetic resonance study of the proton exchange rate in the operator-promoter DNA sequence of the trp operon of Escherichia coli

The dynamic behavior of a palindromic oligonucleotide (C-G-T-A-C-T-A-G-T-T-A-A-C-T-A-G-T-A-C-G) representative of the operator sequence and containing the Pribnow box of the trp operon of Escherichia coli was investigated. The resonances of the imino protons and of the H2 protons of the adenosine residues were all assigned. The opening rate constants of the base-pairs were calculated by monitoring the exchange rate of the observable imino protons (nine out of ten), using selective temperature (T1) measurements, which avoid the complication of cross-relaxation and spin diffusion. These measurements have to be performed in conditions where the exchange process is much faster than the opening and closing of the base-pairs, so that the observed exchange rate is equal to the opening rate. It is shown that the catalysis of the exchange process by phosphate dianions is not very efficient (kB approximately equal to 7 X 10(4) M-1 S-1). Hence, in phosphate buffer, the necessary opening-rate limiting condition is met only at high pH values (approximately equal to 9.5) where efficient catalysis by OH- takes place, or at very high buffer concentration. While G X C base-pairs show very little exchange, acting in the sequence as molecular "staples", the A X T base-pairs that are protected from the fraying have very different opening and closing rates, depending on the sequence. Although it seems possible that the opening process could occur at the base-pair level, it is localized at most to two base-pairs in that particular sequence. The activation energies for the opening process of all non-fraying base-pairs are very similar (19 +/- 1 kcal mol-1; 1 cal = 4.184 J), and the differences in the opening rates are essentially due to differences in the activation entropies. With regard to the role of this sequence in the promoter, it is observed that the end of the Pribnow box exchanges relatively easily, and that the activation parameters for the "breathing" process and for the isomerization step of the promoter--RNA polymerase are not very different.

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.

Nucleotide sequence of the trpD and trpC genes of Salmonella typhimurium

We have completed the nucleotide sequence determination of trpD and trpC, the second and third genes of the trp operon of Salmonella typhimurium. These genes encode two bifunctional proteins thought to have arisen by gene fusions: the trpD polypeptide contains the glutamine amido transferase and the phosphoribosyl anthranilate transferase activities, and the trpC protein possesses the N-(5'-phosphoribosyl)-anthranilic acid isomerase and the indole-3-glycerol phosphate synthetase activities. The trpD gene consists of 1593 nucleotides encoding 531 amino acids, and possesses an internal promoter (p2) located within a region from about 1400 to 1441 of the nucleotide sequence. The trpC gene contains 1356 nucleotides encoding 452 amino acids. In this paper we compare the trpD and trpC genes of S. typhimurium to those of Escherichia coli with respect to codon usage, nucleotide and amino acid conservation, p2 promoter characteristics and intercistronic regions. The sequence of the two genes we present here completes the sequence determination of the trp operon of S. typhimurium and should prove useful in comparisons with the E. coli trp operon and in future studies of operon structure in S. typhimurium.

In vitro synthesis of the tryptophan operon leader peptides of Escherichia coli, Serratia marcescens, and Salmonella typhimurium

We used an in vitro DNA-dependent protein-synthesizing system to demonstrate de novo synthesis of the leader peptide specified by the tryptophan (trp) operons of several bacterial species. Peptide synthesis was directed by self-ligated short restriction fragments containing the trp promoter and leader regions. Synthesis of leader peptides was established by demonstrating that they were labeled in vitro only by those amino acids predicted to be present in the peptides. Leader peptide synthesis was abolished by the addition of the Escherichia coli trp repressor. The E. coli trp leader peptide was found to be extremely labile in vitro; it had a half-life of 3-4 min. In a highly purified DNA-dependent peptide-synthesizing system, synthesis of the di- and tripeptides predicted from the Salmonella typhimurium trp operon leader sequence, fMet-Ala and fMet-Ala-Ala, also was observed. Using this dipeptide synthesis system, we demonstrated that translation initiation at the ribosome binding site used for trp leader peptide synthesis was reduced 10-fold when the transcript contained a segment complementary to the ribosome binding site.

Evolutionary divergence of the Citrobacter freundii tryptophan operon regulatory region: comparison with other enteric bacteria

The regulatory region of the trp operon of Citrobacter freundii was sequenced and compared with the corresponding regions of other enteric bacteria. Significant differences were noted in the promoter region. These differences are presumably responsible for the weak expression of the cloned trp operon in Escherichia coli. The presumed operator region, although nonfunctional in E. coli, has dyad symmetry, but the sequence of the symmetrical region differs appreciably from those of operators that can be regulated by the E. coli trp repressor. The sequence of the trp leader region of C. freundii resembles that of other enteric bacteria, suggesting that the C. freundii operon is also regulated by attenuation. Comparison of the sequence of the initial portion of trpE with the homologous regions of E. coli and Salmonella typhimurium indicates that the three organisms probably are evolutionary equidistant.

Regulatory region of the Klebsiella aerogenes tryptophan operon

The trp operon of Klebsiella aerogenes was cloned, and its regulatory region was sequenced. Comparison with previously reported trp regulatory sequences of other enteric bacteria indicates that the K. aerogenes trp promoter-operator region is most similar to the corresponding region of Salmonella typhimurium. The trp leader regions of K. aerogenes and other enteric bacteria are organized similarly, but there are significant differences in the stabilities of the predicted secondary structures in their leader transcripts. These differences should make the K. aerogenes attenuator a weaker transcription termination site than any of the other attenuator regions studied; this was confirmed in in vitro transcription experiments. The sequence of the leader transcript and the precise site of in vitro termination were determined.

Sequence and properties of operator mutations in the bio operon of Escherichia coli

The nucleotide-sequence changes occurring in newly isolated operator-constitutive mutations of the divergently transcribed bio operon have been determined. The observed point mutations are single GC leads to AT changes which occur at two symmetrical points in the hyphenated inverted repeat present in the control region. The changes at position -15 (with respect to the center of the inverted repeat) cause constitutivity of leftward operon expression and decreased expression of bioB, due to alteration of the -35 region of the rightward promoter. The change at position +15 is identical to one of the changes that Otsuka and Abelson (1978) detected in the bio p98 bio o34 double mutant. The location of the bio p131::IS1 insertion, which affects both leftward and rightward transcription, is also within the operator region. Both of the operator-constitutive mutations and the bio p131 insertion cause decreased repressor binding in vivo as shown by repressor titration tests on multicopy plasmids which bear them. The operator-constitutive mutations also decrease repressor binding in vitro, where added repressor fails to protect the TaqI site that is protected by repressor in bio o+ DNA. These results confirm several aspects of the model for bio operon regulation proposed by Otsuka and Abelson (1978).

Conservation and variation of nucleotide sequences within related bacterial genomes: enterobacteria

We have assessed the degree of relatedness of several portions of the Escherichia coli genome to the corresponding portions of the genomes of representative enteric bacteria, using the Southern transfer and hybridization technique (E. Southern, J. Mol. Biol. 98:503-517, 1975). The degree of relatedness varied among the regions examined. Judging both by the relative amounts of deoxyribonucleic acid in the various enteric genomes that are highly homologous and by the conservation of positions of restriction enzyme cleavage sites in these regions, the enteric genomes have diverged to greater extents in some parts of the genomes than in others. Portions of the genomes (including the tnaA and thyA genes, the trp operon, and one other unassigned segment) appear to have evolved in concert with the genome as a whole. By contrast, the lacZ gene and portions of the genome that are homologous to phage lambda vary more widely, perhaps reflecting a separate evolutionary origin for these segments of deoxyribonucleic acid.

Expression of early genes of origin-defective mutants of simian virus 40

The nucleotide sequences of eight origin-defective mutants of simian virus 40 have been determined. All of the mutants have suffered deletions, which range in size from 4 to 241 nucleotides. Some of the mutants induce the synthesis of tumor (T) antigen, others do not. Viral mRNA extracted from rat cells transformed by two of the T-antigen-positive mutants has been analyzed by the S1 nuclease technique of Berk and Sharp. Irrespective of the size or the location of the deletions, the 5' ends of viral mRNAs are located approximately the same distance from the A+T-rich region (A-T-T-T-A-T) rather than at a specific site in the viral genome.

The regulatory region of the trp operon of Serratia marcescens

The nucleotide sequence of the regulatory region of the trp operon of Serratia marcescens is presented. It contains a transcription termination control site in the transcribed leader region preceding the first structural gene of the operon as well as a regulated promoter/operator transcription initiation region. The structural organisation of the leader region differs substantially from that of Escherichia coli.