Selection for new amino acids at position 211 of the tryptophan synthetase alpha chain of Escherichia coli

A molecular characterization of spontaneous frameshift mutagenesis within the trpA gene of Escherichia coli

Spontaneous frameshift mutations are an important source of genetic variation in all species and cause a large number of genetic disorders in humans. To enhance our understanding of the molecular mechanisms of frameshift mutagenesis, 583 spontaneous Trp+ revertants of two trpA frameshift alleles in Escherichia coli were isolated and DNA sequenced. In order to measure the contribution of methyl-directed mismatch repair to frameshift production, mutational spectra were constructed for both mismatch repair-proficient and repair-defective strains. The molecular origins of practically all of the frameshifts analyzed could be explained by one of six simple models based upon misalignment of the template or nascent DNA strands with or without misincorporation of primer nucleotides during DNA replication. Most frameshifts occurred within mononucleotide runs as has been shown often in previous studies but the location of the 76 frameshift sites was usually outside of runs. Mismatch repair generally was most effective in preventing the occurrence of frameshifts within runs but there was much variation from site to site. Most frameshift sites outside of runs appear to be refractory to mismatch repair although the small number of occurrences at most of these sites make firm conclusions impossible. There was a dense pattern of reversion sites within the trpA DNA region where reversion events could occur, suggesting that, in general, most DNA sequences are capable of undergoing spontaneous mutational events during replication that can lead to small deletions and insertions. Many of these errors are likely to occur at low frequencies and be tolerated as events too costly to prevent or repair. These studies also revealed an unpredicted flexibility in the primary amino acid sequence of the trpA product, the alpha subunit of tryptophan synthase.

Combinatorial approaches to protein stability and structure

Why do proteins adopt the conformations that they do, and what determines their stabilities? While we have come to some understanding of the forces that underlie protein architecture, a precise, predictive, physicochemical explanation is still elusive. Two obstacles to addressing these questions are the unfathomable vastness of protein sequence space, and the difficulty in making direct physical measurements on large numbers of protein variants. Here, we review combinatorial methods that have been applied to problems in protein biophysics over the last 15 years. The effects of hydrophobic core composition, the most important determinant of structure and stability, are still poorly understood. Particular attention is given to core composition as addressed by library methods. Increasingly useful screens and selections, in combination with modern high-throughput approaches borrowed from genomics and proteomics efforts, are making the empirical, statistical correlation between sequence and structure a tractable problem for the coming years.

Advancing our knowledge in biochemistry, genetics, and microbiology through studies on tryptophan metabolism

I was fortunate to practice science during the last half of the previous century, when many basic biological and biochemical concepts could be experimentally addressed for the first time. My introduction to research involved isolating and identifying intermediates in the niacin biosynthetic pathway. These studies were followed by investigations focused on determining the properties of genes and enzymes essential to metabolism and examining how they were alterable by mutation. The most challenging problem I initially attacked was establishing the colinear relationship between gene and protein. Subsequent research emphasized identification and characterization of regulatory mechanisms that microorganisms use to control gene expression. An elaborate regulatory strategy, transcription attenuation, was discovered that is often based on selection between alternative RNA structures. Throughout my career I enjoyed the excitement of solving basic scientific problems. Most rewarding, however, was the feeling that I was helping young scientists experience the pleasure of performing creative research.

Allosteric changes in the cAMP receptor protein of Escherichia coli: hinge reorientation

The cAMP receptor protein (CRP) of Escherichia coli is a dimer of a two-domain subunit. It requires binding of cAMP for a conformational change in order to function as a site-specific DNA-binding protein that regulates gene activity. The hinge region connecting the cAMP-binding domain to the DNA-binding domain is involved in the cAMP-induced allosteric change. We studied the structural changes in CRP that are required for gene regulation by making a large number of single and double amino acid substitutions at four different positions in or near the hinge. To achieve cAMP-independent transcription by CRP, amino acid residues 138 (located within the hinge region) and 141 (located in the D alpha-helix adjacent to the hinge) must be polar. This need for polar residues at positions 138 and 141 suggests an interaction that causes the C and D alpha-helices to come together. As a consequence, the F alpha-helix is released from the D alpha-helix and can interact with DNA. At position 144 in the D alpha-helix and within interacting distances of the F alpha-helix, replacement of alanine by an amino acid with a larger side chain, regardless of its nature, allows cAMP independence. This result indicates that pushing against the F alpha-helix may be a way of making the helix available for DNA binding. We believe that the cAMP-induced allosteric change involves similar hinge reorientation to adjust the C and D alpha-helices, allowing outward movement of the F alpha-helix.

Selection and analysis of non-interactive mutants in the Escherichia coli tryptophan synthase alpha subunit

The inherent infidelity of Taq DNA polymerase in the polymerase chain reaction was exploited to produce random mutations in the trp A gene. Screening of the resulting clones allowed selection of non-interactive mutant alpha subunits retaining their intrinsic catalytic activity. Two single changes responsible for this phenotype were identified by DNA sequencing as: alpha 126 valine (GTG)----glutamic acid (GAG) and alpha 128 valine (GTT)----aspartic acid (GAT). Three single changes giving a non-interactive phenotype with an impaired intrinsic catalytic activity were identified by DNA sequencing as alpha 66 asparagine (AAC)----aspartic acid (GAC); alpha 109 lysine (AAA)----arginine (AGA); alpha 118 cysteine (TGC)----arginine (CGC). Where possible, we individually assessed the importance of these residues in alpha beta interaction in light of structural information from X-ray crystallography and by intergeneric protein sequence comparison.

Suppression of a double missense mutation by a mutant tRNA(Phe) in Escherichia coli

We report here the isolation of a mutant tRNAPhe that suppresses a double missense auxotrophic mutation in trpA of Escherichia coli, trpA218. The doubly mutant protein product differs from wild-type TrpA by the replacements of Phe22 by Leu and Gly211 by Ser. A partial revertant TrpA phenotype can be obtained from trpA218 by changing either Leu22 back to Phe or Ser211 back to Gly. Translational suppressors were previously obtained that act at codon 211, replacing the Ser211 in the TrpA218 protein, presumably with Gly. In the present study, we selected for trpA218 suppressors caused by mutation of a cloned tRNAPhe gene, pheV. DNA sequence analysis of the suppressor isolated reveals a singular structural alteration, changing the anticodon from 5'-GAA-3' to 5'-GAG-3'. Sequencing of trpA218 confirmed the likely identity of Leu22 as CUC. The new missense suppressor, designated pheV(SuCUC), is lethal to the cell when highly expressed, as from a high copy number plasmid. This may be due to efficient replacement of Leu by Phe at CUC (and, probably, CUU) codons throughout the genome. We anticipate that pheV(SuCUC) will prove, like other missense suppressors, to be extremely useful in studies on the specificity and accuracy of decoding.

Third position base changes in codons 5' and 3' adjacent UGA codons affect UGA suppression in vivo

The base sequence around nonsense codons affects the efficiency of nonsense codon suppression. Published data, comparing different nonsense sites in a mRNA, implicate the two bases downstream of the nonsense codon as major determinants of suppression efficiency. However, the results we report here indicate that the nature of the contiguous upstream codon can also affect nonsense suppression, as can the third (wobble) base of the contiguous downstream codon. These conclusions are drawn from experiments in which the two Ser codons UCU233 and UCG235 in a nonsense mutant form (UGA234) of the trpA gene in Escherichia coli have been replaced with other Ser codons by site-directed mutagenesis. Suppression of these trpA mutants has been studied in the presence of a UGA nonsense suppressor derived from glyT. We speculate that the non-site-specific effects of the two adjacent downstream bases may be largely at the level of the termination process, whereas more site-specific or codon-specific effects may operate primarily on the activity of the suppressor tRNA.

Multiple replacements at position 211 in the alpha subunit of tryptophan synthase as a probe of the folding unit association reaction

Equilibrium and kinetic studies on the folding of a series of amino acid replacements at position 211 in the alpha subunit of tryptophan synthase from Escherichia coli were performed in order to determine the role of this position in the rate-limiting step in folding. Previous studies [Beasty, A. M., Hurle, M. R., Manz, J. T., Stackhouse, T., Onuffer, J. J., & Matthews, C. R. (1986) Biochemistry 25, 2965-2974] have shown that the rate-limiting step corresponds to the association/dissociation of the amino (residues 1-188) and carboxy (residues 189-268) folding units. In terms of the secondary structure, the amino folding unit consists of the first six strands and five alpha helices of this alpha/beta barrel protein. The carboxy folding unit comprises the remaining two strands and three alpha helices; position 211 is in strand 7. Replacement of the wild-type glycine at position 211 with serine, valine, and tryptophan at most alters the rate of dissociation of the folding units; association is not changed significantly. In contrast, glutamic acid and arginine dramatically decelerate and accelerate, respectively, both association and dissociation. The difference in effects is attributed to long-range electrostatic interactions for these charged side chains; steric effects and/or hydrogen bonding play lesser roles. When considered with previous data on replacements at other positions in the alpha subunit [Hurle, M. R., Tweedy, N. B., & Matthews, C. R. (1986) Biochemistry 25, 6356-6360], it is clear that beta strands 6 (in the amino folding unit) and 7 (in the carboxy folding unit and containing position 211) dock late in the folding process.

Reversion of trpA nonsense mutations by deletion of the chain-termination codons

This paper describes a novel mechanism for reversion of nonsense mutations in the trpA gene of Escherichia coli. This mechanism, deletion of the nonsense codon, was discovered in the course of selecting for missense revertants of trpA(UGA211) and for catalytically active tryptophan synthetase alpha chain revertants of trpA(UAA234) and trpA(UAG234). Each type of revertant trpA was cloned and its DNA sequence determined. trpA(UGA211) gave rise to two previously unidentified types of missense revertant. The first type was expected, namely trpA(CGA211), the result of a base substitution event. The other type, representing approximately 1% of the missense revertants, was unexpected on the basis of single base substitutions and an understanding of which amino acids are functional at alpha chain position 211. It was found to be the result of a 21 base-pair deletion of a region containing codon 211. The tryptophan-independent revertants of both position 234 nonsense mutants occurred at a frequency of approximately 2 per 10(9) viable cells. They were identical in that they both resulted from a 3 base-pair deletion, namely deletion of the chain-terminating codon at position 234. One of them, however, also displayed an A instead of the normal G in the third position of codon 235. The revertants were characterized according to growth in different media and tryptophan synthetase assays performed on crude extracts. These types of mutants should prove interesting and important for the elucidation of alpha chain structure-function relationships, for insight into the assembly and interaction of subunits in this model multienzyme complex, and for the study of mechanisms by which deletions can be generated.

Missense and nonsense suppressors can correct frameshift mutations

Missense and nonsense suppressor tRNAs, selected for their ability to read a new triplet codon, were observed to suppress one or more frameshift mutations in trpA of Escherichia coli. Two of the suppressible frameshift mutants, trpA8 and trpA46AspPR3, were cloned, sequenced, and found to be of the +1 type, resulting from the insertion of four nucleotides and one nucleotide, respectively. Twenty-two suppressor tRNAs were examined, 20 derived from one of the 3 glycine isoacceptor species, one from lysT, and one from trpT. The sequences of all but four of the mutant tRNAs are known, and two of those four were converted to suppressor tRNAs that were subsequently sequenced. Consideration of the coding specificities and anticodon sequences of the suppressor tRNAs does not suggest a unitary mechanism of frameshift suppression. Rather, the results indicate that different suppressors may shift frame according to different mechanisms. Examination of the suppression windows of the suppressible frameshift mutations indicates that some of the suppressors may work at cognate codons, either in the 0 frame or in the +1 frame, and others may act at noncognate codons (in either frame) by some as-yet-unspecified mechanism. Whatever the mechanisms, it is clear that some +1 frameshifting can occur at non-monotonous sequences. A striking example of a frameshifting missense suppressor is a mutant lysine tRNA that differs from wild-type lysine tRNA by only a single base in the amino acid acceptor stem, a C to U70 transition that results in a G.U base pair. It is suggested that when this mutant lysine tRNA reads its cognate codon, AAA, the presence of the G.U base pair sometimes leads either to a conformational change in the tRNA or to an altered interaction with some component of the translation machinery involved in translocation, resulting in a shift of reading frame. In general, the results indicate that translocation is not simply a function of anticodon loop size, that different frameshifting mechanisms may operate with different tRNAs, and that conformational features, some far removed from the anticodon region, are involved in maintaining fidelity in translocation.

Synergism in folding of a double mutant of the alpha subunit of tryptophan synthase

The urea-induced unfolding of the inactive single mutants Tyr-175----Cys and Gly-211----Glu and the active double mutant Cys-175/Glu-211 of the alpha subunit of tryptophan synthase from Escherichia coli was examined by using ultraviolet difference spectroscopy. Equilibrium techniques were used to determine the equilibrium free energies of unfolding for the mutant proteins to permit comparison with the wild-type protein. The sum of the changes in stability for the single mutants is not equal to the change seen in the double mutant. This inequality is evidence for a structural interaction between these two residues. Kinetic studies show that this synergism, which destabilizes the native form by 1.5-2.0 kcal/mol at pH 7.8, 25 degrees C, occurs only after the final rate-limiting step of domain association.

Sequence verification of mutant codon assignments in trpA of Escherichia coli

Over the past 30 years, a variety of mutations have been characterized in trpA, the gene for the alpha-subunit of tryptophan synthetase in Escherichia coli. On the basis of amino acid sequence analyses, reversion studies, or suppressibility by codon-specific translational suppressors, base substitutions were deduced and codons assigned for each mutation. In the present study, three of the trpA mutants obtained over 25 years ago and a series of codon position 234 trpA mutants isolated more recently by specific selection methods have been cloned and characterized by DNA sequence analysis. Our results establish the reliability of the mutant codon assignments, confirm the validity of the selection and detection procedures used to obtain missense and nonsense mutations in trpA, and demonstrate that the trpA sequence has been stably maintained throughout 30 years of laboratory culturing and mutagenic treatments.

Comparative analysis of UV-induced mutability of ten different codon units in position 211 of the Escherichia coli trpA gene

To study the influence of the local base composition upon UV-induced mutability the reversion frequencies of ten trpA mutants with known codon sequences at position 211 were compared. Comparison of mutant strains reverting by the same base substitution type but with different dipyrimidinic sequences reveals the mutagenic character of the pyrimidine-pyrimidine (6-4) photoproduct. The codons GAC and GAT, both reverting by AT-GC transitions and AT-CG transversions in the middle position and harboring the dipyrimidinic sequence CT in the opposite strand, differ in their reversion frequencies sixfold. This difference can only be due to the influence of the different bases in the third codon position upon the mutability of adjacent second bases.

Codon context effects in missense suppression

After our first observation of codon context effects in missense suppression ( Murgola & Pagel , 1983), we measured the suppression of missense mutations at two positions in trpA in Escherichia coli. The suppressible codons in the trpA messenger RNA were the lysine codons, AAA and AAG, and the glutamic acid codons, GAA and GAG. The mRNA sites of the codons correspond to amino acids 211 and 234 of the trpA polypeptide, positions at which glycine is the wild-type amino acid. Our data demonstrated codon context effects with both pairs of codons. The results indicate that suppression of AAA and AAG by mutant lysine transfer RNAs was more efficient at 211 than at 234, whereas suppression of GAA and GAG by two different mutant glycine tRNAs was more efficient at 234 than at 211. In general, the context effects were more pronounced with GAG and AAG than with GAA and AAA. (In some instances it appeared that suppression of GAA or AAA at a given position was more effective than suppression of GAG or AAG.) By contrast, no context effects were observed with a glyT suppressor of AAA and AAG, a glyT GAA/G-suppressor, and a glyU suppressor of GAG. Our observation of this phenomenon in missense suppression demonstrates that codon context can affect polypeptide elongation and that the effects can be different depending on the codons and tRNAs examined. It is suggested that tRNA-tRNA interaction on the ribosome is involved in the observed context effects.

Suppressors of lysine codons may be misacylated lysine tRNAs

We describe a novel class of missense suppressors that read the codons for lysine at two positions (211 and 234) in the trpA polypeptide of Escherichia coli. The suppressor mutations are highly linked to lysT, a gene for lysine tRNA. The results suggest that the suppressors are misacylated lysine tRNAs that carry glycine or alanine. The mutant codons are apparently suppressed better at position 211 than at position 234, indicating the existence of codon context effects in missense suppression.

Anticodon shift in tRNA: a novel mechanism in missense and nonsense suppression

In a previous publication, an unusual UGG-reading missense suppressor caused by insertion of an extra adenylate residue in the anticodon loop of an Escherichia coli glycine tRNA was described. In this study, we provide in vivo evidence that the additional nucleotide causes an "anticodon shift" by one nucleotide in the 3' direction and that the "new" anticodon can explain the unanticipated coding properties of the suppressor. We converted the UGG suppressor with ethyl methanesulfonate, a base-substitution mutagen, to suppressors that read codons related to UGG by a single base change. Sequence analysis of each mutant tRNA revealed that its mutational alteration was an anticipated base change in one of the three nucleotides of the "new" anticodon. Although the new suppressors read codons beginning with A or U, the mutant tRNAs lack the customary hypermodified nucleosides on the 3' side of the anticodon. As determined on the basis of their in vivo coding specificities, the new mutant tRNAs do not continue to utilize the original anticodon triplet for decoding. Furthermore, the failure of the UGG suppressor to correct frameshift mutations throughout each of three genes of the trp operon suggests that the addition of a nucleotide to the anticodon loop of a tRNA does not necessarily result in out-of-frame decoding by the tRNA. Therefore, a "frameshift" mutation in a tRNA has principally changed the triplet codon recognition properties of the molecule.

Effect of a single amino acid substitution on the folding of the alpha subunit of tryptophan synthase

The urea-induced unfolding of a missense mutant of the alpha subunit of tryptophan synthase from Escherichia coli involving the replacement of Gly by Glu at position 211 has been monitored by absorbance changes at 286 nm. Like the wild-type protein, the equilibrium unfolding curve demonstrates the presence of one or more stable intermediates. Comparison of these results with those from the wild-type alpha subunit [Matthews, C. R., & Crisanti, M. M. (1981) Biochemistry 20, 784] shows that the transition from the native conformation to the stable intermediates is displaced to higher urea concentration in the mutant alpha subunit; however, the transition from the intermediates to the unfolded form is unaffected. Kinetic studies show that the amino acid replacement slows the rate of unfolding by an order of magnitude. The effect on refolding rates is complex. One phase, previously assigned to proline isomerization [Crisanti, M. M., & Matthews, C. R. (1981) Biochemistry 20, 2700], is unaffected by the substitution. The rate of the second phase, which is urea dependent down to about 1 M urea, is slower than the corresponding phase in the wild-type protein by approximately a factor of 2. Below about 1 M urea, the rate of this phase becomes urea independent and identical with that of the wild-type alpha subunit. This change in urea dependence has been ascribed to a change in the nature of the rate-limiting step for this process from one involving folding to one involving proline isomerization. The results support the folding model for the alpha subunit proposed previously [Matthews, C. R., & Crisanti, M. M. (1981) Biochemistry 20, 784] and clarify the role of proline isomerization in limiting the rate of folding.

Suppressors of a UGG missense mutation in Escherichia coli

As part of our investigation of tRNA structure-function relationships, we isolated and preliminarily characterized translational suppressors of the tryptophan codon UGG in a trpA missense mutant of Escherichia coli. the parent strain also contained two other mutant alleles relevant to the suppressor search; these were supD, which codes for a serine-inserting amber suppressor tRNA, and gly V55, the gene for a GGA/G-reading mutationally altered glycine tRNA. On the basis of map location, reversed-phase (RPC-5) column chromatography of glycyl-tRNA, and codon response, several classes have been distinguished so far. The number of suppressors in each class, their codon responses, and their apparent genic identities, respectively, are as follows: class 1--4 suppressors, UGG, supD; class 2--12 suppressors, UGG, glyU; class 3--9 suppressors, UGA and UGG, glyT; class 4--2 suppressors, UGG, glyT; class 5--7 suppressors, UGG, gly V55. Besides these, one suppressor retains supD activity, but so far its map location has not been distinguished from that of supD. Another suppressor clearly does not map near supD or any of the glycine tRNA genes mentioned. These last two suppressors may represent novel missense suppressors such as misacylated tRNA's or mutationally altered aminoacyl-tRNA synthetases, tRNA modification enzymes, or ribosomes. Finally, three other suppressors were obtained from a strain containing glyT56, the gene for an AGA/G-reading form of glyT tRNA. All three occurred at the expense of glyT56 activity and exhibited the the transductional linkage to argH that is characteristic of glyT.

Glutamic acid codon suppressors derived from a unique species of glycine transfer ribonucleic acid

In this paper we describe the successful isolation of glyT-derived GAA suppressors. A glyT+ strain containing glyV55, the gene for a GGA/G-reading, methane sulfonate and hydroxylamine. The cells were plated to select for reversal of auxotrophy due to a trpA(GAA211) mutation. With either mutagen, greater than 85% of the prototrophs obtained were due to suppressors of the trpA mutation. Approximately 12% of the ethyl methane sulfonate-induced and 37% of the hydroxylamine-induced suppressors were shown to be about 25% cotranscucible with metB, as is glyT. The transfer ribonucleic acid from four metB-linked suppressor strains (two from each mutagen) was examined by reversed-phase column (RPC-5) chromatography. In all four cases, the glycyl-transfer ribonucleic acid profile displayed an alteration of glyT transfer ribonucleic acid. All four suppressors responded to GAG in addition to GAA but did not suppress the known mutant codons of several other trpA mutants. Other properties are discussed, along with possible reasons for our success in obtaining these suppressors.

Variations among glyV-derived glycine tRNA suppressors of glutamic acid codons

Glutamic acid codon suppressors in 18 isogenic strains of Escherichia coli have been further characterized as to map location, dominance, growth rates in various media, suppression of the GAG codon, and tRNA profiles after reversed-phase column chromatography. In general the evidence supports the conclusion that all of these suppressors are due to mutations in glyV55, the gene for a GGA/G-reading mutant form of glyV tRNA, and that they represent several different classes that may correspond to at least as many different nucleotide changes. Furthermore, 17 of the 18 suppressors can coexist in a haploid genome with a glyT suppressor that is devoid of GGA-reading ability. This result indicates the retention by those glyV suppressors of some ability to respond to GGA as well as the acquisition of the ability to read GAA, and suggests the possibility of "wobble" in the middle position of the anticodons of those tRNA's.

Intragenic mutational spectra and hot spots

In this review we outline the various factors which may contribute to the non-randomness of intragenic mutational spectra and the occurrence of hot spots. These factors include sample size limitation, particularly for sites of low mutability, and possible regions of low recombination potential. In addition, the nature of the gene product places great restraint on the detectability of either frameshift and premature chain-terminating mutations on one hand, or of the majority of missense mutations on the other. The nature of the Genetic Code itself also limits the mutational spectrum in so far as specific base pair substitutions lead only to a limited number of detectable amino acid replacements. Mutational hot spots may be a special example of the influence of neighbouring base pairs in the mutability of any given base pair. This is apparently true for frameshift mutations which tend to occur in runs of repeated base pairs or base pair doublets. Neighbouring base effects could operate not only at the level of initial reactivity with a mutagen, but also subsequently at the levels of DNA repair, recombination or replication. In some cases rare or modified bases may be responsible for neighbour effects. We suggest specific experimental approaches which seem likely to aid in the elucidation of these problems.

Genetic and biochemical characterization of some missense mutations in the lacZ gene of Escherichia coli K-12

Some preparations of beta-galactosidase from strains of Escherichia coli carrying point mutations in their lacZ genes did not precipitate with antibody as effectively as wild-type enzyme, but did not appear to be chain-terminating mutations as judged by polarity measurements and suppression. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of crude extracts of induced Lac+ strains revealed that the monomer of beta-galactosidase ran as a band uncontaminated by other cellular proteins. This method was used to identify missense mutations in the alpha and beta portions of the lacZ gene. Six of 13 mutations investigated were judged to be missense by this criterion. Measurement of the degree of polarity, the ability to complement a nonsense mutation at the operator-distal extremity of the gene (omega-complementation), and suppressibility by 12 nonsense suppressors allowed the assignment of six other mutations as either number or ochre. The protein figments produced by these six nonsense mutations appeared to be degraded in vivo. One mutation that could not be classified was either a missense mutation whose protein product was degraded or a very leak nonsense mutation. Two lacZ alleles were suppressed by the ochre suppressors supM and supN, although they were missense by other criteria. The ability of supM to suppress both nonsense and missense mutations can be explained if it is derived from a tyrosine transfer ribonucleic acid with a modified base in the first position of the anticodon. The mutations assigned to the missense class were not suppressed by the missense suppressors supH, supQ, glyV, glyU, or glyT. Our results suggest that the criteria used in the past to distinguish between nonsense and missense mutations may not be conclusive even when used together.

Naturally occurring sites within the Shigella dysenteriae tryptophan operon severely limit tryptophan biosynthesis

We investigated the structural, functional, and regulatory properties of the Shigella dysenteriae tryptophan (trp.) operon in transduction hybrids in which the cysB-trp-region of Escherichia coli is replaced by the corresponding region from S. dysenteriae. Tryptophan biosynthesis was largely blocked in the hybrids, although the order of the structural genes was identical with that of E. coli. Nutritional tests and enzyme assays revealed that the hybrids produced a defective anthranilate synthetase (ASase). Deletion mapping identified two distinct sites in trpE, each of which was partially responsible for the instability and low activity of ASase. We also discovered a pleiotropic site trpP (S) that maps outside the structural gene region and is closely linked to the S. dysenteriae trp operator. trpP (S) reduced the rate of trp messenger ribonucleic acid synthesis, and consequently trp enzyme levels, 10-fold relative to wild-type E. coli. In recombinants in which the structural genes of E coli were under the control of the S. dysenteriae promoter, enzyme levels were also reduced 10-fold. In some fast-growing revertants of the original hybrids, the rates of trp messenger ribonucleic acid synthesis and levels of tryptophan synthetase were restored to values characteristic of wild-type E.coli. Thus, the Trp auxotrophy associated with the S dysenteriae trp operon derives from the combination of a defective ASase and decreased expression of the entire operon imposed by trpP (S).