THE COMPLETE AMINO ACID SEQUENCE OF THE TRYPTOPHAN SYNTHETASE A PROTEIN (alpha SUBUNIT) AND ITS COLINEAR RELATIONSHIP WITH THE GENETIC MAP OF THE A GENE

The discovery of archaea: from observed anomaly to consequential restructuring of the phylogenetic tree

Observational and experimental discoveries of new factual entities such as objects, systems, or processes, are major contributors to some advances in the life sciences. Yet, whereas discovery of theories was extensively deliberated by philosophers of science, very little philosophical attention was paid to the discovery of factual entities. This paper examines historical and philosophical aspects of the experimental discovery by Carl Woese of archaea, prokaryotes that comprise one of the three principal domains of the phylogenetic tree. Borrowing Kuhn's terminology, this discovery of a major biological entity was made during a 'normal science' project of building molecular taxonomy for prokaryotes. Unexpectedly, however, an observed anomaly instigated the discovery of archaea. Substantiation of the existence of the new archaeal entity and consequent reconstruction of the phylogenetic tree prompted replacement of a long-held model of a prokarya and eukarya bipartite tree of life by a new model of a tripartite tree comprising of bacteria, archaea, and eukarya. This paper explores the history and philosophical implications of the progression of Woese's project from normal science to anomaly-instigated model-changing discovery. It is also shown that the consequential discoveries of RNA splicing and of ribozymes were similarly prompted by unexpected irregularities during normal science activities. It is thus submitted that some discoveries of factual biological entities are triggered by unforeseen observational or experimental anomalies.

The Evolving Definition of the Term "Gene"

This paper presents a history of the changing meanings of the term "gene," over more than a century, and a discussion of why this word, so crucial to genetics, needs redefinition today. In this account, the first two phases of 20th century genetics are designated the "classical" and the "neoclassical" periods, and the current molecular-genetic era the "modern period." While the first two stages generated increasing clarity about the nature of the gene, the present period features complexity and confusion. Initially, the term "gene" was coined to denote an abstract "unit of inheritance," to which no specific material attributes were assigned. As the classical and neoclassical periods unfolded, the term became more concrete, first as a dimensionless point on a chromosome, then as a linear segment within a chromosome, and finally as a linear segment in the DNA molecule that encodes a polypeptide chain. This last definition, from the early 1960s, remains the one employed today, but developments since the 1970s have undermined its generality. Indeed, they raise questions about both the utility of the concept of a basic "unit of inheritance" and the long implicit belief that genes are autonomous agents. Here, we review findings that have made the classic molecular definition obsolete and propose a new one based on contemporary knowledge.

Dissolution of hypotheses in biochemistry: three case studies

The history of biochemistry and molecular biology is replete with examples of erroneous theories that persisted for considerable lengths of time before they were rejected. This paper examines patterns of dissolution of three such erroneous hypotheses: The idea that nucleic acids are tetrads of the four nucleobases ('the tetranucleotide hypothesis'); the notion that proteins are collinear with their encoding genes in all branches of life; and the hypothesis that proteins are synthesized by reverse action of proteolytic enzymes. Analysis of these cases indicates that amassed contradictory empirical findings did not prompt critical experimental testing of the prevailing theories nor did they elicit alternative hypotheses. Rather, the incorrect models collapsed when experiments that were not purposely designed to test their validity exposed new facts.

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.

On the role of alphaThr183 in the allosteric regulation and catalytic mechanism of tryptophan synthase

The catalytic activity and substrate channeling of the pyridoxal 5'-phosphate-dependent tryptophan synthase alpha(2)beta(2) complex is regulated by allosteric interactions that modulate the switching of the enzyme between open, low activity and closed, high activity states during the catalytic cycle. The highly conserved alphaThr183 residue is part of loop alphaL6 and is located next to the alpha-active site and forms part of the alpha-beta subunit interface. The role of the interactions of alphaThr183 in alpha-site catalysis and allosteric regulation was investigated by analyzing the kinetics and crystal structures of the isosteric mutant alphaThr183Val. The mutant displays strongly impaired allosteric alpha-beta communication, and the catalytic activity of the alpha-reaction is reduced one hundred fold, whereas the beta-activity is not affected. The structural work establishes that the basis for the missing inter-subunit signaling is the lack of loop alphaL6 closure even in the presence of the alpha-subunit ligands, 3-indolyl-D-glycerol 3'-phosphate, or 3-indolylpropanol 3'-phosphate. The structural basis for the reduced alpha-activity has its origins in the missing hydrogen bond between alphaThr183 and the catalytic residue, alphaAsp60.

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.

Role of diffusion in the folding of the alpha subunit of tryptophan synthase from Escherichia coli

The rate-limiting step in the folding of the alpha subunit of tryptophan synthase has been proposed to be the association of two folding units. To probe the role of diffusion in this rate-limiting step, the urea-induced unfolding and refolding of the protein was examined in the presence of a number of viscosity-enhancing agents. The analysis was simplified by studying the effect of these agents on folding unit dissociation, the rate-limiting unfolding reaction, and the reverse of the rate-limiting step in refolding. In the presence of ethylene glycol, the relaxation times for unfolding to the same final conditions increased with increasing concentration of the cosolvent. When the effects of the cosolvent on protein stability were taken into account, the rates were found to show a unitary linear dependence on the viscosity of the solution. Similar results were obtained with glycerol and low concentrations of glucose, demonstrating that the effect is general and not specific to any viscogenic agent. These results clearly demonstrate that the rate-limiting folding unit association/dissociation reaction in the alpha subunit of tryptophan synthase involves a diffusional process.

Transcription stimulates recombination. II. Generalized transduction of Escherichia coli by phages T1 and T4

Phage Mu was inserted in the trpE gene of one donor Escherichia coli strain and in the lac promoter of another. Strains with Mu prophage mutations which permitted transcription of genes whose transcription had been polarly blocked by the Mu insertion were isolated and called "bypass" strains. The transducing phages T1am, and T1am,ST, and, in one instance, T4GT7 were grown on both the bypass and the original strains. After growth on the bypass strains transducing phages were able to transduce Trp+ and Lac+, respectively, to a variety of Trp- and Lac- strains more efficiently than after growth on nonbypass strains. These results support the idea that crossovers required for generalized transduction occur more efficiently if the specific region is transcribed by both interacting parental molecules.

Characterization of a slow folding reaction for the alpha subunit of tryptophan synthase

The equilibria and kinetics of urea-induced unfolding and refolding of the alpha subunit of tryptophan synthase of E. coli have been examined for their dependences on viscosity, pH, and temperature in order to investigate the properties of one of the rate-limiting steps, domain association. A viscosity enhancer, 0.58 M sucrose, was found to slow unfolding and accelerate refolding. This apparently anomalous result was shown to be due to the stabilizing effect of sucrose on the folding reaction. After accounting for this stabilization effect by using linear free-energy plots, the unfolding and refolding kinetics were found to have a viscosity dependence. A decrease in pH was found to stabilize the domain association reaction by increasing the refolding rate and decreasing the unfolding rate. This effect was accounted for by protonation of a single residue with a pK value of 8.8 in the native state and 7.1 in the intermediate, in which the two domains are not yet associated. The activation energy of unfolding is 4.8 kcal/mol, close to the diffusion limit. The negative activation entropy of unfolding, -47 cal/deg-mol, which controls this reaction, may result from ordering of solvent about the newly exposed domain interface of the transition state. These results may provide information on the types of noncovalent interactions involved in domain association and improve the ability to interpret the folding of mutants with single amino-acid substitutions at the interface.

Effects of the phenylalanine-22----leucine, glutamic acid-49----methionine, glycine-234----aspartic acid, and glycine-234----lysine mutations on the folding and stability of the alpha subunit of tryptophan synthase from Escherichia coli

The effects of four single amino acid replacements on the stability and folding of the alpha subunit of tryptophan synthase from Escherichia coli have been investigated by ultraviolet differences spectroscopy. In previous studies [Miles, E. W., Yutani, K., & Ogasahara, K. (1982) Biochemistry 21, 2586], it had been shown that the urea-induced unfolding at pH 7.8, 25 degrees C, proceeds by the initial unfolding of the less stable carboxyl domain (residues 189-268) followed by the unfolding of the more stable amino domain (residues 1-188). The effects of the Phe-22----Leu, Glu-49----Met, Gly-234----Asp, and Gly-234----Lys mutants on the equilibrium unfolding process can all be understood in terms of the domain unfolding model. With the exception of the Glu-49----Met replacement, the effects on stability are small. In contrast, the effects of three of the four mutations on the kinetics of interconversion of the native form and one of the stable partially folded intermediates are dramatic. The results for the Phe-22----Leu and Gly-234----Asp mutations indicate that these residues play a key role in the rate-limiting step. The Glu-49----Met mutation increases the stability of the native form with respect to that of the intermediate but does not affect the rate-limiting step. The Gly-234----Lys mutation does not affect either the stability or the kinetics of folding for the transition between native and intermediate forms. The changes in stability calculated from the unfolding and refolding rate constants agree quantitatively with those obtained from the equilibrium data. When considered with the results from a previous study on the Gly-211----Glu replacement [Matthews, C. R., Crisanti, M. M., Manz, J. T., & Gepner G. L. (1983) Biochemistry 22, 1445], it can be concluded that the rate-limiting step in the conversion of the intermediate to the native conformation involves either domain association or some other type of molecule-wide phenomenon.

Alteration of capsular type of encapsulated strains of Staphylococcus aureus during freeze-drying and storage

Remarkable alteration was shown in capsular type antigen production in encapsulated strains of Staphylococcus aureus stored by lyophilization for 10 years. This alteration was further elucidated by antibody production in rabbits immunized with the altered strain and by absorbing the antibodies with representative capsular type strains.

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.

Construction and characterization of Escherichia coli polA-lacZ gene fusions

The promoter of the polA gene of Escherichia coli K-12 was fused to the lacZ gene by selecting deletions within a lambda lacZ polA transducing phage. Four fusions, deleting varying amounts of the polA gene, were characterized. The polA promoter was found to be approximately 3% as active as the fully induced lac promoter. This figure is compatible with the normal intracellular level of deoxyribonucleic acid polymerase I. No evidence was found for outogenous regulation of transcription from the polA promoter. Expression from this promoter was influenced by neither recA nor mitomycin C, but uvrD and uvrE mutations reduced expression slightly.

Spontaneous mutational specificity of drug resistance plasmid pKM101 in Escherichia coli

Plasmid pKM101 enhances the frequency of spontaneous and ultraviolet light-induced mutations in Escherichia coli and protects the cells against the lethal effects of ultraviolet irradiation. By analyzing reversion patterns of defined trpA alleles, we showed that pKM101 caused all types of spontaneous base-pair substitution mutations with the possible exception of guanine . cytosine leads to adenine. thymine transitions. Neither insertion nor deletion frameshift mutations were enhanced. Transversions were more strongly enhanced than transitions, and adenine . thymine base pairs appeared more susceptible to pKM101 mutator activity than guanine . cytosine base pairs. In addition, there were effects from neighboring base pairs and genetic background that influenced the mutator activity of pKM101.

HindII and HindIII restriction maps of the attphi80-tonB-trp region of the Escherichia coli genome, and location of the tonB gene

The HindII and HindIII restriction maps of the attphi80-tonB-trp region of the Escherichia coli chromosome are presented. Analysis of phage DNAs carrying tonB mutations has allowed identification of a 1,730-base pair HindII fragment containing at least part of the tonB gene. This fragment is 4,020 base pairs from the end of trpA, with the total distance from attphi80 to trpA being 6,550 +/- 800 base pairs. Properties of hybrid plasmids containing insertions of various tonB+ restriction fragments suggest that tonB lies completely within the 1,730-base pair fragment. In addition, apparent fusions of beta-galactoside to proteins within the tonB region suggest that the entire region codes for more than one polypeptide.

Context effects on nonsense codon suppression in Escherichia coli

The influence of mRNA context on nonsense codon suppression has been studied by suppression measurements at one site in the Escherichia coli trpE gene and at two sites in the trpA gene. The ratio of suppression efficiencies of amber and ochre codons at each site (homotopic pairs) has been compared using ochre suppressing derivatives of tRNATyr. This ratio is independent of differential effects of the inserted amino acid on enzyme function. We have found that mRNA context can change the ratio of suppression efficiencies of homotopic nonsense codons at the three sites in the trp gene system over a ten-fold range. The causes of such variation, and, in particular the effect of certain adjacent nucleotides on nonsense codon suppression are considered.

Tryptophan synthetase alpha(5.7-S): novel molecular species formed within Escherichia coli

A novel molecular species contributes about 5% of the total tryptophan synthetase of Escherichia coli derepressed for the trp operon enzymes. The new species is identified under conditions in which the dissociation of the two nonidentical subunits of the tryptophan synthetase complex is favored. The new species sediments at 5.7S, catalyzes the conversion of indole-3-glycerol phosphate to indole, and has been designated alpha(5.7-S). Although alpha(5.7-S) is not observed in extracts of trpA or trpB mutant strains deficient in the ability to form tryptophan synthetase alpha or beta2 subunits, respectively, a mixture of the two extracts allows the formation of alpha(5.7-S). Similar results are obtained when a homogeneous alpha protein is mixed with an extract of a trpA mutant strain, suggesting that the interaction of alpha and beta2 proteins is obligatory for alpha(5.7-S) formation. One can obtain a beta2 protein preparation that when mixed with a pure alpha protein gives no alpha(5.7-S). Therefore, the interaction of alpha and beta2 proteins alone is not sufficient for the formation of alpha(5.7-S). When a mixture of alpha and beta2 proteins devoid of alpha(5.7-S) is added to extracts of trp deletion mutants, the novel species can be reconstituted in vitro only when deletions are used that carry at least the operator-proximal part of the trpB gene. Therefore, it is concluded that the alpha(5.7-S) species of tryptophan synthetase results from the interaction of the alpha protein, the beta2 protein, and a third component, beta', specified by the deoxyribonucleic acid defined by the end points of two trp deletion mutants.

Genetic map of the lactose repressor gene (i) of Escherichia coli

39 tonB i(-) deletions were used to map 57 independently isolated i gene mutants. Methods selective for i(+) recombinants from various types of i mutants are described. i(+) recombination frequencies of 6 x 10(-6) to 6 x 10(-7) can be detected in the different selective systems. Twenty i(s) mutations and 12 i(-d) mutations map in distinct but different regions of the gene. i(-) (sus) mutations are scattered over the gene.

Pseudomonas putida tryptophan synthetase

The two protein components of Pseudomonas putida tryptophan synthetase have been purified to homogeneity. Although there is general similarity between the Pseudomonas enzyme and that of the enteric bacteria, many differences were found. Components from Escherichia coli and P. putida do not stimulate each other enzymatically, and the enzymes differ in their response to monovalent cations. Serine deamination occurs best with the intact enzyme of P. putida, not with the beta(2) subunit alone as in E. coli. The amino acid compositions of the alpha subunits differ appreciably. These findings extend earlier studies showing differences between enteric organisms and pseudomonads in the regulation and genetic organization of the enzymes of the tryptophan pathway.

Pseudomonas putida tryptophan synthetase: partial sequence of the subunit

There is 50% identity in the sequences of the first 50 residues of the alpha chains of Escherichia coli and Pseudomonas putida. No deletions or additions of residues are found in this region, except for the N-terminal methionine residue which is missing in the polypeptide isolated from P. putida. Most of the residues which differ are chemically dissimilar, and half of them are specified by codons which differ by more than a single base. The two residues known by mutational analysis to be essential for catalysis in E. coli are conserved in P. putida. The potential taxonomic usefulness of information of this sort is analyzed.

ICR-induced frameshift mutations in the histidine operon of Salmonella

Both the acridine half-mustard, ICR191, and the nonalkylating azaacridine derivative, ICR364-OH, induce three classes of frameshift mutations in the histidine operon of Salmonella typhimurium. (i) One class is completely stable in reversion tests and is presumed to represent deletion of one or a few critical nucleotide pairs or two nearby frameshifts. One extended deletion was found out of 11 stable mutations. (ii) Of two spontaneously reverting classes which also are considered to predominantly involve base deletions, one is unaffected in reversion with ICR191, nitrosoguanidine, and diethylsulfate, and the other is induced to revert with ICR191. (iii) A third class, considered to predominantly involve base additions, responds in reversion tests with ICR191 as well as with nitrosoguanidine and diethylsulfate. Other investigators have shown that one mutant of this class is a "plus" frameshift and that nitrosoguanidine acts in reversion to delete a guanine plus cytosine base pair. Although such plus frameshifts are found with high frequency among mutations selected from acridine-treated bacteria or when strong selection pressure is applied for their detection in reversion tests, data from this laboratory indicate that this class of plus frameshifts is rare among mutations derived spontaneously or after treatment with a variety of other mutagens. Finally, we demonstrate that the alkylating ICR191 and the nonalkylating ICR364-OH preferentially cause mutations in different chromosome regions and that their spectra of activity only partially overlap that found for spontaneous frameshift mutations.

The sequence of amino acids in insulin isolated from islet tissue of the cod (Gadus callarias)

1. S-Aminoethylcysteinyl derivatives of the A and B chains of cod insulin were prepared from the individual S-sulpho chains. 2. Studies on small peptides derived from the S-aminoethylated peptide chains by treatment with trypsin allowed the amino acid sequences in the region of the cysteinyl residues of the A and B peptide chains to be defined. 3. The six amide groups in cod insulin were located by complete digestion of small peptides from the A and B chains with aminopeptidase followed by amino acid analyses. 4. The results, together with previous studies on the oxidized A and B chains, define the sequences of the 51 amino acids that constitute cod insulin.

T4 bacteriophage mutants suppressible by a missense suppressor which inserts glycine in place of arginine for the codon AGA

Phage mutants of T4 have been isolated which can multiply only on Escherichia coli strains which contain a missense suppressor which is known to cause the substitution of glycine for arginine in response to the AGA codon. Mutations producing the suppressible phenotype were mapped and shown to occur in six different phage cistrons. Two of the cistrons were concerned with deoxyribonucleic acid synthesis, two were concerned with phage structural components, and two were concerned with functions required for growth in E. coli K-12 but not in E. coli B. The burst size of the different phage mutants grown on strains carrying the same suppressor was dependent upon the efficiency of suppression, which in turn is known to be dependent upon the glycyl-transfer ribonucleic acid synthetase activity.

Substrate binding properties of mutant and wild-type A proteins of Escherichia coli tryptophan synthetase

Most of the mutant A proteins studied appear to be similar to the normal enzyme both in their apparent conformation about the critical cysteine residues and their ability to bind substrate. Two mutant proteins, in which a glutamic acid or arginine residue is substituted for a glycine residue, do appear abnormal suggesting that these primary structural changes radically affect the conformation in regions at or near the site or sites of substrate binding.