Threonine Deaminase from Escherichia coli

Metabolic engineering of threonine catabolism enables Saccharomyces cerevisiae to produce propionate under aerobic conditions

BACKGROUND

Propionate is widely used as a preservative in the food and animal feed industries. Propionate is currently produced by petrochemical processes, and fermentative production of propionate remains challenging.

METHODS AND RESULTS

In this study, a synthetic propionate pathway was constructed in the budding yeast Saccharomyces cerevisiae, for propionate production under aerobic conditions. Through expression of tdcB and aldH from Escherichia coli and kivD from Lactococcus lactis, L-threonine was converted to propionate via 2-ketobutyrate and propionaldehyde. The resulting yeast aerobically produced 0.21 g/L propionate from glucose in a shake flask. Subsequent overexpression of pathway genes and elimination of competing pathways increased propionate production to 0.37 g/L. To further increase propionate production, carbon flux was pulled into the propionate pathway by weakened expression of pyruvate kinase (PYK1), together with overexpression of phosphoenolpyruvate carboxylase (ppc). The final propionate production reached 1.05 g/L during fed-batch fermentation in a fermenter.

CONCLUSIONS AND IMPLICATIONS

In this work, a yeast cell factory was constructed using synthetic biology and metabolic engineering strategies to enable propionate production under aerobic conditions. Our study demonstrates engineered S. cerevisiae as a promising alternative for the production of propionate and its derivatives. This article is protected by copyright. All rights reserved.

Identification of Core Regulatory Genes and Metabolic Pathways for the n-Propanol Synthesis in Saccharomyces cerevisiae

The n-propanol produced by Saccharomyces cerevisiae has a remarkable effect on the taste and flavor of Chinese Baijiu. The n-propanol metabolism-related genes were deleted to evaluate the role in the synthesis of n-propanol to ascertain the key genes and pathways for the production of n-propanol by S. cerevisiae. The results showed that CYS3, GLY1, ALD6, PDC1, ADH5, and YML082W were the key genes affecting the n-propanol metabolism in yeast. The n-propanol concentrations of α5ΔGLY1, α5ΔCYS3, and α5ΔALD6 increased by 121.75, 22.75, and 17.78%, respectively, compared with α5. The n-propanol content of α5ΔPDC1, α5ΔADH5, and α5ΔYML082W decreased by 24.98, 8.35, and 8.44%, respectively, compared with α5. The contents of intermediate metabolites were measured, and results showed that the mutual transformation of glycine and threonine in the threonine pathway and the formation of propanal from 2-ketobutyrate were the core pathways for the formation of n-propanol. Additionally, YML082W played important role in the synthesis of n-propanol by directly producing 2-ketobutyric acid through l-homoserine. This study provided valuable insights into the n-propanol synthesis in S. cerevisiae and the theoretical basis for future optimization of yeast strains in Baijiu making.

Allosteric regulation of Bacillus subtilis threonine deaminase, a biosynthetic threonine deaminase with a single regulatory domain

The enzyme threonine deaminase (TD) is a key regulatory enzyme in the pathway for the biosynthesis of isoleucine. TD is inhibited by its end product, isoleucine, and this effect is countered by valine, the product of a competing biosynthetic pathway. Sequence and structure analyses have revealed that the protomers of many TDs have C-terminal regulatory domains, composed of two ACT-like subdomains, which bind isoleucine and valine, while others have regulatory domains of approximately half the length, composed of only a single ACT-like domain. The regulatory responses of TDs from both long and short sequence varieties appear to have many similarities, but there are significant differences. We describe here the allosteric properties of Bacillus subtilis TD ( bsTD), which belongs to the short variety of TD sequences. We also examine the effects of several mutations in the regulatory domain on the kinetics of the enzyme and its response to effectors. The behavior of bsTD can be analyzed and rationalized using a modified Monod-Wyman-Changeux model. This analysis suggests that isoleucine is a negative effector, and valine is a very weak positive effector, but that at high concentrations valine inhibits activity by competing with threonine for binding to the active site. The behavior of bsTD is contrasted with the allosteric behavior reported for TDs from Escherichia coli and Arabidopsis thaliana, TDs with two subdomains. We suggest a possible evolutionary pathway to the more complex regulatory effects of valine on the activity of TDs of the long sequence variety, e.g., E. coli TD.

Amino acid biosynthesis: new architectures in allosteric enzymes

This review focuses on the allosteric controls in the Aspartate-derived and the branched-chain amino acid biosynthetic pathways examined both from kinetic and structural points of view. The objective is to show the differences that exist among the plant and microbial worlds concerning the allosteric regulation of these pathways and to unveil the structural bases of this diversity. Indeed, crystallographic structures of enzymes from these pathways have been determined in bacteria, fungi and plants, providing a wonderful opportunity to obtain insight into the acquisition and modulation of allosteric controls in the course of evolution. This will be examined using two enzymes, threonine synthase and the ACT domain containing enzyme aspartate kinase. In a last part, as many enzymes in these pathways display regulatory domains containing the conserved ACT module, the organization of ACT domains in this kind of allosteric enzymes will be reviewed, providing explanations for the variety of allosteric effectors and type of controls observed.

A Mathematical Model for the Branched Chain Amino Acid Biosynthetic Pathways of Escherichia coli K12

As a first step toward the elucidation of the systems biology of the model organism Escherichia coli, it was our goal to mathematically model a metabolic system of intermediate complexity, namely the well studied end product-regulated pathways for the biosynthesis of the branched chain amino acids L-isoleucine, L-valine, and L-leucine. This has been accomplished with the use of kMech (Yang, C.-R., Shapiro, B. E., Mjolsness, E. D., and Hatfield, G. W. (2005) Bioinformatics 21, in press), a Cellerator (Shapiro, B. E., Levchenko, A., Meyerowitz, E. M., Wold, B. J., and Mjolsness, E. D. (2003) Bioinformatics 19, 677-678) language extension that describes a suite of enzyme reaction mechanisms. Each enzyme mechanism is parsed by kMech into a set of fundamental association-dissociation reactions that are translated by Cellerator into ordinary differential equations. These ordinary differential equations are numerically solved by Mathematica. Any metabolic pathway can be simulated by stringing together appropriate kMech models and providing the physical and kinetic parameters for each enzyme in the pathway. Writing differential equations is not required. The mathematical model of branched chain amino acid biosynthesis in E. coli K12 presented here incorporates all of the forward and reverse enzyme reactions and regulatory circuits of the branched chain amino acid biosynthetic pathways, including single and multiple substrate (Ping Pong and Bi Bi) enzyme kinetic reactions, feedback inhibition (allosteric, competitive, and non-competitive) mechanisms, the channeling of metabolic flow through isozymes, the channeling of metabolic flow via transamination reactions, and active transport mechanisms. This model simulates the results of experimental measurements.

An enzyme mechanism language for the mathematical modeling of metabolic pathways

MOTIVATION

As a first step toward the elucidation of the systems biology of complex biological systems, it was our goal to mathematically model common enzyme catalytic and regulatory mechanisms that repeatedly appear in biological processes such as signal transduction and metabolic pathways.

RESULTS

We describe kMech, a Cellerator language extension that describes a suite of enzyme mechanisms. Each enzyme mechanism is parsed by kMech into a set of fundamental association-dissociation reactions that are translated by Cellerator into ordinary differential equations that are numerically solved by Mathematica. In addition, we present methods that use commonly available kinetic measurements to estimate rate constants required to solve these differential equations.

Production of polyesters in transgenic plants

Polyhydroxyalkanoates (PHAs) are bacterial polyesters having the properties of biodegradable thermoplastics and elastomers. Synthesis of PHAs has been demonstrated in transgenic plants. Both polyhydroxybutyrate and the co-polymer poly(hydroxybutyrate-co-hydroxyvalerate) have been synthesized in the plastids of Arabidopsis thaliana and Brassica napus. Furthermore, a range of medium-chain-length PHAs has also been produced in plant peroxisomes. Development of agricultural crops to produce PHA on a large scale and at low cost will be a challenging task requiring a coordinated and stable expression of several genes. Novel extraction methods designed to maximize the use of harvested plants for PHA, oil, carbohydrate, and feed production will be needed. In addition to their use as plastics, PHAs can also be used to modify fiber properties in plants such as cotton. Furthermore, PHA can be exploited as a novel tool to study the carbon flux through various metabolic pathways, such as the fatty acid beta-oxidation cycle.

Interim report on genomics of Escherichia coli

We present a summary of recent progress in understanding Escherichia coli K-12 gene and protein functions. New information has come both from classical biological experimentation and from using the analytical tools of functional genomics. The content of the E. coli genome can clearly be seen to contain elements acquired by horizontal transfer. Nevertheless, there is probably a large, stable core of >3500 genes that are shared among all E. coli strains. The gene-enzyme relationship is examined, and, in many cases, it exhibits complexity beyond a simple one-to-one relationship. Also, the E. coli genome can now be seen to contain many multiple enzymes that carry out the same or closely similar reactions. Some are similar in sequence and may share common ancestry; some are not. We discuss the concept of a minimal genome as being variable among organisms and obligatorily linked to their life styles and defined environmental conditions. We also address classification of functions of gene products and avenues of insight into the history of protein evolution.

A new method for evaluation and dietary therapy of congenital: deficiencies of amino acid metabolic enzymes. Linear system analysis and optimization of feedback inputs for the metabolic pathways of lysine, methionine and isoleucine

We intended to elucidate an integrated mathematical model of amino acid metabolism and we propose a system for optimization treatment of disturbed metabolic states caused by congenital enzyme deficiencies. Our analysis focused on the metabolic pathway starting at asparaginic acid proceeding to isoleucine, methionine and lysine. The rate of change in the concentration of the biochemical species was expressed as 21 linear rate equations. We obtained the rate constants and the magnitude of feedback from reported experimental data. Linear systems analysis revealed that the metabolic system under study was stable but uncontrollable. These properties were insensitive to changes in the magnitude of feedback. To show the effect of optimizing the feedback so that it minimizes the square of the concentration of the species and the control input, we analyzed the impulse response of the species, transient response and the singular value of the system for four cases; (1) at the physiological state without optimizing the feedback, (2) at the physiological state attained after optimizing the feedback, (3) at the pathophysiological state attained with enzyme deficiency states for lysine and methionine metabolism without optimizing the feedback, and (4) at the pathophysiological state attained after optimizing the feedback for enzyme deficiencies. In the enzyme deficient model, the impulse response oscillated and lasted longer than that in the physiological state. These changes appeared even in the species on other branched pathways. The singular value was elevated in the enzyme deficient state. By optimizing the feedback, all the impulse responses in the enzyme deficient state recovered to nearly those in the normal physiological state. Similarly, the transient response and the singular value in the enzyme deficient state recovered to nearly the normal physiological values. We elucidated the numerical value of the feedback gain for this optimization. The present analysis is useful for the evaluation of the integrated properties of amino acid metabolism and the optimization technique is potentially of use for determining a treatment course for congenital metabolic enzyme deficiencies.

Growth rate-related regulation of the ilvGMEDA operon of Escherichia coli K-12 is a consequence of the polar frameshift mutation in the ilvG gene of this strain

In Escherichia coli K-12 the intracellular levels of threonine deaminase and transaminase B, products of ilvA and ilvE, respectively, in the ilvGMEDA operon, increase with increasing growth rates (S. Pedersen, P. L. Bloch, S. Reeh, and F. C. Neidhardt, Cell 14:179-190, 1978). However, the transcriptional activities of the upstream ilvpG and the internal ilvpE promoters do not increase. Therefore, the growth rate-related expression of this operon is not regulated at the level of transcription initiation. Unlike other wild-type E. coli strains, E. coli K-12 contains a polar frameshift mutation in the ilvG gene (R. P. Lawther, D. H. Calhoun, C. W. Adams, C. A. Hauser, J. Gray, and G. W. Hatfield, Proc. Natl. Acad. Sci. USA 78:922-925, 1981). In an E. coli K-12 (IlvG+) derivative strain, where the reading frame of the ilvG gene is restored, no growth rate-related expression of the ilvGMEDA operon is observed. Thus, the growth rate-related expression of the ilvGMEDA operon in E. coli K-12 is the fortuitous consequence of the polar frameshift mutation in the ilvG gene of this strain.

Dissociation of enzyme oligomers: a mechanism for allosteric regulation

Most enzymes exist as oligomers or polymers, and a significant subset of these (perhaps 15% of all enzymes) can reversibly dissociate and reassociate in response to an effector ligand. Such a change in subunit assembly usually is accompanied by a change in enzyme activity, providing a mechanism for regulation. Two models are described for a physical mechanism, leading to a change in activity: (1) catalytic activity depends on subunit conformation, which is modulated by subunit dissociation; and (2) catalytic or regulatory sites are located at subunit interfaces and are disrupted by subunit dissociation. Examples of such enzymes show that both catalytic sites and regulatory sites occur at the junction of 2 subunits. In addition, for 9 enzymes, kinetic studies supported the existence of a separate regulatory site with significantly different affinity for the binding of either a substrate or a product of that enzyme. Over 40 dissociating enzymes are described from 3 major metabolic areas: carbohydrate metabolism, nucleotide metabolism, and amino acid metabolism. Important variables that influence enzyme dissociation include: enzyme concentration, ligand concentration, other cellular proteins, pH, and temperature. All these variables can be readily manipulated in vitro, but normally only the first two are physiological variables. Seven of these enzymes are most active as the dissociated monomer, the others as oligomers, emphasizing the importance of a regulated equilibrium between 2 or more conformational states. Experiments to test whether enzyme dissociation occurs in vivo showed this to be the case in 6 out of 7 studies, with 4 different enzymes.

An efficient approach to identify ilvA mutations reveals an amino-terminal catalytic domain in biosynthetic threonine deaminase from Escherichia coli

High-level expression of the regulatory enzyme threonine deaminase in Escherichia coli strains grown on minimal medium that are deficient in the activities of enzymes needed for branched-chain amino acid biosynthesis result in growth inhibition, possibly because of the accumulation of toxic levels of alpha-ketobutyrate, the product of the committed step in isoleucine biosynthesis. This condition affords a means for selecting genetic variants of threonine deaminase that are deficient in catalysis by suppression of growth inhibition. Strains harboring mutations in ilvA that decreased the catalytic activity of threonine deaminase were found to grow more rapidly than isogenic strains containing wild-type ilvA. Modification of the ilvA gene to introduce additional unique, evenly spaced restriction enzyme sites facilitated the identification of suppressor mutations by enabling small DNA fragments to be subcloned for sequencing. The 10 mutations identified in ilvA code for enzymes with significantly reduced activity relative to that of wild-type threonine deaminase. Values for their specific activities range from 40% of that displayed by wild-type enzyme to complete inactivation as evidenced by failure to complement an ilvA deletion strain to isoleucine prototrophy. Moreover, some mutant enzymes showed altered allosteric properties with respect to valine activation and isoleucine inhibition. The location of the 10 mutations in the 5' two-thirds of the ilvA gene is consistent with suggestions that threonine deaminase is organized functionally with an amino-terminal domain that is involved in catalysis and a carboxy-terminal domain that is important for regulation.

Functional and structural analyses of threonine dehydratase from Corynebacterium glutamicum

Threonine dehydratase activity is an important element in the flux control of isoleucine biosynthesis. The enzyme of Corynebacterium glutamicum demonstrates a marked sigmoidal dependence of initial velocity on the threonine concentration, a dependence that is consistent with substrate-promoted conversion of the enzyme from a low-activity to a high-activity conformation. In the presence of the negative allosteric effector isoleucine, the K0.5 increased from 21 to 78 mM and the cooperativity, as expressed by the Hill coefficient increased from 2.4 to 3.7. Valine promoted opposite effects: the K0.5 was reduced to 12 mM, and the enzyme exhibited almost no cooperativity. Sequence determination of the C. glutamicum gene for this enzyme revealed an open reading frame coding for a polypeptide of 436 amino acids. From this information and the molecular weight determination of the native enzyme, it follows that the dehydratase is a tetramer with a total mass of 186,396 daltons. Comparison of the deduced polypeptide sequence with the sequences of known threonine dehydratases revealed surprising differences from the C. glutamicum enzyme in the carboxy-terminal portion. This portion is greatly reduced in size, and a large gap of 95 amino acids must be introduced to achieve homology. Therefore, the C. glutamicum enzyme must be considered a small variant of threonine dehydratase that is typically controlled by isoleucine and valine but has an altered structure reflecting a topological difference in the portion of the protein most likely to be important for allosteric regulation.

An improved method for purification of L-threonine deaminase from rat liver

L-threonine deaminase was obtained at a high degree of purity from rat liver. Two main steps were added to the previously reported procedure: cryoprecipitation and chromatofocusing (in the presence of a specific KCl concentration). The purification factor was 3,090 and the specific activity 989. The method is very reproducible and convenient. It gives the highest specific activity and the highest degree of purity of the enzyme recorded to date.

The complete nucleotide sequence of the ilvGMEDA cluster of Escherichia coli K-12

The ilvGMEDA gene cluster of Escherichia coli K-12 has been the focus of intensive genetic and biochemical analysis for the past 30 years. Genetic regulation of the ilvGMEDA cluster involves attenuation, internal promoters, internal Rho-dependent termination sites, a site of polarity in the ilvG pseudogene of the wild-type organism, and autoregulation by the ilvA gene product, the biosynthetic L-threonine deaminase. We have now completed the nucleotide sequence of the 6600-bp cluster and have analyzed it, along with the ilvYC, ilvBN, and ilvIH genes, for codon frequencies and possible evolutionary relationships. The isoleucine content of each of the gene products of the ilvGMEDA cluster is quite similar (less than a two-fold variation), thus excluding one possible interpretation of the isoleucine-specific downstream amplification phenomenon. There is no evidence for retrograde evolution in the cluster since no significant homologies are detectable among genes that catalyze sequential reactions of the pathway. A highly significant homology does exist, however, between the threonine deaminases of yeast mitochondria and E. coli. The sequence at the boundary of the ilvA and ilvD genes is TAATAATG, so that the second TAA stop codon of ilvD overlaps the ATG initiation codon of ilvA.

Role of small subunit (IlvN polypeptide) of acetohydroxyacid synthase I from Escherichia coli K-12 in sensitivity of the enzyme to valine inhibition

Most of the coding sequence for the IlvN polypeptide subunit of acetohydroxyacid synthase I was deleted from the ilvB+ ilvN+ plasmid pTCN12 by in vitro methods. Several ilvB+ delta ilvN derivatives of pTCN12 were identified among transformants of a strain otherwise lacking any acetohydroxyacid synthase. Deletion derivatives produced an enzymatically active IlvB polypeptide, as shown by the Ilv+ phenotype of transformed cells and by immunologic and enzymatic assays. However, whereas the growth of pTCN12 transformants was sensitive to valine inhibition, growth of the ilvB+ delta ilvN transformants was relatively resistant. Moreover, in vitro analyses confirmed that both acetolactate and acetohydroxybutyrate synthesis in extracts of the ilvB+ delta ilvN transformants was resistant to valine inhibition, in comparison with that in extracts of pTCN12 transformants or with that catalyzed by purified acetohydroxyacid synthase I. The IlvN polypeptide had a minimal effect, if any, on IlvB polypeptide accumulation as measured by immunoprecipitation, but its absence resulted in a greater than 10-fold reduction in enzyme specific activity.

Cloning of the ilvA538 gene coding for feedback-hypersensitive threonine deaminase from Escherichia coli K-12

A variety of experimental results implicate the ilvA gene product, threonine deaminase, as an autoregulatory protein that affects the expression of its own gene and those coding for some related proteins. Some of the most direct evidence comes from the analysis of mutations in the ilvA gene with pleiotropic genetic regulatory effects. The most extensively documented mutation, ilvA538, lowers the expression of and abolishes repression control of the ilvGEDA transcription unit. A pleiotropic effect of the ilvA538 mutation, which may be either incidental or mechanistically related to the loss of repression control, renders threonine deaminase feedback hypersensitive to the inhibition of catalytic activity by the pathway end product, isoleucine. We transferred this mutation to lambda dilv phage and pBR322 derivatives. Direct enzyme assay of the plasmid- and phage-coded ilvA538 gene product in delta ilv hosts confirmed the feedback hypersensitivity of the enzyme product. In conjunction with the ilvG671 (phenotype, ILvG+ Valr; previously designated ilvO671) allele located in cis, high levels of the plasmid and lambda dilv phage-coded mutant enzyme suitable for protein purification were observed. Deletion mapping experiments with lambda dilv phage confirmed that the ilvA538 mutation, and not mutations promoter proximal to ilvD (transcription is from ilvG to ilvA), confer a loss of repression control. These genetic mapping studies indicate, however, that an additional mutation(s) may be present that contributes, at least in part, to the reduced enzyme levels in strains with the ilvA538 mutation.

Identification of the protein products of the rrnC, ilv, rho region of the Escherichia coli K-12 chromosome

Two methods have been used to identify the protein products of the Escherichia coli K-12 ilv region at 84 min and the flanking rrnC (counterclockwise) and rho (clockwise) loci. First, a set of lambda dilv specialized transducing phages, including some phages that carry rho and others that carry part of rrnC, was used to infect UV irradiated cells. The proteins produced by the infecting lambda dilv phage were selectively labelled with radioactivity amino acids and identified by SDS gel electrophoresis and autoradiography. Second, restriction enzyme fragments were cloned from the lambda dilv phage into pBR322 and the plasmid specific gene products produced in maxicells were similarly identified by SDS gel electrophoresis and autoradiography. The proteins produced were correlated with specific genes and restriction enzyme fragments present in the lambda dilv phage and the pBR322 derivatives. Several ilv gene products that have previously been refractory to protein purification attempts have been identified for the first time by this technique. The presence of mutations at the ilvO site is shown to activate the cryptic ilvG gene and to result in the production of a 62,000 dalton protein. A 15,000 dalton protein of unknown function is synthesized from a DNA segment between ilv and rrnC. The rho gene was cloned from lambda dilv phage into pBR322 and shown to be dominant to a rho mutation on the host chromosome. The rho gene product and four additional proteins coded by genes near or between rho and ilv have been detected.

Genetical and structural analysis of a group of lambda ilv and lambda rho transducing phages

Eight lambda ilv C transducing phages generated from E. coli K12 secondary site lysogens have been analysed genetically and physically. Two of them carry, in addition, the rho gene and its promotor region, but not the cya gene. The ilv O 603 mutation has been located between ilv G and ilv E. Electrophoretic analysis of the proteins synthesized by these phages in a system of UV irradiated cells allowed us to assign molecular weights of 55000 and 66000 daltons to the ilv C and the ilv D gene products, respectively, and to show that an ilv G-encoded polypeptide of 60000 daltons is made from an ilv O- but not from an ilv O+ phage. The expression of the ilv G gene is discussed in the light of the recent finding of a promoter-attenuator region lying upstream to ilv G. Finally, we have found that one of the lambda ilv phages does not have the classical structure of a transducing phage.

Suppressors of a genetic regulatory mutation affecting isoleucine-valine biosynthesis in Escherichia coli K-12

Escherichia coli K-12 mutant PS187 carries a mutation, ilvA538, in the structural gene for the biosynthetic L-threonine deaminase that leads to a leucine-sensitive growth phenotype, an isoleucine- and leucine-hypersensitive L-threonine deaminase, and pleiotropic effects resulting in abnormally low and invariant expression of some of the isoleucine-valine biosynthetic enzymes. Fifty-eight derivatives of strain PS187 were isolated as resistant to growth inhibition by leucine, by valine, or by valine plus glycly-valine and were biochemically, genetically, and physiologically characterized. All of these derivatives produced the feedback-hypersensitive L-threonine deaminase, and thus presumably possess the ilvA538 allele of the parent strain. Elevated synthesis of L-threonine deaminase was observed in 41 of the 58 isolates. Among 18 strains analyzed genetically, only those with mutations linked to the ilv gene clusters at 83 min produced elevated levels of L-threonine deaminase. One of the strains, MSR91, isolated as resistant to valine plus glycyl-valine, was chosen for more detailed study. The locus in strain MSR91 conferring resistance was located in four factor crosses between ilvE and rbs, and is in or near the ilvO gene postulated to be a site controlling the expression of the ilvEDA genes. Synthesis of the ilvEDA gene products in strain MSR91 is constitutive and derepressed approximately 200-fold relative to the parent strain, indicating that the genetic regulatory effects of the ilvA538 allele have been suppressed. Strain MSR91 should be suitable for use in purification of the ilvA538 gene product, since enzyme synthesis is fully derepressed and the suppressor mutation is clearly not located within the ilvA gene.

Enhanced allosteric regulation of threonine deaminase and acetohydroxy acid synthase from Escherichia coli in a permeabilized-cell assay system

A permeabilized-cell technique for rapid assay of enzyme activity has revealed enhanced allosteric regulation of both threonine deaminase (L-threonine hydrolyase (deaminating), EC 4.2.1.16) and acethohydroxy acid synthease (acetolactate pyruvate-lyase (carboxylating), EC 4.1.3.18) in Escherichia col K-12. In the permeabilized cell assay threonine deaminase exhibited a higher Hill coefficient for inhibition by L-isoleucine, and acetohydroxy acid synthase exhibited a hypersensensitivity to allosteric inhibition by L-valine when compared to studies on crude extracts. We propose that these effects reflect the in situ microenvironments of both enzymes. Preliminary evidence further indicates that acetohydroxy acid synthase may loosely associate with the cell membrane.

A bacterial phenylalanine aminotransferase lacking pyridoxal 5'-phosphate as cofactor

A bacterium has been isolated from soil which metabolises phenylalanine initially through the action of a phenylalanine aminotransferase. This enzyme has been purified by conventional techniques and affinity chromatography and shown to be unusual among aminotransferases in not containing pyridoxal 5'-phosphate as cofactor.

Threonine deaminase from a nonsense mutant of Escherichia coli requiring isoleucine or pyridoxine: evidence for half-of-the-sites reactivity

The mutant IP7 of Escherichia coli B requires isoleucine or pyridoxine for growth as a consequence of a mutation in the gene coding for biosynthetic threonine deaminase. The mutation of IP7 was shown to be of the nonsense type by the following data: (1) reversion to isoleucine prototrophy involves the formation of external suppression at a high frequency, as shown by transduction experiments; and (ii) the isoleucine requirement is suppressed by lysogenization with a phage carrying the amber suppressor su-3. Cell extracts of the mutant strain contain a low activity of threonine deaminase. The possibility that this activity is biodegradative was ruled out by kinetic experiments. The mutant threonine deaminase was purified to homogeneity by conventional procedures. The enzyme is a dimer of identical subunits of an approximate molecular weight of 43,000 (Grimminger and Feldner, 1974), whereas the wild-type enzyme is a tetramer of 50,000-dalton subunits (Calhoun et al., 1973; Grimminger et al., 1973). The mutant enzyme is not inhibited by isoleucine and does not bind isoleucine, as shown by equilibrium dialysis experiments. Pyridoxal phosphate enhances the maximum catalytic activity of the mutant enzyme by a factor of five, whereas the wild-type enzyme is not affected. In wild-type and mutant threonine deaminase the ratio of protein subunits and bound pyridoxal phosphate is 2:1. The activation of threonine deaminase from strain IP7 is due to a second coenzyme binding site, as shown by (i) spectrophotometric titration of the enzyme with pyridoxal phosphate and by (ii) measurement the pyridoxal phosphate content of the enzyme after sodium borohydride reduction of the protein. The observation of one pyridoxal phosphate binding site per peptide dimer in the wild-type enzyme and of two binding sites per dimer in the mutant strongly suggests that one of the potential sites in the wild-type enzyme is masked by allosteric effects. The factors responsible for the half-of-the-sites reactivity of the coenzyme sites appear to be nonoperative in the mutant protein.

Threonine deaminase from Escherichia coli: feedback-hypersensitive enzyme from a genetic regulatory mutant

A mutation, ilvA538, in the gene coding for the biosynthetic L-threonine deaminase of Escherichia coli K-12 has previously been demonstrated to have pleiotropic regulatory effects leading to low and invariant expression of some of the isoleucine-valine biosynthetic enzyme, and altered expression of the branched-chain aminoacyl-tRNA synthetases. Strain PS187, which carries the ilvA538 allele, has a partial growth requirement for L-isoleucine and is characterized by a sensitivity to growth inhibition by L-leucine. The experiments reported here demonstrate that the L-threonine deaminase produced by strain PS187 is hypersensitive to inhibition by the pathway end product L-isoleucine. In addition, L-leucine, which acts at relatively high concentrations in vitro as an inhibitor of L-threonine deaminase from the wild type, is a more potent inhibitor of the activity of the mutant enzyme. Forty-six derivatives of strain PS187 were isolated as spontaneous mutants resistant to the growth-inhibitory effects of L-leucine. Two of these, strains MSR14 and MSR16, produce an L-threonine deaminase that is more resistant than the wild type to L-isoleucine inhibition, and intermediate between the wild type and strain PS187 with respect to L-leucine inhibition. Strains MSR14 and MSR16 produce L-threonine deaminase and dihydroxyacid dehydrase, the ilvD gene product, at the low levels characteristic of the parent strain. Other L-leucine-resistant derivatives of strain PS187 produce higher levels of the feedback-hypersensitive L-threonine deaminase. Thus, the sensitivity to growth inhibition by L-leucine observed with strain PS187 appears to be related both to the hypersensitivity of L-threonine deaminase to inhibition of catalytic activity and to the low level of ilv gene expression. The results reported here indicated that L-threonine deaminase is structurally altered in strain PS187, and thus provide further support for the proposal that L-threonine deaminase participates as a genetic regulatory element for the expression of the branched-chain amino acid biosynthetic enzymes.

Purification and properties of threonine deaminase from Saccharomyces cerevisiae

Threonine deaminase (L-theonine hydro-lyase (deaminating), E.C. 4.2.1.16) has been purified to homogeneity from extracts of Saccharomyces cerevisiae. When purified 1200-fold, the enzyme is homogeneous by the criterion of sodium dodecyl sulfate-polyacrylamide electrophoresis. The reduced and alkylated protein has a molecular weight of approximately 50,000 daltons, one-fourth the value determined previously for the intact enzyme. The purified enzyme exhibits homotropic effects with the substrate; these effects are descresed in the presence of DL-allothreonine, a competitive inhibitor. Half-maximal velocity is achieved at 34 mM L-threonine in the absence of other effectors. L-isoleucine both stimulates at low (0.01-0.05 mM) concentrations and inhibits at high (0.1-1.0 mM) concentrations. Valine activates the enzyme in the absence of isoleucine ; in the presence of isoleucine it reverses inhibition.

Physiological and biochemical studies on the function of 5-methyluridine in the transfer ribonucleic acid of Escherichia coli

Matched pairs of transductant strains differing by the presence of absence of 5-methyluridine (ribothymidine) (m5U) in their transfer ribonucleic acid (tRNA) were used to study the function of this modified nucleoside in Escherichia coli. Ordinary measurements of growth rate in different media revealed no effect of the loss of m5U in tRNA. A gene located close to trmA (the structural cistron for the methyltransferase that produces m5U in tRNA), however, was found to reduce the growth rates significantly, depending on the medium and the temperature of cultivation. Measurement of codon recognition, macromolecular composition, tRNA binding to the ribosome, and the rate of protein chain elongation in vivo indicated no disadvantage caused by the lack of m5U. The regulation of ilv and his operons seemed also to be unaffected by the absence of m5U in the tRNA. In a mixed population experiment, however, cells possessing m5U in their tRNA seemed to have a distinct advantage over cells lacking this modified nucleoside. This experiment provides the first indication of the overall value of m5U in tRNA.

Studies of homogeneous "biosynthetic" L-threonine dehydratase from Escherichia coli K-12. Some kinetic properties and molecular multiplicity

"Biosynthetic" L-threonine dehydratase (EC 4.2.1.16) was purified to a homogeneous state with 29% yield of total activity from Escherichia coli K-12. The homogeneity of the enzyme was shown by polyacrylamide gel disc electrophoresis in the presence of dodecyl sulphate. The enzyme consisted of equal subunits having a molecular weight of about 57 000. The polyacrylamide gel disc electrophoresis has shown that the native enzyme consisted of a set of oligomeric forms. The multiplicity of molecular organization of the enzyme was reflected in complicated kinetic behaviour: at pH greater than 9 on the plots of initial reaction rate (v) versus initial substrate concentration ([S]o) there were four inflexion points (two intermediate plateaux), the position and deepness of which depended on enzyme concentration. At pH 8.3 on the v versus [S]o plots appeared two inflexion points (one intermediate plateu), the position of which practically did not depend on enzyme concentration in the reaction mixture, but strongly depended on the enzyme concentration in the stock solution. Repeated polyacrylamide gel disc electrophoresis of several oligomeric forms, isolated by the first electrophoresis, has shown that the oligomeric forms underwent a slow polymerization. It was suggested that "biosynthetic" L-threonine dehydratase from E. coli K-12 is a set of multiple oligomeric forms, having different kinetic parameters. Probably, each form of the enzyme has a "simple" kinetics characterized by hyperbolic or sigmoidal shape of v versus [S]o plots. The rate of equilibrium installation between the oligomeric forms was small in comparison with the enzyme reaction velocity, that lead to the complex kinetic curves, appearing as a result of summing up of the kinetics inherent to theindividual forms.

Purification of biosynthetic threonine deaminase from Escherichia coli

Biosynthetic threonine deaminase (L-threonine hydro-lyase (deaminating), EC 4.2.1.16) was purified to apparent homogeneity from cell extracts of Escherichia coli by chromatographic procedures using valine-Sepharose, isoleucine-N-hexamethyleneamine-Sepharose, and hydroxyapatite with an overall yield of 40%. Analytical ultracentrifugation shows a molecular weight of 214 000. In sodium dodecyl sulfate gel electrophoresis, the enzyme migrates as a single band corresponding to a molecular weight of about 50 000. These data confirm that the enzyme is a tetramer. The sedimentation coefficient, s-020,w, determined by differential sedimentation experiments is 9.2 S. The enzyme shows absorption maxima at 415 and 280 nm. Determination of pyridoxal phosphate by three indenpendent methods shows the presence of two molecules of pyridoxal phosphate per enzyme molecule, the different methods being in excellent agreement equilibrium dialysis experiments establish the presence of two isoleucine binding sites. The Scatchard plot suggests non-cooperativity of these sites. The association constant for isoleucine is 1.2 - 10(5)M-1.

Synthesis of branced-chain aminoacyl-transfer ribonucleid acid synthetases in a Salmonella typhimurium mutant with an altered biosynthetic L-threonine deaminase

The differential rates of synthesis of the three branched-chain aminoacyl-transfer ribonucleic acid synthetases were measured in Salmonella typhimurium LT-2 and a mutant, ilvA504. The mutant produced an l-threonine deaminase with a decreased affinity for its cofactor, pyridoxal-5'-monophosphate. The addition of pyridoxal-5'-monophosphate to cultures of strain ilvA504 growing in excess isoleucine, valine, and leucine resulted in an increased rate of growth and repression of the synthesis of the isoleucine and valine biosynthetic enzymes. No differences in the rate of synthesis of the branched-chain aminoacyl-transfer ribonucleic acid synthetases were observed in cultures of ilvA504 growing with or without added pyridoxal-5'-monophosphate. The differential rates of synthesis of all three enzymes were similar to the rates measured in strain LT-2. These experiments suggest that different forms of the ilvA gene product are involved in the regulation of the branched-chain amino acid biosynthetic enzymes and the branched-chain aminoacyl-transfer ribonucleic acid synthetases.

Complementation between different mutations in the ilvA gene of Escherichia coli K-12

An ilvA mutation carried by a ø80i(lambda)dilv transducing phage complemented some ilvA mutations and did not complement others. Complementation was accompanied by appearance of threonine deaminase activity in vivo. These results divided the ilvA mutations into two sets which formerly appeared to define two cistrons.

Phosphate-induced protein chromatography

High phosphate concentration is shown to cause a large proportion of the proteins of a cell-free extract of Escherichia coli to bind to agarose columns to which L-valine is attached. With a decreasing concentration gradient of potassium phosphate, the proteins elute in relation to their solubility in concentrated ammonium sulfate. This column technique appears to provide a general tool for the purification of proteins.