Autoregulation: a role for a biosynthetic enzyme in the control of gene expression

Impact of negative feedback in metabolic noise propagation

Synthetic biology combines different branches of biology and engineering aimed at designing synthetic biological circuits able to replicate emergent properties useful for the biotechnology industry, human health and environment. The role of negative feedback in noise propagation for a basic enzymatic reaction scheme is investigated. Two feedback control schemes on enzyme expression are considered: one from the final product of the pathway activity, the other from the enzyme accumulation. Both schemes are designed to provide the same steady-state average values of the involved players, in order to evaluate the feedback performances according to the same working mode. Computations are carried out numerically and analytically, the latter allowing to infer information on which model parameter setting leads to a more efficient noise attenuation, according to the chosen scheme. In addition to highlighting the role of the feedback in providing a substantial noise reduction, our investigation concludes that the effect of feedback is enhanced by increasing the promoter sensitivity for both schemes. A further interesting biological insight is that an increase in the promoter sensitivity provides more benefits to the feedback from the product with respect to the feedback from the enzyme, in terms of enlarging the parameter design space.

Threonine deaminase: autogenous regulator of the ilv genes in Escherichia coli K-12

In this paper we analyze the effect of mutations in three genes, ilvO, ilvA and rho, on the expression of the ilvEJGDA gene cluster of Escherichia coli K-12. The ilvO603 mutation causes a cis-dominant derepression of the ilvEJGDA genes. In particular, the ilvG gene, not expressed in the wild type, becomes expressed in the ilvO603 strain. We have introduced ilvA mutations (ilvA454 or ilvA628) in the ilvO603 strain and we show that ilvG expression requires the presence in cis of both an ilvO603 mutation and of an ilvA+ allele. The ilvG gene is not expressed when in trans is present an ilvO+, ilvA+ genotype. However, it is expressed when the chromosome in trans is ilvO603, ilvA+ (ilvG-). We suggest that ilvO603 is part of ilvA, the structural gene for threonine deaminase, and that threonine deaminase from the ilvO603 mutant binds the ilvO603 site and not the ilvO+ site. Therefore, the ilvA gene product would be a cis-acting protein. Mutations in the rho gene cause derepression of the ilvEJGDA gene cluster without a concomitant expression of the ilvG gene. We show that introduction of either a rho-218 or a rho-115 mutation into the ilvO603, ilvA454 double mutant causes expression of ilvG. We therefore suggest that the ilvA gene product, threonine deaminase, is involved in termination of transcription as an antagonist of the rho gene product. Introduction of ilvA454 into an ilvO603 strain causes also a decrease in expression of the ilvE, ilvJ and ilvD genes. This effect is maximum in the case of the ilvD gene and we studied it in detail in isogenic strains containing also the rho-218 mutation.

A site of action for tRNA mediated regulation of the ilvOEDA operon of Escherichia coli K12

Transfer RNA (tRNA), rho factor threonine deaminase and the ilvO locus are molecular participants in the regulation of isoleucine-valine (ilv) biosynthesis. Isogenic strains have been constructed with the hisT76 mutation in pairwise combination with ilvO mutations, the rho221 mutation and the ilvDAC115 deletion mutation. The role of the altered tRNA of the hisT76 mutation was found to be independent of the sites of action of the ilvO- mutation, rho factor, and threonine deaminase. The expression of the ilvOEDA operon is stimulated 2-fold when the hisT76 mutation is present in strains containing either ilvO- or rho221 mutations. The expression of the ilvOEDA operon remains nonrepressed in a hisT76 strain deleted for threonine deaminase. These results indicate that the hisT76 undermodified tRNAs are influencing the initiation of transcription of the ilvOEDA operon.

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.

Dual autogenous regulatory role of threonine deaminase in Escherichia coli K-12

We describe the regulatory properties of two strains carrying either the ilvA624 or the ilvA625 mutations, located in the structural gene for threonine deaminase. Crude extracts of both these strains possess a threonine deaminase activity migrating on polyacrylamide gels, differently from the wild type enzyme. Growth studies demonstrate that these mutations do not cause a limitation of isoleucine biosynthesis, suggesting normal catalytic activity of deaminase. A regulatory consequence of the ilvA624 allele is a derepression of the isoleucine-valine biosynthetic enzymes, which is recessive to an ilvA+ allele. The ilvA625 mutation causes a derepression which is dominant in an ilvA625/ILVA+ diploid. We interpret these data assuming that threonine deaminase, previously shown to be an autogenous regulator of the ilv genes, lacks a repressor function in the ilvA624 mutant, while in the ilvA625 mutant it is a better activator than wild type threonine deaminase. The data are discussed in terms of a model requiring that threonine deaminase, or a precursor of it, is in equilibrium between two forms, one being an activator of gene expression and the other being a repressor.

In vitro synthesis of beta-galactosidase with ilv-lac fusion deoxyribonucleic acid as template

An in vitro protein-synthesizing system has been developed to study the mechanism of induction of ilvC gene in Escherichia coli strain K-12. Deoxyribonucleic acid (DNA) from a lambda phage carrying an ilvC-lac fusion was employed as a template for the in vitro synthesis of beta-galactosidase under the control of the ilvC promoter. The use of this template allowed an investigation of the components required for induction of the ilvC gene and the kinetics of the induction. The in vitro synthesis of beta-galactosidase under the control of the ilvC promoter was found to be DNA, acetohydroxy acid, and guanosine-3'-diphosphate-5'-diphosphate dependent, and sensitive to rifampin, actinomycin D, and chloramphenicol. Uncoupling experiments indicate that the inducer, acetohydroxybutyrate, acts at the transcriptional level. Investigation of a proposed noninducible ilvC regulatory mutant has shown normal induction in vitro. It was also observed that an intact ilvA gene is not required for the induction of the ilvC gene.

Inhibition of aminoacyl-transfer ribonucleic acid synthetases and the regulation of amino acid biosynthetic enzymes in Neurospora crassa

Growth conditions that result in the accumulation of the tryptophan intermediate indoleglycerol phosphate or of the histidine intermediate imidazoleglycerol phosphate cause mycelia of Neurospora crassa to exhibit an immediate and sustained increase in the differential rate at which the biosynthetic enzymes of the tryptophan, histidine, and arginine pathways are synthesized. These accumulated intermediates are shown to be inhibitors of the activity of aminoacyltransfer ribonucleic acid (tRNA) synthetases, as judged by an in vitro esterification assay. The tryptophan intermediate is shown to inhibit the charging of tryptophan, and the histidine intermediate is shown to inhibit charging of histidine. The inhibitions noted are consistent with the finding that the level of charged tRNATrp is decreased significantly in cells that have accumulated indoleglycerol phosphate and that of tRNAHis is decreased significantly in cells that have accumulated imidazoleglycerol phosphate. These results are interpreted as support for the involvement of aminoacyl-tRNA species in mediating cross-pathway regulation of the tryptophan, histidine, and arginine biosynthetic pathways as proposed in Lester's polyrepressor hypothesis (G. Lester, 1971). the correlations noted lead to the conclusion that Neurospora utilizes regulatory mechanisms that have the ability to react to changes in the level of charging of tRNA species.

Regulation of branched-chain amino acid transport in Escherichia coli

The repression and derepression of leucine, isoleucine, and valine transport in Escherichia coli K-12 was examined by using strains auxotrophic for leucine, isoleucine, valine, and methionine. In experiments designed to limit each of these amino acids separately, we demonstrate that leucine limitation alone derepressed the leucine-binding protein, the high-affinity branched-chain amino acid transport system (LIV-I), and the membrane-bound, low-affinity system (LIV-II). This regulation did not seem to involve inactivation of transport components, but represented an increase in the differential rate of synthesis of transport components relative to total cellular proteins. The apparent regulation of transport by isoleucine, valine, and methionine reported elsewhere was shown to require an intact leucine, biosynthetic operon and to result from changes in the level of leucine biosynthetic enzymes. A functional leucyl-transfer ribonucleic acid synthetase was also required for repression of transport. Transport regulation was shown to be essentially independent of ilvA or its gene product, threonine deaminase. The central role of leucine or its derivatives in cellular metabolism in general is discussed.

The influence of mutations upon the synthesis of RNA polymerase subunits in Escherichia coli cells

The influence of mutations in structural genes of beta and beta subunits of RNA polymerase upon the synthesis of these subunits in E. coli cells have been investigated. An amber-mutation ts22 in the beta subunit gene decreases the intracellular concentration of this subunit and the rate of its synthesis. At the same time the concentration and the rate of beta subunit synthesis is increased. These suggest the compensatory activation of the RNA polymerase operon that takes place under the conditions of shortage of one of the subunits. Reversions as well as more effective suppression of ts22 amber mutation, achieved by streptomycin addition, substitution of su2 by sul, or by specific mutations, result in a rise of beta and drop of beta subunit concentration and synthesis in ts22 mutant. TsX missense-mutation in the beta subunit gene alters the properties of the enzyme increasing, at the same time, the concentration and the rate of synthesis of both beta and beta subunits, particularly at a nonpermissive temperature. This points to an inversely proportional relationship between the rate of synthesis of RNA polymerase subunits and the total intracellular activity of the enzyme. Extra subunits are rapidly degraded in ts22 and tsX mutants. The whole complex of our data and those of others suggest that the regulation of the synthesis of RNA polymerase subunits is accomplished by interaction of a negative and a positive mechanisms of regulation which include not only activators and repressors but the enzyme itself as well.

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.

Regulation of the ilv 1 multifunctional gene in Saccharomyces cerevisiae

The ilv 1 gene in S. cerevisiae codes for a regulatory protein involved in depression of the ilv 2 and ilv 3 genes as well as a biosynthetic enzyme, threonine deaminase. 2. The ilv 1 gene does not autogenously regulate its catalytic product threonine deaninase. 3. Regulation of the ilv 2 and ilv 3 gene products involve different aporepressors than regulation of the ilv 1 gene product. 4. The ilv I multifunctional gene in S. cerevisiae may be a duplication and fusion of a bacterial like ilv 1 gene where ilv 1 catalytic and regulatory function have been differentially conserved.

Significance of autogenously regulated and constitutive synthesis of regulatory proteins in repressible biosynthetic systems

The functional implications of the different modes of regulation have been examined systematically. The results lead to certain predictions. The regulatory protein in repressor-controlled systems is constitutively synthesised. In activator-controlled systems synthesis of the regulatory protein is autogenously regulated. There is favourable agreement between these predictions and published experimental evidence.

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.

Transcriptional control of the isoleucine-valine messenger RNA's in E. coli K-12

Hybridization of messenger ribonucleic acid (mRNA) isolated from Escherichia Coli K-12 to deoxyribonucleic acid (DNA) from lambdaCI857st68h80dilv was used to detect isoleucine-valine (ilv) specific mRNA. A number of strains partially constitutive for the isoleucine-valine enzymes had levels of ilv mRNA 2 to 3-fold higher than the parent strain. Starvation for any of the branched-chain amino acids resulted in a 20 to 23-fold increase in ilv mRNA as compared to repressed levels. These differences were not due to altered growth rates or to changes in the stability of ilv mRNA. These data indicate that regulation of the isoleucine-valine enzymes by multivalent repression occurs mainly at the level of transcription. Kinetics of elongation of ilv mRNA after repression are consistent with the assumption that the mechanism of multivalent repression involves the prevention of further initiations by RNA polymerase.

Isolation and characterization of mutants with a feedback resistant N-acetylglutamate synthase in Escherichia coli K 12

Mutants with a feedback resistant N-acetylglutamate synthase have been isolated from a proA/B, argD, argR strain by screening for proline excretion on minimal medium with arginine. The feedback resistant character of three mutants was transduced into an argA (N-acetylglutamate synthase negative) strain. It was cotransducible with argA at a frequency of greater than 99%. N-acetylglutamate synthase extracted from the three mutants was approximately one hundred times less sensitive to L-arginine than the enzyme from the feedback sensitive parent strain.

Autogenous regulation of the inducible tryptophan synthase of Pseudomonas putida

Mutants blocked before indole-3-glycerol phosphate formation in the tryptophan biosynthetic pathway of P. putida ("early-blocked" mutants) are unable to use indole as a source of tryptophan for growth on minimal medium. The uninduced level of tryptophan synthase [EC 4.2.1.20; L-serine hydro-lyase (adding indole)] in such mutants was thought to be responsible for this property. We have shown that levels of indole higher than those previously tested will support growth of these mutants. In addition, the growth rate of these mutants on a given indole concentration was shown to be proportional to the synthase level induced under the same conditions. This apparent induction of tryptophan synthase by indole in "early-blocked" mutants was shown to be caused by formation of the normal effector molecule, indole-3-glycerol-P, from indole. Secondary mutations occur in "early-blocked" trp strains, which enable them to grow on low concentrations of indole. One type of "indole-utilization" mutation occurs in the trpA gene, inactivating its product. Tryptophan synthase is readily induced by low concentrations of indole in these mutants, even though they are unable to convert indole to indole-3-glycerol-P. We propose that the alpha-chain of the synthase has an autogenous regulatory function, serving as the repressor or the indole-3-glycerol-P recognition component of the repressor of the trpAB operon (synthase alpha-and beta-chains). Our hypothesis holds that the trpA type of "indole-utilization" mutation alters the repressor (synthase alpha-chain) so that indole as well as indole-3-glycerol-P serves as an effector molecule for tryptophan synthase induction.

Regulation of branched-chain aminoacyl-transfer ribonucleic acid synthetases in an ilvDAC deletion strain of Escherichia coli K-12

Valyl-, isoleucyl-, and leucyl-transfer ribonucleic acid synthetase formation was compared in isogenic strains of Escherichia coli K-12 that differed only in that one strain carried a deletion of three genes of the ilv gene cluster, ilvD, -A, and -C. It was found that: (i) the activities of these synthetases in the deletion strain were less than those in the normal strain during growth in minimal medium supplemented with excess isoleucine, valine, and leucine, and (ii) their stability was reduced in the deletion strain during specific branched-chain amino acid limitations. The results of density-labeling experiments suggest that the in vivo stability of valyl-, isoleucyl-, and leucyl-transfer ribonucleic acid synthetases requires some product missing in the ilvDAC deletion strain.

Deoxyribonucleic acid-directed in vitro synthesis of ilv-specific messenger ribonucleic acid by extracts of Escherichia coli K-12

The synthesis of ilv-specific messenger ribonucleic acid (mRNA) by extracts of Escherichia coli K-12 has been demonstrated in a deoxyribonucleic acid (DNA)-dependent, coupled transcription-translation system. ilv-Specific mRNA was determined by hybridization either to double-stranded lambdacI857St68h80dilv DNA (lambdah80dilv DNA) immobilized on nitrocellulose filters or to its separate l and r strands in liquid. During conditions optimal for protein synthesis, slightly more than 6% of the total [(3)H]RNA synthesized by S-30 extracts of the threonine deaminase-negative strain CU5136 was ilv-specific. Of this RNA, nearly 30% was complementary to the l (correct) strand. Total ilv-specific mRNA synthesis in vitro was not affected by omission of valine or all 20 amino acids from the reaction mixture. Hybridization of ilv-specific mRNA made in vitro to the l strand of lambdah80dilv DNA was effectively reduced in the presence of unlabeled RNA extracted from an ilv derepressed strain but not from an ilv deletion strain. In a purified transcription system, employing commercial RNA polymerase, twofold more ilv-specific mRNA was synthesized than in the coupled system, but this increase was entirely due to greater transcription of the r (incorrect) strand. An S-30 extract prepared from a strain isogenic to strain CU5136 but derepressed for ilvA gene expression synthesized twofold more ilv-specific mRNA in the coupled system. The significance of these findings is discussed.

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.

Pleiotropy of hisT mutants blocked in pseudouridine synthesis in tRNA: leucine and isoleucine-valine operons

The hisT gene codes for an enzyme responsible for the conversion of uridine to pseudouridine (Psi) in the anticodon region of many tRNA species in Salmonella typhimurium. We have previously shown that a hisT mutant has tRNA(His) which lacks pseudouridine in this region and as a consequence has an altered chromatographic behavior. We show here a similar alteration in chromatographic behavior of all tRNA(Leu) and one tRNA(Ile) species from a hisT mutant. By contrast, tRNA(Val), which contains no pseudouridine except for the one in the TPsiCG sequence, is chromatographically unaltered in a hisT mutant. The absence of pseudouridine in the anticodon region of tRNA in hisT mutants has been previously shown to cause derepression of the histidine operon. We show here that in hisT mutants the regulation of the leucine and the isoleucine and valine operons is also affected: the enzymes of these operons are refractory to repression by the branched chain amino acids. However, there is no difference between hisT and wild type in the pattern of derepression caused by isoleucine or valine limitation and only a slight difference in the enzyme levels in cells grown on minimal medium. The alteration in the regulation of branched chain amino acid operons may also explain why hisT mutants are resistant to inhibition of growth by the amino acid analogues 5,5,5-trifluoroleucine, beta-hydroxyleucine, and norleucine and by the oligopeptides glycylglycylnorleucine and norleucylnorleucine.

Autogenous regulation of gene expression

A new term, autogenous regulation, is used to describe a phenomenon that is not a new discovery but rather is newly appreciated as a mechanism common to a number of systems in both prokaryotic and eukaryotic organisms. In this mechanism the product of a structural gene regulates expression of the operon in which that structural gene resides. In many (perhaps all) cases, the regulatory gene product has several functions, since it may act not only as a regulatory protein but also as an enzyme, structural protein, or antibody, for example. In a few cases, this protein is the multimeric allosteric enzyme that catalyzes the first step of a metabolic pathway, gearing together the two most important mechanisms for controlling the biosynthesis of metabolites in bacterial cells-feedback inhibition and repression. Autogenous regulation may provide a mechanism for amplification of gene expression (84); for severe and prolonged inactivation of gene expression (85); for buffering the response of structural genes to changes in the environment (45, 52); and for maintaining a constant intracellular concentration of a protein, independent of cell size or growth rate (86). Thus, autogenous regulation provides the cell with means for accomplishing a number of different regulatory tasks, each suited to better satisfying the needs of the organism for its survival.