Multivalent repression of aspartic semialdehyde dehydrogenase in Escherichia coli K-12

Protein cost allocation explains metabolic strategies in Escherichia coli

In-depth understanding of microbial growth is crucial for the development of new advances in biotechnology and for combating microbial pathogens. Condition-specific proteome expression is central to microbial physiology and growth. A multitude of processes are dependent on the protein expression, thus, whole-cell analysis of microbial metabolism using genome-scale metabolic models is an attractive toolset to investigate the behaviour of microorganisms and their communities. However, genome-scale models that incorporate macromolecular expression are still inhibitory complex: the conceptual and computational complexity of these models severely limits their potential applications. In the need for alternatives, here we revisit some of the previous attempts to create genome-scale models of metabolism and macromolecular expression to develop a novel framework for integrating protein abundance and turnover costs to conventional genome-scale models. We show that such a model of Escherichia coli successfully reproduces experimentally determined adaptations of metabolism in a growth condition-dependent manner. Moreover, the model can be used as means of investigating underutilization of the protein machinery among different growth settings. Notably, we obtained strongly improved predictions of flux distributions, considering the costs of protein translation explicitly. This finding in turn suggests protein translation being the main regulation hub for cellular growth.

Mismatch-CRISPRi Reveals the Co-varying Expression-Fitness Relationships of Essential Genes in Escherichia coli and Bacillus subtilis

Essential genes are the hubs of cellular networks, but lack of high-throughput methods for titrating gene expression has limited our understanding of the fitness landscapes against which their expression levels are optimized. We developed a modified CRISPRi system leveraging the predictable reduction in efficacy of imperfectly matched sgRNAs to generate defined levels of CRISPRi activity and demonstrated its broad applicability. Using libraries of mismatched sgRNAs predicted to span the full range of knockdown levels, we characterized the expression-fitness relationships of most essential genes in Escherichia coli and Bacillus subtilis. We find that these relationships vary widely from linear to bimodal but are similar within pathways. Notably, despite ∼2 billion years of evolutionary separation between E. coli and B. subtilis, most essential homologs have similar expression-fitness relationships with rare but informative differences. Thus, the expression levels of essential genes may reflect homeostatic or evolutionary constraints shared between the two organisms.

Mutagenesis of Key Residues in the Binding Center of l-Aspartate-b-Semialdehyde Dehydrogenase from Escherichia coli Enhances Utilization of the Cofactor NAD(H)

L-Aspartate-β-semialdehyde dehydrogenase (ASADH) is a key enzyme in the aspartate pathway. In bacteria, ASADH is highly specific for the cofactor NADP(+) rather than NAD(+). Limited information on cofactor utilization is available, and neither the wild-type protein nor the available mutants could utilize NAD(+) efficiently. In this study, we identified several residues crucial for cofactor utilization by Escherichia coli ASADH (ecASADH) by mutating residues within the cofactor binding center. Among the investigated mutants, ecASADH-Q350N and ecASADH-Q350N/H171A, which exhibited markedly improved NAD(+) utilization, were further investigated by various biochemical approaches and molecular modeling. Relative to the wild type, the two mutants showed approximately 44-fold and 66-fold increases, respectively, in the constant kcat /Km of NAD(+). As desired, they could also utilize NADH efficiently to synthesize l-homoserine in cascade reactions in vitro.

Whole-genome transcriptional analysis of Escherichia coli during heat inactivation processes related to industrial cooking

Escherichia coli K-12 was grown to the stationary phase, for maximum physiological resistance, in brain heart infusion (BHI) broth at 37°C. Cells were then heated at 58°C or 60°C to reach a process lethality value \[\mathbf{\left(}{{\mathit{F}}^{\mathit{o}}}_{\mathbf{70}}^{\mathbf{10}}\mathbf{\right)} \] of 2 or 3 or to a core temperature of 71°C (control industrial cooking temperature). Growth recovery and cell membrane integrity were evaluated immediately after heating, and a global transcription analysis was performed using gene expression microarrays. Only cells heated at 58°C with F(o) = 2 were still able to grow on liquid or solid BHI broth after heat treatment. However, their transcriptome did not differ from that of bacteria heated at 58°C with F(o) = 3 (P value for the false discovery rate [P-FDR] > 0.01), where no growth recovery was observed posttreatment. Genome-wide transcriptomic data obtained at 71°C were distinct from those of the other treatments without growth recovery. Quantification of heat shock gene expression by real-time PCR revealed that dnaK and groEL mRNA levels decreased significantly above 60°C to reach levels similar to those of control cells at 37°C (P < 0.0001). Furthermore, despite similar levels of cell inactivation measured by growth on BHI media after heating, 132 and 8 genes were differentially expressed at 71°C compared to 58°C and 60°C at F(o) = 3, respectively (P-FDR < 0.01). Among them, genes such as aroA, citE, glyS, oppB, and asd, whose expression was upregulated at 71°C, may be worth investigating as good biomarkers for accurately determining the efficiency of heat treatments, especially when cells are too injured to be enumerated using growth media.

Microbial metabolic engineering for L-threonine production

L-threonine, one of the three major amino acids produced throughout the world, has a wide application in industry, as an additive or as a precursor for the biosynthesis of other chemicals. It is predominantly produced through microbial fermentation the efficiency of which largely depends on the quality of strains. Metabolic engineering based on a cogent understanding of the metabolic pathways of L-threonine biosynthesis and regulation provides an effective alternative to the traditional breeding for strain development. Continuing efforts have been made in revealing the mechanisms and regulation of L-threonine producing strains, as well as in metabolic engineering of suitable organisms whereby genetically-defined, industrially competitive L-threonine producing strains have been successfully constructed. This review focuses on the global metabolic and regulatory networks responsible for L-threonine biosynthesis, the molecular mechanisms of regulation, and the strategies employed in strain engineering.

Methionine production by fermentation

Fermentation processes have been developed for producing most of the essential amino acids. Methionine is one exception. Although microbial production of methionine has been attempted, no commercial bioproduction exists. Here, we discuss the prospects of producing methionine by fermentation. A detailed account is given of methionine biosynthesis and its regulation in some potential producer microorganisms. Problems associated with isolation of methionine overproducing strains are discussed. Approaches to selecting microorganism having relaxed and complex regulatory control mechanisms for methionine biosynthesis are examined. The importance of fermentation media composition and culture conditions for methionine production is assessed and methods for recovering methionine from fermentation broth are considered.

The threonine story

L-Threonine is an essential amino acid which has recently been brought into agricultural industry for balancing the livestock feed. L-Threonine is produced by microbial synthesis using glucose or sucrose as substrates. For the process to be cost-effective, the microbial strain must be capable of threonine overproduction. This paper reviews the biochemical pathways of L-threonine synthesis in bacteria and the regulation of these pathways, the principles and the techniques of constructing high-producing strains, and the most efficient strains thus developed.

Lysine production byBrevibacterium linens and its mutants: Activities and regulation of enzymes of the lysine biosynthetic pathway

Activity and regulation of key enzymes of the lysine biosynthetic pathway were investigated inBrevibacterium linens, a natural excretor of lysine, its lysine-overproducing homoserine auxotroph (Hom(-1)) and its auxotrophic and multianalogue-resistant high-yielding mutant (AEC NV 20(r)50). The activity of aspartate kinase (AK) and aspartaldehydate dehydrogenase (AD) was maximum during the mid-exponential phase of growth and decreased therafter. The mutants showed 10 and 20% more activity of AK and AD than the wild-type lysine excretor.B. linens (natural excretor) has a single AK and AD repressed and inhibited bivalently by lysine and threonine. Lysine slightly repressed and inhibited dihydrodipicolinate synthase (DS) and diaminopimelate decarboxylase (DD) of the wild type and of the mutant Hom(-1). The mutant AEC NV 20(r)50 showed DS and DD to be insensitive to lysine inhibition and repression. Persistence of a major part of the maximal activity of these enzymes during the late stationary phase of growth allowed prolonged synthesis and excretion of lysine. Stepwise addition of resistance to the different analogues of lysine in the mutant AEC NV20(r)50 resulted in an increase of enzyme activity and reduced repressibilities of enzymes that contributed to the high yield of lysine.

Methionine production by microorganisms

Microbial production of methionine is reviewed with 73 references. The review describes different methionine-producing organisms, as well as analog-resistant regulatory mutants, their optimum cultural conditions and yields. The pathways of methionine biosynthesis and their regulation are discussed.

Methionine biosynthesis in Enterobacteriaceae: biochemical, regulatory, and evolutionary aspects

The genes coding for the enzymes involved in methionine biosynthesis and regulation are scattered on the Escherichia coli chromosome. All of them have been cloned and most have been sequenced. From the information gathered, one can establish the existence (upstream of the structural genes coding for the biosynthetic genes and the regulatory gene) of "methionine boxes" consisting of two or more repeats of an octanucleotide sequence pattern. The comparison of these sequences allows the extraction of a consensus operator sequence. Mutations in these sequences lead to the constitutivity of the vicinal structural gene. The operator sequence is the target of a DNA-binding protein--the methionine aporepressor--which has been obtained in the pure state, for which S-adenosylmethionine acts as the corepressor. Mutations in the corresponding gene lead to the constitutive expression of all the methionine structural genes. The physicochemical properties of the methionine aporepressor are being investigated.

Molecular cloning, characterization, and chromosomal localization of dapF, the Escherichia coli gene for diaminopimelate epimerase

The Escherichia coli dapF gene was isolated from a cosmid library as a result of screening for clones overproducing diaminopimelate epimerase. Insertional mutagenesis was performed on the cloned dapF gene with a mini-Mu transposon, leading to chloramphenicol resistance. One of these insertions was transferred onto the chromosome by a double-recombination event, allowing us to obtain a dapF mutant. This mutant accumulated large amounts of LL-diaminopimelate, confirming the blockage in the step catalyzed by the dapF product, but did not require meso-diaminopimelate for growth. The dapF gene was localized in the 85-min region of the E. coli chromosome between cya and uvrD.

Cloning and expression in Escherichia coli of the homoserine kinase (thrB) gene from Brevibacterium lactofermentum

Five DNA fragments carrying the thrB gene (homoserine kinase E.C. 2.7.1.39) of Brevibacterium lactofermentum were cloned by complementation of Escherichia coli thrB mutants using pBR322 as vector. All the cloned fragments contained a common 3.1 kb DNA sequence. The cloned fragments hybridized among themselves and with a 9 kb BamHI fragment of the chromosomal DNA of B. lactofermentum but not with the DNA of E. coli. None of the cloned fragments were able to complement thrA and thrC mutations of E. coli. Plasmids pULTH2, pULTH8 and pULTH11 had the cloned DNA fragments in the same orientation and were very stable. On the contrary, plasmid pULTH18 was very unstable and showed the DNA inserted in the opposite direction. E. coli minicells transformed with plasmids pULTH8 or pULTH11 (both carrying the common 3.1 kb fragment) synthesize a protein with an Mr of 30,000 that is similar in size to the homoserine kinase of E. coli.

Chromosomal location and nucleotide sequence of the Escherichia coli dapA gene

In Escherichia coli, the first enzyme of the diaminopimelate and lysine pathway is dihydrodipicolinate synthetase, which is feedback-inhibited by lysine and encoded by the dapA gene. The location of the dapA gene on the bacterial chromosome has been determined accurately with respect to the neighboring purC and dapE genes. The complete nucleotide sequence and the transcriptional start of the dapA gene were determined. The results show that dapA consists of a single cistron encoding a 292-amino acid polypeptide of 31,372 daltons.

Nucleotide sequence of the promoter region of the E. coli lysC gene

The regulatory region of the lysC gene (that encodes the lysine-sensitive aspartokinase of Escherichia coli) has been identified and purified by the use of lysC-lacZ fusions. Its regulatory sequence has been determined. No signals similar to those described in the case of an attenuation mechanism could be found in the long leader sequence existing between the starts of transcription and of translation.

Regulation of aspartokinase III synthesis in Escherichia coli: isolation of mutants containing lysC-lac fusions

Mutants containing fusions of the lac gene to the lysC gene were isolated. In these, the expression of beta-galactosidase was regulated by lysine (and arginine), as previously described for aspartokinase III.

Isolation and identification of mutants constitutive for aspartokinase III synthesis in Escherichia coli K 12

We devised a procedure in order to isolate, in Escherichia coli, constitutive mutants for aspartokinase III synthesis, the first enzyme of the lysine regulon. It consists of the introduction of a limiting step in lysine biosynthesis, by the use of the partial suppression of a nonsense mutation. For the first time we could isolate many constitutive mutants. Their characteristics (cotransduction with the lysC structural gene; no effect on the synthesis of other enzymes of the regulon; cis-dominance) lead to classify these mutations as operator-type. The fact that no repressor mutations could be isolated is discussed.

Participation of lysine-sensitive aspartokinase in threonine production by S-2-aminoethyl cysteine-resistant mutants of Serratia marcescens

S-2-Aminoethyl cysteine (AEC) reduced both growth rate and final growth level of Serratia marcescens Sr41. The growth inhibition was completely reversed by lysine. AEC inhibited the activity of lysine-sensitive aspartokinase to a lesser extent than lysine. The AEC addition to the medium lowered not only the level of lysine-sensite aspartokinase but also those of homoserine dehydrogenase and threonine deaminase, whereas lysine repressed the aspartokinase alone. To select mutations releasing lysine-sensitive aspartokinase from feedback controls, AEC-resistant colonies were isolated from strains HNr31 and HNr53, both of which were previously found to excrete threonine on the minimal plates but not on the plates containing excess lysine. Two of 280 resistant colonies excreted large amounts of threonine. Strains AECr174 and AECr301, derived from strains HNr31 and HNr53, respectively, lacked both feedback inhibition and repression of lysine-sensitive aspartokinase. These strains produced about 7 mg of threonine per ml in the medium containing glucose and urea.

Thialysine-resistant mutant of Salmonella typhimurium with a lesion in the thrA gene

A mutant of Salmonella typhimurium was selected for its spontaneous resistance to the lysine analog, thialysine (S-2-aminoethyl cysteine). This strain, JB585, exhibits a number of pleiotropic properties including a partial growth requirement for threonine, resistance to thiaisoleucine and azaleucine, excretion of lysine and valine, and inhibition of growth by methionine. Genetic studies show that these properties are caused by a single mutation in the thrA gene which encodes the threonine-controlled aspartokinase-homoserine dehydrogenase activities. Enzyme assays demonstrated that the aspartokinase activity is unstable and the threonine-controlled homoserine dehydrogenase activity absent in extracts prepared from the mutant. These results explain the growth inhibition by methionine because the remaining homoserine dehydrogenase isoenzyme would be repressed by methionine, causing a limitation for threonine. The partial growth requirement for threonine during growth in glucose minimal medium may also, by producing an isoleucine limitation, cause derepression of the isoleucine-valine enzymes and provide an explanation for both the valine excretion, and azaleucine and thiaisoleucine resistance. The overproduction of lysine may confer the thialysine resistance.

Regulation of a metabolic system in vitro: synthesis of threonine from aspartic acid

Six enzymes involved in the conversion of aspartate to threonine have been extracted from Escherichia coli and separated from each other. Two of these enzymes, aspartokinase and homoserine dehydrogenase, have also been partially purified from Rhodopseudomonas spheroides. In an attempt to determine whether small changes in the kinetic properties of individual enzymes are important to the regulation of metabolic flux through a coupled reaction system, the partially purified enzymes were recombined in a variety of ways under reaction conditions designed to resemble the in vivo situation. These conditions include: use of an entire metabolic system rather than a single reaction; high enzyme concentrations at the same relative concentrations as found in the cell; and low, steady-state concentrations of substrates and products. Metabolic flux was followed spectrophotometrically and the concentrations of aspartic semialdehyde, hemoserine, O-phosphohomoserine, and threonine were measured. The results indicate that the threonine concentration is of major importance in regulating metabolic flux by inhibiting aspartokinase, the first reaction in threonine in the pathway. When threonine-insensitive aspartokinases were used, concentrations reached higher levels and the rate of NADPH oxidation remained higher. The fact that neither aspartic semialdehyde nor homoserine accumulated as the threonine concentration increased and the lack of correlation between changes in metabolic flux and ADP/ATP or NADPH/NADP ratios indicate that more subtle forms of metabolic regulation, such as "reverse cascade", secondary feedback sites, or "energy charge", are of little regulatory importance in this isolated, metabolic system. The results also emphasize the need for caution in projecting in vivo control mechanisms from in vitro experiments.

Role of lysyl-tRNA in the regulation of lysine biosynthesis in Escherichia coli K12

A mutant of lysyl-tRNA synthetase has been isolated in Escherichia coli K12. With this strain the Kmapp for lysine is 25 fold higher than with the parental strain. The percentage of charged tRNAlys in vivo is only 7 per cent (as against 65 per cent with HFR H). Under these conditions no derepression of synthesis is observed for three lysine biosynthetic enzymes (AK III, ASA-dehydrogenase, DAP-decarboxylase) ; a partial derepression is obtained in the case of the dhdp-reductase. Thus lysyl-tRNA does not act as the only corepressor molecule in the lysine regulon.

Regulation of the lysine biosynthetic pathway in Escherichia coli K-12: isolation of a cis-dominant constitutive mutant for AK III synthesis

A method for isolating regulatory mutants for the synthesis of lysine biosynthetic enzymes in Escherichia coli is described. One of them is identified as a cis-dominant constitutive mutant for the synthesis of the lysine-sensitive asportokinase AK III (lysC gene).

Existence of two levels of repression in the biosynthesis of methionine in Saccharomyces cerevisiae: effect of lomofungin on enzyme synthesis

Derepression of a methionine biosynthetic enzyme (homocysteine synthase) has been studied after repression either by exogenous methionine or by exogenous S-adenosylmethionine (SAM). Lomofungin, which inhibits the synthesis of ribosomal precursor and messenger ribonucleic acid but not of protein in Saccharomyces cerevisiae, has been used in this system. It has been shown that the addition of this antibiotic prevents the derepression of homocysteine synthase after repression by exogenous methionine but not after repression by exogenous SAM. These experiments with lomofungin and the kinetics of repression after addition of methionine or SAM to the growth medium provide evidence that the repression induced by exogenous methionine acts at the transcriptional level whereas the repression induced by exogenous SAM acts at the translational level.

Regulation of dihydrodipicolinate synthase and aspartate kinase in Bacillus subtilis

The regulation of dihydrodipicolinate synthase (EC 4.2.1.52) and aspartate kinase (EC 2.7.2.4) was studied in Bacillus subtilis 168. Starvation for lysine gave depression of one aspartate kinase isoenzyme but not of dihydrodipicolinate synthase. Strains resistant to growth inhibition by the lysine analogue thiosine exhibited constitutively derepressed synthesis of one aspartate kinase isoenzyme but had normal levels of dihydrodipicolinate synthase. The data provide strong evidence that lysine is not the signal for derepression of dihydrodipicolinate synthase. Nevertheless, dihydrodipicolinate synthase specific activity increased during sporulation, and it is suggested that this increase may result, in part, from resistance to proteolysis of that enzyme.

Mapping of the structural genes of the three aspartokinases and of the two homoserine dehydrogenases of Escherichia coli K-12

Mutants requiring threonine plus methionine (or homoserine), or threonine plus methionine plus diaminopimelate (or homoserine plus diaminopimelate) have been isolated from strains possessing only one of the three isofunctional aspartokinases. They have been classified in several groups according to their enzymatic defects. Their mapping is described. Several regions of the chromosome are concerned: thrA (aspartokinase I-homoserine dehydrogenase I) is mapped in the same region as thrB and thrC (0 min). lysC (aspartokinase III) is mapped at 80 min, far from the other genes coding for diaminopimelate synthesis. metLM (aspartokinase II-homoserine dehydrogenase II) lies at 78 min closely linked to metB, metJ, and metF.