Dynamic flux balance analysis of diauxic growth in Escherichia coli

Flux Balance Analysis (FBA) has been used in the past to analyze microbial metabolic networks. Typically, FBA is used to study the metabolic flux at a particular steady state of the system. However, there are many situations where the reprogramming of the metabolic network is important. Therefore, the dynamics of these metabolic networks have to be studied. In this paper, we have extended FBA to account for dynamics and present two different formulations for dynamic FBA. These two approaches were used in the analysis of diauxic growth in Escherichia coli. Dynamic FBA was used to simulate the batch growth of E. coli on glucose, and the predictions were found to qualitatively match experimental data. The dynamic FBA formalism was also used to study the sensitivity to the objective function. It was found that an instantaneous objective function resulted in better predictions than a terminal-type objective function. The constraints that govern the growth at different phases in the batch culture were also identified. Therefore, dynamic FBA provides a framework for analyzing the transience of metabolism due to metabolic reprogramming and for obtaining insights for the design of metabolic networks.     

Regulation of peptidoglycan biosynthesis in relA+ and relA- strains of Escherichia coli during diauxic growth on glucose and lactose.

In both relA+ and relA- derivatives, the biosynthesis of peptidoglycan, lipid intermediates, and nucleotide precursors abruptly halted at the onset of diauxic lag from glucose to lactose with a concomitant accumulation of guanosine 5'-diphosphate 3'-diphosphate (ppGpp). These results are consistent with the proposal that ppGpp is involved in inhibiting the incorporation of disaccharide-pentapeptide into peptidoglycan and in regulating nucleotide precursor synthesis.     

Bacterial gene regulation in diauxic and non-diauxic growth

When bacteria are grown in a batch culture containing a mixture of two growth-limiting substrates, they exhibit a rich spectrum of substrate consumption patterns including diauxic growth, simultaneous consumption, and bistable growth. In previous work, we showed that a minimal model accounting only for enzyme induction and dilution captures all the substrate consumption patterns [Narang, A., 1998a. The dynamical analogy between microbial growth on mixtures of substrates and population growth of competing species. Biotechnol. Bioeng. 59, 116-121, Narang, A., 2006. Comparitive analysis of some models of gene regulation in mixed-substrate microbial growth, J. Theor. Biol. 242, 489-501]. In this work, we construct the bifurcation diagram of the minimal model, which shows the substrate consumption pattern at any given set of parameter values. The bifurcation diagram explains several general properties of mixed-substrate growth. (1) In almost all the cases of diauxic growth, the "preferred" substrate is the one that, by itself, supports a higher specific growth rate. In the literature, this property is often attributed to the optimality of regulatory mechanisms. Here, we show that the minimal model, which accounts for induction and growth only, displays the property under fairly general conditions. This suggests that the higher growth rate of the preferred substrate is an intrinsic property of the induction and dilution kinetics. It can be explained mechanistically without appealing to optimality principles. (2) The model explains the phenotypes of various mutants containing lesions in the regions encoding for the operator, repressor, and peripheral enzymes. A particularly striking phenotype is the "reversal of the diauxie" in which the wild-type and mutant strains consume the very same two substrates in opposite order. This phenotype is difficult to explain in terms of molecular mechanisms, such as inducer exclusion or CAP activation, but it turns out to be a natural consequence of the model. We show furthermore that the model is robust. The key property of the model, namely, the competitive dynamics of the enzymes, is preserved even if the model is modified to account for various regulatory mechanisms. Finally, the model has important implications for the problem of size regulation in development. It suggests that protein dilution may be the mechanism coupling patterning and growth.     

Macromolecular replication during lignin biosynthesis

Lignins play a crucial role in the cell-wall architecture of all vascular plants. They are composed of p-hydroxyphenylpropanoid units interconnected through covalent bonds formed during lignol radical coupling between six different pairs of atomic centers. For 50 years, the primary structures of lignins have been thought to be random, but for a number of reasons such an assumption is not tenable. For example, it has been reported that, by simple physicochemical means, the rather recalcitrant lignins in spruce wood can be decisively separated into two fractions containing quite dissimilar biopolymer chains. Thus, a paradigm shift should be imminent, and a detailed working hypothesis for the mechanism of lignin biosynthesis would be invaluable in delineating how the process of macromolecular lignin assembly can be properly investigated. In conjunction with an earlier experimental result, an explicit model for a template dehydropolymerization process has been developed that describes how lignin primary structure is replicated. The strengths of the powerful noncovalent interactions have been calculated that control the transient placement of lignol radicals about to undergo coupling on a double-stranded lignin template. These elementary steps engender, in the growing daughter chain, a primary structure identical to that of the distal template strand. The interactions are governed by dynamical electron correlation in the π-orbitals of each immobilized lignol radical and the complementary aromatic ring in the antiparallel proximal strand. The resulting noncovalent forces are computed to be stronger than those stabilizing GC/CG base pairs in DNA double-helices, but the mechanism of replication is fundamentally different from that of any other biopolymer.     

Repression of biotin biosynthesis in Escherichia coli during growth on biotin vitamers.

A strain of Escherichia coli in which the lacZ gene was fused to the bioA promoter was constructed. Colonies of this strain formed Lac(+) colonies on low-biotin agar (1.6 to 4.1 nM) and Lac(-) colonies on high-biotin agar (41 nM). This lac-bio fusion strain was used to study the question of whether cells growing on the biotin vitamers d-biotin-d-sulfoxide (BDS) and dethiobiotin (DTB) generate enough biotin to give maximal repression of beta-galactosidase synthesis. Repression by high concentrations (400 nM) of BDS was almost maximal (about 96%), whereas DTB repression reached a saturation level of about 80% with increasing DTB concentrations. The levels of repression obtained with both vitamers were sufficient to cause the colonies to appear Lac(-). When the lac-bio fusion was transduced into lines carrying mutations (bis) that prevent reduction of BDS to biotin, the transductants were not repressed by added BDS. Repression by BDS is unlikely to result from accumulation of extracellular biotin-related substances because (i) washed bis(+) cells were not detectably derepressed when transferred into medium containing BDS and (ii) washed bis cells were not detectably repressed when transferred into medium in which bis(+) cells had grown. Lactose agar plates containing high concentrations of DTB or BDS comprise an efficient selective medium for bioB or bis mutants and were used to isolate spontaneous mutations of these genes. This method should be adaptable to the selection of mutations in any biosynthetic pathway subject to end-product repression.     

Role of inducer exclusion in preferential utilization of glucose over melibiose in diauxic growth of Escherichia coli

The role of inducer exclusion in diauxic growth of Escherichia coli on glucose and melibiose was investigated. The amounts of glucose and melibiose in the culture medium were determined during the diauxie. Glucose was consumed during the first growth cycle of the diauxie, and melibiose was consumed during the second cycle. The addition of adenosine 3',5'-cyclic monophosphate to the culture medium released both transient and catabolite repressions on the melibiose operon by glucose. Biphasic growth without a transient lag phase was observed in the presence of adenosine 3',5'-cyclic monophosphate. Preferential utilization of glucose over melibiose was observed even under such conditions. Thus, it is clear that inducer exclusion alone is sufficient to ensure the preferential utilization of glucose over melibiose. Similar results were obtained from a glucose-lactose diauxie. Inducer exclusion itself was not affected by adenosine 3',5'-cyclic monophosphate.     

Macromolecular syntheses in an Escherichia coli adk mutant

Preferential inhibition by high temperatures of synthesis of newly induced enzymes in Escherichia coli K-12 CR341T28 adk is only apparent; syntheses of all macromolecules cease simultaneously.     

Enzyme biosynthesis in Escherichia coli

Escherichia coli B synthesized beta-galactosidase and an enzyme system for D-xylose when exposed to lactose and xylose respectively in nitrogen-free media. The amount of beta-galactosidase formed in the absence of external nitrogen depended upon the nature of the medium in which the cells had originally been grown. Half as much of this enzyme was synthesized without exogenous nitrogen by cells taken from a nitrogen-rich medium as was formed by cells under favorable conditions with an external supply of nitrogen. Escherichia coli B contained a pool of nitrogen compounds soluble in 80 per cent ethanol and made up of several ninhydrin-positive components. One of these was identified chromatographically as glycine using an authentic radioactive sample. Another substance behaved like serine on the chromatograms. The internal pool of amino acids and peptides was large enough to account for the beta-galactosidase synthesized by cells exposed to lactose in a medium free of nitrogen. Some degree of interaction of the syntheses of the beta-galactosidase and xylose enzyme systems was observed in nitrogen-free media. This interaction produced a greater effect on the formation of beta-galactosidase and was attributed to a limiting factor(s) in the internal nitrogenous pool or to a limiting intermediate in enzyme synthesis.     

In situ recovery of lycopene during biosynthesis with recombinant Escherichia coli

Lycopene is produced by recombinant Escherichia coli expressing genes to encode for the lycopene biosynthesis. However, the productivity of lycopene seemed to be limited by many factors including product toxicity. In the present study, we have investigated physiology of recombinant E. coli during biosynthesis and in situ recovery of lycopene based on an organic/aqueous two-phase system. Lycopene, the 40-carbon molecule product, was little extracted from recombinant E. coli cells to octane or decane phase. However, partial digestion of cell walls with lysozyme promoted extraction of lycopene into the organic phases. Engineering of an organic/aqueous two-phase system allowed recombinant E. coli cells to produce ca. 40% larger amount of lycopene compared to that in a conventional aqueous single-phase system. Optimization of the in situ product recovery process will lead to further increase of product concentration and productivity.     

Effect of Trimethoprim on Macromolecular Synthesis in Escherichia coli

Trimethoprim is a specific inhibitor of dihydrofolate reductase. When added to amino acid supplemented cultures of Escherichia coli, protein, ribonucleic acid (RNA), and deoxyribonucleic acid synthesis are rapidly inhibited. It is shown that thymidylate and purine synthesis must continuously occur if the inhibition is to be maintained. These results are interpreted as demonstrating that in vivo trimethoprim can reduce but not totally inhibit the action of dihydrofolate reductase and therefore reduce the amount of tetrahydrofolate derivatives available for formylmethionyl transfer RNA formylation, purine, and thymidylate synthesis.     

Pyrimidine Pools and Macromolecular Composition of Pyrimidine-Limited Escherichia coli

The growth rate of a pyrimidine-requiring strain was controlled by limiting the concentration of exogenous orotic acid. As the steady state, pyrimidine-limited growth rate was decreased, the intracellular pyrimidine pools and the total nucleic acid per unit mass of culture also decreased. The ratio of deoxyribonucleic acid to protein remained constant, whereas the ratio of ribonucleic acid to protein decreased 30% over a threefold variation in growth rate (50- to 150-min doubling times). The intracellular uridine triphosphate and cytosine triphosphate pools also decreased (although not coordinately), and the pyrimidine biosynthetic enzymes were derepressed. Cell size was unaffected by pyrimidine-mediated variation of the growth rate.     

Bacterial growth in space flight: logistic growth curve parameters for Escherichia coli and Bacillus subtilis

Previous investigations have reported that bacterial suspension cultures grow to higher stationary concentrations in space flight than on Earth; however, none of these investigations included extensive ground controls under varied inertial conditions. This study includes extensive controls and cell-growth data taken at several times during lag phase, log phase, and stationary phase of Escherichia coli and Bacillus subtilis. The Marquardt-Levenberg, least-squares fitting algorithm was used to calculate kinetic growth parameters from the logistic bacterial growth equations for space-flight and control growth curves. Space-flight cultures grew to higher stationary-phase concentrations and had shorter lag-phase durations. Also, evidence was found for increased exponential growth rate in space. Received: 27 February 1998 / Received revision: 21 August 1998 / Accepted: 3 September 1998     

Pervasive compensatory adaptation in Escherichia coli

To investigate compensatory adaptation (CA), we used genotypes of Escherichia coli which were identical except for one or two deleterious mutations. We compared CA for (i) deleterious mutations with large versus small effects, (ii) genotypes carrying one versus two mutations, and (iii) pairs of deleterious mutations which interact in a multiplicative versus synergistic fashion. In all, we studied 14 different genotypes, plus a control strain which was not mutated. Most genotypes showed CA during 200 generations of experimental evolution, where we define CA as a fitness increase which is disproportionately large relative to that in evolving control lines, coupled with retention of the original deleterious mutation(s). We observed greater CA for mutations of large effect than for those of small effect, which can be explained by the greater benefit to recovery in severely handicapped genotypes given the dynamics of selection. The rates of CA were similar for double and single mutants whose initial fitnesses were approximately equal. CA was faster for synergistic than for multiplicative pairs, presumably because the marginal gain which results from CA for one of the component mutations is greater in that case. The most surprising result in our view, is that compensation should be so readily achieved in an organism which is haploid and has little genetic redundancy This finding suggests a degree of versatility in the E. coil genome which demands further study from both genetic and physiological perspectives.