Microcalorimetric study of aerobic growth of Escherichia coli in batch culture

Thermograms of an aerobic batch culture of Escherichia coli K-12 in synthetic medium were obtained by using a newly designed mecrocalorimeter. The thermograms reflected sharp changes of metabolic activity in glucose-, nitrogen-, or oxygen-limited cultures. The thermo chemical analysis for each culture condition was done using the data of the heat evolved, the head of combustion of cells, and the elementary analysis of the cells. The efficiency of energy conversion determined experimentally revealed nutritional differences.     

A new batch calorimeter for aerobic growth studies

A microcalorimeter for aerobic growth studies, derived from a Tian Calvet differential apparatus, was successfully constructed. The calorimetric vessel was a short cylinder, which permitted a good exchange between the surface area and the gas phase. The time constant of the calorimeter was 3.6 min and the sensitivity 234 V/W. The thermochemical aspect of the aerobic growth of Escherichia coli on succinate, acetate, and glucose was investigated. This analysis revealed that the contribution of biosynthetic reactions varied with the substrate used and strongly influenced the heat evolution. The experimental metabolic enthalpy change was in good agreement with the predicted value for succinate and glucose growth. To explain the discrepancy between the two values observed for acetate growth we suggest that acetate metabolism may generate a by-product which was not further oxidized.     

The utilisation of glucose/acetate mixtures by Escherichia coli W3110 under aerobic growth conditions

Byproduct acetate is of major concern when considering the growth of Escherichia coli on glucose. Besides the fact that acetate production detracts from the overall yield, acetate itself is also a growth inhibitor. To further complicate matters, E. coli is capable of growth on acetate via the glyoxylate bypass. In an effort to evaluate the influence of acetate on the growth of E. coli, mixed glucose/acetate substrate batch and continuous cultivations have been carried out. The results have been examined in the context of their implications for industrial-scale bioreactors. It was found that acetate was growth inhibitory at relatively low concentrations <1.25 g/l. A batch culture supplied with both glucose and acetate utilised glucose in preference to acetate. Simultaneous utilisation of substrates was observed in continuous cultures at low imposed growth rates, i.e., below ca. 0.30 h^у.     

Control of carbon flux to acetate excretion during growth of Escherichia coli in batch and continuous cultures

During growth of Escherichia coli ML308 on pyruvate in a continuous culture (turbidostat) or batch culture, flux of carbon into the cells exceeds the amphibolic capacity of the central pathways. This is balanced by diversion of carbon flux to acetate excretion which in turn diminishes the efficiency of carbon conversion to biomass [g] dry wt (mol substrate)-1]. However, restriction of carbon supply in a chemostat diminishes flux to acetate excretion and at a dilution rate (D = mu) of 0.35 h-1 or less, no flux to acetate excretion was sustained thus permitting perfect balance between carbon input on the one hand, and the output to biosynthesis and energy generation on the other. This, in turn, improves the efficiency of carbon conversion to biomass. Inclusion of 3-bromopyruvate (an inhibitor of pyruvate dehydrogenase) at a concentration which diminishes growth rate (mu) to 0.35 h-1 or less also prevented flux to acetate excretion. Furthermore, in a family of fluoroacetate-resistant strains, excessive flux of pyruvate was balanced by diversion of carbon flux to lactate excretion rather than acetate and a higher growth rate (mu = 0.63 h-1) was sustained.     

Deletion of cscR in Escherichia coli W improves growth and poly-3-hydroxybutyrate (PHB) production from sucrose in fed batch culture

Sucrose has several advantages over glucose as a feedstock for bioprocesses, both environmentally and economically. However, most industrial Escherichia coli strains are unable to utilize sucrose. E. coli W can grow on sucrose but stops growing when sucrose concentrations become low. This is undesirable in fed-batch conditions where sugar levels are low between feeding pulses. Sucrose uptake rates were improved by removal of the cscR gene, which encodes a protein that represses expression of the sucrose utilization genes at low sucrose concentrations. Poly-3-hydroxybutyrate (PHB) was used as a model compound in order to assess the effect of improved sugar utilization on bio-production. In the cscR knockout strain, production from sucrose was improved by 50%; this strain also produced 30% more PHB than the wild-type using glucose. This result demonstrates the feasibility of utilizing sucrose as an industrial feedstock for E. coli-based bioprocesses in high cell density culture.     

Deletion of cscR in Escherichia coli W improves growth and poly-3-hydroxybutyrate (PHB) production from sucrose in fed batch culture

Sucrose has several advantages over glucose as a feedstock for bioprocesses, both environmentally and economically. However, most industrial Escherichia coli strains are unable to utilize sucrose. E. coli W can grow on sucrose but stops growing when sucrose concentrations become low. This is undesirable in fed-batch conditions where sugar levels are low between feeding pulses. Sucrose uptake rates were improved by removal of the cscR gene, which encodes a protein that represses expression of the sucrose utilization genes at low sucrose concentrations. Poly-3-hydroxybutyrate (PHB) was used as a model compound in order to assess the effect of improved sugar utilization on bio-production. In the cscR knockout strain, production from sucrose was improved by 50%; this strain also produced 30% more PHB than the wild-type using glucose. This result demonstrates the feasibility of utilizing sucrose as an industrial feedstock for E. coli-based bioprocesses in high cell density culture.     

Superoxide dismutase protects against aerobic heat shock in Escherichia coli.

Exposure of a superoxide dismutase-null (sodA sodB) strain of Escherichia coli to aerobic heat stress (45 to 48 degrees C) caused a profound loss of viability, whereas the same heat stress applied anaerobically had a negligible effect. A superoxide dismutase-competent parental strain was resistant to the lethal effect of the aerobic heating. It follows that aerobic heating imposes an oxidative burden of which O2- must be a major component. This effect is not seen at 53 degrees C, presumably because, at this higher temperature, direct thermolability of vital cell components overrides the effect of superoxide radicals.     

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.     

The effect of acetate on population heterogeneity in different cellular characteristics of Escherichia coli in aerobic batch cultures

Acetate as the major by-product in industrial-scale bioprocesses with Escherichia coli is found to decrease process efficiency as well as to be toxic to cells, which has several effects like a significant induction of cellular stress responses. However, the underlying phenomena are poorly explored. Therefore, we studied time-resolved population heterogeneity of the E. coli growth reporter strain MG1655/pGS20PrrnBGFPAAV expressing destabilized green fluorescent protein during batch growth on acetate and glucose as sole carbon sources. Additionally, we applied five fluorescent stains targeting different cellular properties (viability as well as metabolic and respiratory activity). Quantitative analysis of flow cytometry data verified that bacterial populations in the bioreactor are more heterogeneous in growth as well as stronger metabolically challenged during growth on acetate as sole carbon source, compared to growth on glucose or acetate after diauxic shift. Interestingly, with acetate as sole carbon source, significant subpopulations were found with some cells that seem to be more robust than the rest of the population. In conclusion, following batch cultures population heterogeneity was evident in all measured parameters. Our approach enabled a deeper study of heterogeneity during growth on the favored substrate glucose as well as on the toxic by-product acetate. Using a combination of activity fluorescent dyes proved to be an accurate and fast alternative as well as a supplement to the use of a reporter strain. However, the choice of combination of stains should be well considered depending on which population traits to aim for.     

Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.

Flux balance models of metabolism use stoichiometry of metabolic pathways, metabolic demands of growth, and optimality principles to predict metabolic flux distribution and cellular growth under specified environmental conditions. These models have provided a mechanistic interpretation of systemic metabolic physiology, and they are also useful as a quantitative tool for metabolic pathway design. Quantitative predictions of cell growth and metabolic by-product secretion that are experimentally testable can be obtained from these models. In the present report, we used independent measurements to determine the model parameters for the wild-type Escherichia coli strain W3110. We experimentally determined the maximum oxygen utilization rate (15 mmol of O2 per g [dry weight] per h), the maximum aerobic glucose utilization rate (10.5 mmol of Glc per g [dry weight] per h), the maximum anaerobic glucose utilization rate (18.5 mmol of Glc per g [dry weight] per h), the non-growth-associated maintenance requirements (7.6 mmol of ATP per g [dry weight] per h), and the growth-associated maintenance requirements (13 mmol of ATP per g of biomass). The flux balance model specified by these parameters was found to quantitatively predict glucose and oxygen uptake rates as well as acetate secretion rates observed in chemostat experiments. We have formulated a predictive algorithm in order to apply the flux balance model to describe unsteady-state growth and by-product secretion in aerobic batch, fed-batch, and anaerobic batch cultures. In aerobic experiments we observed acetate secretion, accumulation in the culture medium, and reutilization from the culture medium. In fed-batch cultures acetate is cometabolized with glucose during the later part of the culture period.(ABSTRACT TRUNCATED AT 250 WORDS)     

The effect of controlled feeding of glycerol on beta-galactosidase production by Escherichia coli in batch culture

A mutant of E. coli constitutive for β-galactosidase has been grown in batch culture with the carbon source, glycerol, fed at various fixed rates to the culture. High feeding rates where growth was only slightly restricted gave final enzyme levels similar to those obtained in cultures where all the glycerol was added initially. Low feeding rates resulted in breakdown of the β-galactosidase formed and gave reduced final levels of the enzyme.     

On-line monitoring of growth of Escherichia coli in batch cultures by bioluminescence

Bioluminescence was used to monitor growth of Escherichia coli in batch cultures on-line. Light emission of a strain engineered for constitutive bioluminescence was monitored with a simple set-up consisting of a photodiode, a photodetector amplifier and a recorder. Bioluminescence and colony forming units (CFU) of the cultures increased and decreased proportionally and were correlated during every growth phase at temperatures between 28 °C and 40 °C. Up to the late log (deceleration) phase, both light emission and CFU increased rapidly. Beyond the stationary phase these characteristics decreased very slowly at lower temperatures, while at higher ones they declined more rapidly. Towards the end of the cultivation, light emission of the cultures dropped to undetectable levels, even though CFU were recovered. This was particularly marked at lower temperatures where non-luminescent cultures retained very high CFU. This indicates that the actual metabolism of cells in a culture can be at a very low level or completely shut down, yet cells retain their capability to be culturable. The on-line technology described here has a number of potential uses in the laboratory and industry. Received: 30 September 1999 / Received revision: 29 November 1999 / Accepted: 3 December 1999     

Acetate metabolism in a pta mutant of Escherichia coli W3110: importance of maintaining acetyl coenzyme A flux for growth and survival.

In order to study the physiological role of acetate metabolism in Escherichia coli, the growth characteristics of an E. coli W3100 pta mutant defective in phosphotransacetylase, the first enzyme of the acetate pathway, were investigated. The pta mutant grown on glucose minimal medium excreted unusual by-products such as pyruvate, D-lactate, and L-glutamate instead of acetate. In an analysis of the sequential consumption of amino acids by the pta mutant growing in tryptone broth (TB), a brief lag between the consumption of amino acids normally consumed was observed, but no such lag occurred for the wild-type strain. The pta mutant was found to grow slowly on glucose, TB, or pyruvate, but it grew normally on glycerol or succinate. The defective growth and starvation survival of the pta mutant were restored by the introduction of poly-beta-hydroxybutyrate (PHB) synthesis genes (phbCAB) from Alcaligenes eutrophus, indicating that the growth defect of the pta mutant was due to a perturbation of acetyl coenzyme A (CoA) flux. By the stoichiometric analysis of the metabolic fluxes of the central metabolism, it was found that the amount of pyruvate generated from glucose transport by the phosphoenolpyruvate-dependent phosphotransferase system (PTS) exceeded the required amount of precursor metabolites downstream of pyruvate for biomass synthesis. These results suggest that E. coli excretes acetate due to the pyruvate flux from PTS and that any method which alleviates the oversupply of acetyl CoA would restore normal growth to the pta mutant.     

Fed-batch culture of Escherichia coli for L-valine production based on in silico flux response analysis

We have previously reported the development of a 100% genetically defined engineered Escherichia coli strain capable of producing L ‐valine from glucose with a high yield of 0.38 g L ‐valine per gram glucose (0.58 mol L ‐valine per mol glucose) by batch culture. Here we report a systems biological strategy of employing flux response analysis in bioprocess development using L ‐valine production by fed‐batch culture as an example. Through the systems‐level analysis, the source of ATP was found to be important for efficient L ‐valine production. There existed a trade‐off between L ‐valine production and biomass formation, which was optimized for the most efficient L ‐valine production. Furthermore, acetic acid feeding strategy was optimized based on flux response analysis. The final fed‐batch cultivation strategy allowed production of 32.3 g/L L ‐valine, the highest concentration reported for E. coli. This approach of employing systems‐level analysis of metabolic fluxes in developing fed‐batch cultivation strategy would also be applicable in developing strategies for the efficient production of other bioproducts. Biotechnol. Bioeng. 2011; 108:934–946. © 2010 Wiley Periodicals, Inc.     

A metabolic model of cellular energetics and carbon flux during aerobic Escherichia coli fermentation

An integrated metabolic model for the production of acetate by Escherichia coli growing on glucose under aerobic conditions was presented previously (Ko et al., 1993). The resulting model equations can be used to explain phenomena often observed with industrial fermentations, i.e., increased acetate production which follows from high glucose uptake rate, a low dissolved oxygen concentration, a high specific growth rate, or a combination of these conditions. However, several questions still need to be addressed. First, cell composition is growth rate and media dependent. Second, the macromolecular composition varied between E. coli strains. And finally, a model that represents the carbon fluxes between the Embden-Meyerhof-Parnas (EMP) and the hexose monophosphate (HMP) pathways when cells are subject to internal and/or external stresses is still not well defined. In the present work, we have made an effort to account for these effects, and the resulting model equations show good agreement for wild-type and recombinant E. coli experimental data for the acetate concentration, the onset of acetate secretion, and cell yield based on glucose. These results are useful for optimizing aerobic E. coli fermentation processes. More specifically, we have determined the EMP pathway carbon flux profiles required by the integrated metabolic model for an accurate fit of the acetic acid profile data from a wild-type E. coli strain ML308. These EMP carbon flux profiles were correlated with a dimensionless measurement of biomass and then used to predict the acetic acid profiles for E. coli strain F-122 expressing human immunodeficiency virus-(HIV(528)) beta-galactosidase fusion protein. The effect of different macromolecular compositions and growth rates between these two E. coli strains required a constant scaling factor for improved quantitative predictions.     

Batch culture characterization and metabolic flux analysis of succinate-producing Escherichia coli strains

This study presents an in-depth analysis of the anaerobic metabolic fluxes of various mutant strains of Escherichia coli overexpressing the Lactococcus lactis pyruvate carboxylase (PYC) for the production of succinate. Previously, a metabolic network design that includes an active glyoxylate pathway implemented in vivo increased succinate yield from glucose in an E. coli mutant to 1.6 mol/mol under fully anaerobic conditions. The design consists of a dual succinate synthesis route, which diverts required quantities of NADH through the traditional fermentative pathway and maximizes the carbon converted to succinate by balancing the carbon flux through the fermentative pathway and the glyoxylate pathway (which has a lower NADH requirement). Mutant strains previously constructed during the development of high-yield succinate-producing strains were selected for further characterization to understand their metabolic response as a result of several genetic manipulations and to determine the significance of the fermentative and the glyoxylate pathways in the production of succinate. Measured fluxes obtained under batch cultivation conditions were used to estimate intracellular fluxes and identify critical branch point flux split ratios. The comparison of changes in branch point flux split ratios to the glyoxylate pathway and the fermentative pathway at the oxaloacetate (OAA) node as a result of different mutations revealed the sensitivity of succinate yield to these manipulations. The most favorable split ratio to obtain the highest succinate yield was the fractional partition of OAA to glyoxylate of 0.32 and 0.68 to the fermentative pathway obtained in strains SBS550MG (pHL413) and SBS990MG (pHL413). The succinate yields achieved in these two strains were 1.6 and 1.7 mol/mol, respectively. In addition, an active glyoxylate pathway in an ldhA, adhE, ack-pta mutant strain is shown to be responsible for the high succinate yields achieved anaerobically. Furthermore, in vitro activity measurements of seven crucial enzymes involved in the pathways studied and intracellular measurements of key intermediate metabolite pools provided additional insights on the physiological perturbations caused by these mutations. The characterization of these recombinant mutant strains in terms of flux distribution pattern, in vitro enzyme activity and intracellular metabolite pools provides useful information for the rational modification of metabolic fluxes to improve succinate production.     

Use of a novel air separation system in a fed-batch fermentative culture of Escherichia coli

A novel air separation system based on permeable membrane gas separation technology was used to cultivate Escherichia coli. The system fulfilled the dissolved oxygen requirements of a culture of E. coli grown on a glucose synthetic medium at a high and constant growth rate of 0.55 h-1. A biomass yield of 45 g (dry weight) per liter was achieved, and no by-product inhibition by acetate or CO2 was observed.