Systematic phenome analysis of Escherichia coli multiple‐knockout mutants reveals hidden reactions in central carbon metabolism

Central carbon metabolism is a basic and exhaustively analyzed pathway. However, the intrinsic robustness of the pathway might still conceal uncharacterized reactions. To test this hypothesis, we constructed systematic multiple‐knockout mutants involved in central carbon catabolism in Escherichia coli and tested their growth under 12 different nutrient conditions. Differences between in silico predictions and experimental growth indicated that unreported reactions existed within this extensively analyzed metabolic network. These putative reactions were then confirmed by metabolome analysis and in vitro enzymatic assays. Novel reactions regarding the breakdown of sedoheptulose‐7‐phosphate to erythrose‐4‐phosphate and dihydroxyacetone phosphate were observed in transaldolase‐deficient mutants, without any noticeable changes in gene expression. These reactions, triggered by an accumulation of sedoheptulose‐7‐phosphate, were catalyzed by the universally conserved glycolytic enzymes ATP‐dependent phosphofructokinase and aldolase. The emergence of an alternative pathway not requiring any changes in gene expression, but rather relying on the accumulation of an intermediate metabolite may be a novel mechanism mediating the robustness of these metabolic networks.     

Dynamic modeling of the central carbon metabolism of Escherichia coli

Application of metabolic engineering principles to the rational design of microbial production processes crucially depends on the ability to describe quantitatively the systemic behavior of the central carbon metabolism to redirect carbon fluxes to the product-forming pathways. Despite the importance for several production processes, development of an essential dynamic model for central carbon metabolism of Escherichia coli has been severely hampered by the current lack of kinetic information on the dynamics of the metabolic reactions. Here we present the design and experimental validation of such a dynamic model, which, for the first time, links the sugar transport system (i.e., phosphotransferase system [PTS]) with the reactions of glycolysis and the pentose-phosphate pathway. Experimental observations of intracellular concentrations of metabolites and cometabolites at transient conditions are used to validate the structure of the model and to estimate the kinetic parameters. Further analysis of the detailed characteristics of the system offers the possibility of studying important questions regarding the stability and control of metabolic fluxes.     

Engineering Escherichia coli native metabolism for efficient biosynthesis of orotate

Orotate (OA) is a precursor of pyrimidine nucleotides and is widely used in food, pharmaceutical, and cosmetic industries. Although various microorganisms have been used for OA production, the production efficiency needs to be further improved for industrial application. In this study, we engineered Escherichia coli native metabolism for efficient OA production. The entire pathway was divided into the downstream OA synthesis, the midstream aspartate/glutamine supply, and the upstream glycolysis modules. First, the downstream module was optimized by disrupting pyrE to block OA consumption and release the feedback inhibition, and tuning expression of the biosynthetic genes. Second, the midstream pathway was enhanced by increasing the supply of the precursors and the cofactor nicotinamide adenine dinucleotide phosphate (NADPH). More importantly, we observed that pyrE disruption may lead to metabolic disorder as indicated by the accumulation of large amount of acetate. This problem was solved by reducing the flux of glycolysis. With these efforts, the final strain produced 80.3 g/L OA with a yield of 0.56 g/g glucose in fed-batch fermentation, which are the highest titer and yield reported so far. This work paves the way for industrial production of OA and represents as a good example of modulating cell metabolism for efficient chemical production.     

Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism

Shewanella spp. are a group of facultative anaerobic bacteria widely distributed in marine and freshwater environments. In this study, we profiled the central metabolic fluxes of eight recently sequenced Shewanella species grown under the same condition in minimal medium with [3‐¹³C] lactate. Although the tested Shewanella species had slightly different growth rates (0.23–0.29 h^?1) and produced different amounts of acetate and pyruvate during early exponential growth (pseudo‐steady state), the relative intracellular metabolic flux distributions were remarkably similar. This result indicates that Shewanella species share similar regulation in regard to central carbon metabolic fluxes under steady growth conditions: the maintenance of metabolic robustness is not only evident in a single species under genetic perturbations (Fischer and Sauer, 2005; Nat Genet 37(6):636–640), but also observed through evolutionary related microbial species. This remarkable conservation of relative flux profiles through phylogenetic differences prompts us to introduce the concept of metabotype as an alternative scheme to classify microbial fluxomics. On the other hand, Shewanella spp. display flexibility in the relative flux profiles when switching their metabolism from consuming lactate to consuming pyruvate and acetate. Biotechnol. Bioeng. 2009;102: 1161–1169. © 2008 Wiley Periodicals, Inc.     

Use of the flux model of amino acid metabolism of Escherichia coli

A program implementing a flux model of Escherichia coli metabolism was used to analyze the effects of the addition of amino acids (tryptophan, tyrosine, phenylalanine, leucine, isoleucine, valine, histidine, lysine, threonine, cysteine, methionine, arginine, proline) to minimal medium or media lacking nitrogen, carbon, or both. The overall response of the metabolic system to the addition of various amino acids to the minimal medium is similar. Glycolysis and the synthesis of pyruvate with its subsequent degradation to acetate via acetyl-CoA become more efficient, whereas the fluxes through the pentose phosphate pathway and the TCA cycle decrease. If amino acids are used as the sole source of carbon, nitrogen, or both, the changes in the flux distribution are determined mainly by the carbon limitation. The phosphoenolpyruvate to glucose-6-phosphate flux increases; the flux through the pentose phosphate path is directed towards ribulose-5-phosphate. Other changes are determined by the compounds that are the primary products of catabolism of the added amino acid.     

Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS.

We describe here a novel methodology for rapid diagnosis of metabolic changes, which is based on probabilistic equations that relate GC-MS-derived mass distributions in proteinogenic amino acids to in vivo enzyme activities. This metabolic flux ratio analysis by GC-MS provides a comprehensive perspective on central metabolism by quantifying 14 ratios of fluxes through converging pathways and reactions from [1-13C] and [U-13C]glucose experiments. Reliability and accuracy of this method were experimentally verified by successfully capturing expected flux responses of Escherichia coli to environmental modifications and seven knockout mutations in all major pathways of central metabolism. Furthermore, several mutants exhibited additional, unexpected flux responses that provide new insights into the behavior of the metabolic network in its entirety. Most prominently, the low in vivo activity of the Entner-Doudoroff pathway in wild-type E. coli increased up to a contribution of 30% to glucose catabolism in mutants of glycolysis and TCA cycle. Moreover, glucose 6-phosphate dehydrogenase mutants catabolized glucose not exclusively via glycolysis, suggesting a yet unidentified bypass of this reaction. Although strongly affected by environmental conditions, a stable balance between anaplerotic and TCA cycle flux was maintained by all mutants in the upper part of metabolism. Overall, our results provide quantitative insight into flux changes that bring about the resilience of metabolic networks to disruption.     

Characterization of physiological responses to 22 gene knockouts in Escherichia coli central carbon metabolism

Understanding the impact of gene knockouts on cellular physiology, and metabolism in particular, is centrally important to quantitative systems biology and metabolic engineering. Here, we present a comprehensive physiological characterization of wild-type Escherichia coli and 22 knockouts of enzymes in the upper part of central carbon metabolism, including the PTS system, glycolysis, pentose phosphate pathway and Entner–Doudoroff pathway. Our results reveal significant metabolic changes that are affected by specific gene knockouts. Analysis of collective trends and correlations in the data using principal component analysis (PCA) provide new, and sometimes surprising, insights into E. coli physiology. Additionally, by comparing the data-to-model predictions from constraint-based approaches such as FBA, MOMA and RELATCH we demonstrate the important role of less well-understood kinetic and regulatory effects in central carbon metabolism.     

Eco-efficiency of urban material metabolism: a case study in Shenzhen, China

The keys of studying urban sustainable development are material metabolism flux and efficiency. Metabolism flux of urban materials can only reflect the metabolism velocity, while its eco-efficiency can determine the metabolism capacity to support socio-economic development. The general model and the measure model of the eco-efficiency were set up, based on the source recycle (decreasing the consumption of crude resources) and the terminal recycle (decreasing the discharge of pollutants) of production and life. These models were employed to study material metabolism flux and efficiency in Shenzhen, China. Results showed that water, energy and waste metabolism fluxes have increased since 1998 with constant socio-economic development, and their eco-efficiencies have also increased rapidly. When GDP rose by 2.7 times, the metabolism fluxes of urban water and electricity rose by 1.5 and 3.0 times, respectively. When the added value of industry rose by 3.7 times, the metabolism fluxes of industrial water, electricity, energy and waste rose by 1.9, 3.5, 2.7 and 2.0 times, respectively. When population rose by 1.5 times, the metabolism fluxes of residential water and electricity rose by 1.8 and 1.7 times, respectively. During the period, the resource efficiency, environmental efficiency and eco-efficiency rose by 1.8, 3.7 and 2.3 times, respectively. Whereas the efficiency of material metabolism has been improved in Shenzhen, the scarcity of material resources has become more and more serious. Therefore, it is necessary to further improve the efficiency of material metabolism. The keys of improving the eco-efficiency of urban material metabolism are the increasing of resource and environmental efficiencies, and the establishing of the recycling chain of re-utilization of waste resources.     

Eco-efficiency of urban material metabolism: a case study in Shenzhen, China

The keys of studying urban sustainable development are material metabolism flux and efficiency. Metabolism flux of urban materials can only reflect the metabolism velocity, while its eco-efficiency can determine the metabolism capacity to support socio-economic development. The general model and the measure model of the eco-efficiency were set up, based on the source recycle (decreasing the consumption of crude resources) and the terminal recycle (decreasing the discharge of pollutants) of production and life. These models were employed to study material metabolism flux and efficiency in Shenzhen, China. Results showed that water, energy and waste metabolism fluxes have increased since 1998 with constant socio-economic development, and their eco-efficiencies have also increased rapidly. When GDP rose by 2.7 times, the metabolism fluxes of urban water and electricity rose by 1.5 and 3.0 times, respectively. When the added value of industry rose by 3.7 times, the metabolism fluxes of industrial water, electricity, energy and waste rose by 1.9, 3.5, 2.7 and 2.0 times, respectively. When population rose by 1.5 times, the metabolism fluxes of residential water and electricity rose by 1.8 and 1.7 times, respectively. During the period, the resource efficiency, environmental efficiency and eco-efficiency rose by 1.8, 3.7 and 2.3 times, respectively. Whereas the efficiency of material metabolism has been improved in Shenzhen, the scarcity of material resources has become more and more serious. Therefore, it is necessary to further improve the efficiency of material metabolism. The keys of improving the eco-efficiency of urban material metabolism are the increasing of resource and environmental efficiencies, and the establishing of the recycling chain of re-utilization of waste resources.     

Real-time detection of central carbon metabolism in living Escherichia coli and its response to perturbations

The direct tracking of cellular reactions in vivo has been facilitated with recent technologies that strongly enhance NMR signals in substrates of interest. This methodology can be used to assay intracellular reactions that occur within seconds to few minutes, as the NMR signal enhancement typically fades on this time scale. Here, we show that the enhancement of (13)C nuclear spin polarization in deuterated glucose allows to directly follow the flux of glucose signal through rather extended reaction networks of central carbon metabolism in living Escherichia coli. Alterations in central carbon metabolism depending on the growth phase or upon chemical perturbations are visualized with minimal data processing by instantaneous observation of cellular reactions.     

过表达氨基葡萄糖脱氨酶对大肠杆菌氨基葡萄糖合成及中心碳代谢的影响

考察过表达氨基葡萄糖脱氨酶对氨基葡萄糖合成及大肠杆菌（Escherichia coli）中心碳代谢的影响。实验结果表明：过表达氨基葡萄糖脱氨酶使得在36 g/L葡萄糖,pH为9.0的发酵条件下,发酵24 h后,重组菌发酵液中氨基葡萄糖、丙酮酸和乙酸的量分别是对照菌Rosetta的2.1、1.48和1.74倍;而乳酸的量为2.53 g/L,对照菌Rosetta发酵液中的乳酸含量未检测到,重组菌发酵液中柠檬酸及α-酮戊二酸的含量分别是Rosetta的2.99和2.73倍。     

城市物质代谢的生态效率——以深圳市为例

城市可持续发展研究的关键是城市物质代谢通量及其效率研究,但物质代谢通量仅能反映代谢速率,而其生态效率则能反映支持社会经济发展的物质代谢能力。从工业、生活的源头循环(减少原生资源的消耗)和末端循环(减少污染物的产生)角度,构建城市物质代谢生态效率的度量模型,并依据中国城市化发展进程,选定深圳市作为研究区,核算城市水、能量和废物代谢通量以及代谢的生态效率。结果表明:随着深圳市社会经济的快速发展,水、能源和废物代谢通量呈现出增长势头,但代谢的生态效率不断提高。1998～2004年间,GDP增长2.7倍,城市水和电的代谢通量分别增长1.5倍和3.0倍;工业增加值增长3.7倍,工业水、电、能源和废物的代谢通量分别增长1.9、3.5、2.7倍和2.0倍;常住人口增长1.5倍,居民水和电的代谢通量分别增长1.8倍和1.7倍;资源效率提高1.8倍,环境效率提高3.7倍,生态效率提高2.3倍。虽然深圳市物质代谢的生态效率在提高,但是随着物质资源的日益稀缺,物质代谢的生态效率仍需进一步提高,而提高城市物质代谢生态效率的关键是资源效率和环境效率的协同发展,以及逐步构建废物资源化的循环链条。     

A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli

Acrylic acid is a value-added chemical used in industry to produce diapers, coatings, paints, and adhesives, among many others. Due to its economic importance, there is currently a need for new and sustainable ways to synthesise it. Recently, the focus has been laid in the use of Escherichia coli to express the full bio-based pathway using 3-hydroxypropionate as an intermediary through three distinct pathways (glycerol, malonyl-CoA, and β-alanine). Hence, the goals of this work were to use COPASI software to assess which of the three pathways has a higher potential for industrial-scale production, from either glucose or glycerol, and identify potential targets to improve the biosynthetic pathways yields. When compared to the available literature, the models developed during this work successfully predict the production of 3-hydroxypropionate, using glycerol as carbon source in the glycerol pathway, and using glucose as a carbon source in the malonyl-CoA and β-alanine pathways. Finally, this work allowed to identify four potential over-expression targets (glycerol-3-phosphate dehydrogenase (G3pD), acetyl-CoA carboxylase (AccC), aspartate aminotransferase (AspAT), and aspartate carboxylase (AspC)) that should, theoretically, result in higher AA yields.     

Microtubular protein in its polymerized or nonpolymerized states differentially modulates in vitro and intracellular fluxes catalyzed by enzymes of carbon metabolism

The fluxes through HK/G6PDH and PK/LDH coupled-enzymatic reactions were quantified in the presence of physiological concentrations (1–15 μM) of polymerized or non-polymerized microtubular protein (MTP) from rat brain and in a permeabilized yeast cell system. In vitro enzymatic fluxes were increased by either polymerized or nonpolymerized brain MTP mainly in the lower range of MTP concentration. At fixed MTP concentrations in the flux stimulatory range of HK/G6PDH (1 mg/ml MTP) or PK/LDH (0.4 mg/ml MTP), a hyperbolic and sigmoidal response to NADP and PEP, respectively, was detected. That dependence varied according to the polymeric status of MTP. The specificity of the phenomenon observed in vitro, was tested for the PK/LDH and HK/G6PDH enzymatic couples in the presence of neutral polymers such as glycogen (? 10 mg/ml), poly(ethylene glycol) (up to 10% w/w) or G-actin (? 1 mg/ml). In permeabilized Saccharomyces cerevisiae cells, the PK-catalyzed flux was sensitive to microtubule disruption by nocodazole (15 μg/ml). The HK/G6PDH system was not affected by nocodazole showing values of kinetic parameters close to those obtained in vitro in the presence of polymerized brain MTP. Indirect immunofluorescence with specific antibodies against tubulin allowed to confirm the microtubules disruption in the presence of nocodazole in permeabilized yeast cells under the same conditions in which enzymes were assayed intracellularly. The experimental evidence is in agreement with the observed phenomenon of increase in fluxes in the enzymatic reactions assayed to be specifically induced by MTP either in vitro or in situ. The results presented are discussed in terms of the assembly of large supramolecular structures as a supraregulatory mechanism of synchronization of systemic cellular processes such as metabolic fluxes. © 1994 Wiley-Liss, Inc.     

古菌在红树林沉积物中的多样性及其碳代谢机制

红树林湿地生态系统具有维持生物多样性、净化环境及维持海岸带生态平衡等多种功能。古菌普遍存在于红树林沉积物中,在元素的生物地球化学循环中发挥着重要作用。古菌具有丰富的碳代谢多样性,能固定CO_2,参与甲烷循环,产乙酸,降解蛋白质、多聚碳水化合物等有机质,但目前对于红树林沉积物中古菌碳代谢的研究才刚刚起步。高通量测序技术的快速发展促进了大量新的古菌门类的发现,这些新的古菌门类具备多样的碳代谢潜力。本文简要概述古菌的主要类群与分布,综述国内外有关古菌碳代谢多样性的最新研究进展,并阐明这些古菌在红树林生态系统中的生态分布和功能特征,为进一步探究古菌代谢机制提供知识基础。     

Electrical bistability in a neuron model with monostable dendritic and axosomatic membranes

In a two-compartment mathematical model, we studied the reason for and conditions of manifestation of electrical bistability in a neuron composed of monostable parts. One compartment of the model simulated the dendrites; their membrane was monostable at high depolarization and characterized by an N-shaped steady current-voltage (I–V) characteristic endowed by inward synaptic current through voltage-dependent channels sensitive to N-methyl-D-aspartate (NMDA). Another compartment simulated the axosomatic region with a positively sloped linearizedI–V characteristic of the membrane monostable at the resting membrane potential. For the whole cell, bistability was obvious at a subcritical intensity of NMDA activation; the reason was the current directed from the more depolarized dendritic region into the somatic region, and the necessary condition was that the above somatopetal core current must exceed the net inward transmembrane current (the latter was the sum of the inward synaptic and outward passive extrasynaptic currents) of the dendritic compartment. This relation essentially depended on the size of the dendrites. Neirofiziologiya/Neurophysiology, Vol. 32, No. 2, pp. 98–101, March–April, 2000.     

Overexpression of a diacylglycerol acyltransferase gene in Phaeodactylum tricornutum directs carbon towards lipid biosynthesis

Under nutrient deplete conditions, diatoms accumulate between 15% to 25% of their dry weight as lipids, primarily as triacylglycerols (TAGs). As in most eukaryotes, these organisms produce TAGs via the acyl‐CoA dependent Kennedy pathway. The last step in this pathway is catalyzed by diacylglycerol acyltransferase (DGAT) that acylates diacylglycerol (DAG) to produce TAG. To test our hypothesis that DGAT plays a major role in controlling the flux of carbon towards lipids, we overexpressed a specific type II DGAT gene, DGAT2D, in the model diatom Phaeodactylum tricornutum. The transformants had 50‐ to 100‐fold higher DGAT2D mRNA levels and the abundance of the enzyme increased 30‐ to 50‐fold. More important, these cells had a 2‐fold higher total lipid content and incorporated carbon into lipids more efficiently than the wild type (WT) while growing only 15% slower at light saturation. Based on a flux analysis using ¹³C as a tracer, we found that the increase in lipids was achieved via increased fluxes through pyruvate and acetyl‐CoA. Our results reveal overexpression of DAGT2D increases the flux of photosynthetically fixed carbon towards lipids, and leads to a higher lipid content than exponentially grown WT cells.     

Quantification of proteomic and metabolic burdens predicts growth retardation and overflow metabolism in recombinant Escherichia coli

Escherichia coli has been the host organism most frequently investigated for efficient recombinant protein production. However, the production of a foreign protein in recombinant E. coli often leads to growth deterioration and elevated secretion of acetic acid. Such observed phenomena have been widely linked with cell stress responses and metabolic burdens originated particularly from the increased energy demand. In this study, flux balance analysis and dynamic flux balance analysis were applied to investigate the observed growth physiology of recombinant E. coli, incorporating the proteome allocation theory and an adjustable maintenance energy level (ATPM) to capture the proteomic and energetic burdens introduced by recombinant protein synthesis. Model predictions of biomass growth, substrate consumption, acetate excretion, and protein production with two different strains were in good agreement with the experimental data, indicating that the constraint on the available proteomic resource and the change in ATPM might be important contributors governing the growth physiology of recombinant strains. The modeling framework developed in this work, currently with several limitations to overcome, offers a starting point for the development of a practical, model-based tool to guide metabolic engineering decisions for boosting recombinant protein production.     

Time-scale dynamics of proteome predicts the central carbon metabolism involved in triterpenoid accumulation responsive to nitrogen limitation in Ganoderma lucidum

Central carbon metabolism describes the integration of transport pathway of main carbon sources inside the cell. Nitrogen (N) limitation is a favorable approach to stimulate ganoderic triterpenoid (GT) accumulation in Ganoderma lucidum. In this study, the dynamic regulation of metabolism reassignment towards GT biosynthesis responsive to N limitation was investigated by iTRAQ-based proteome. Physiological data suggested that N limitation slightly affected cell growth but significantly enhanced GT contents in the initial 20 days. From day 10, the protein contents were halted by prolonged N limitation duration. Proteomics-based investigations revealed that the carbon skeletons integrated into GT precursors were regenerated by glycolysis and the tricarboxylic acid (TCA) cycle. Cells strategically reserved nitrogen by barely incorporating it into TCA cycle intermediates to form amino acids, and enzymes involved in protein degradation were up regulated. Furthermore, regulation of proteins in response to abiotic stress and oxidation– reduction processes played a critical role in maintaining cellular homeostasis. These findings indicated that the flux of carbon into GT following N deficiency was a consequence of the remodeling of intermediate metabolism in TCA cycle and glycolysis reactions. This study provides a rationale for genetic engineering of G. lucidum, which may enable synchronized biomass and GT synthesis.     

Physiological response of central metabolism in Escherichia coli to deletion of pyruvate oxidase and introduction of heterologous pyruvate carboxylase

We studied the physiological response of Escherichia coli central metabolism to the expression of heterologous pyruvate carboxylase (PYC) in the presence and absence of pyruvate oxidase (POX). These studies were complemented with expression analysis of central and intermediary metabolic genes and conventional in vitro enzyme assays to evaluate glucose metabolism at steady-state growth conditions (chemostats). The absence of POX activity reduced nongrowth-related energy metabolism (maintenance coefficient) and increased the maximum specific rate of oxygen consumption. The presence of PYC activity (i.e., with POX activity) increased the biomass yield coefficient and reduced the maximum specific oxygen consumption rate compared to the wildtype. The presence of PYC in a poxB mutant resulted in a 42% lower maintenance coefficient and a 42% greater biomass yield compared to the wildtype. Providing E. coli with PYC or removing POX increased the threshold specific growth rate at which acetate accumulation began, with an 80% reduction in acetate accumulation observed at a specific growth rate of 0.4 h-1 in the poxB-pyc+ strain. Gene expression analysis suggests utilization of energetically less favorable glucose metabolism via glucokinase and the Entner-Doudoroff pathway in the absence of functional POX, while the upregulation of the phosphotransferase glucose uptake system and several amino acid biosynthetic pathways occurs in the presence of PYC. The physiological and expression changes resulting from these genetic perturbations demonstrate the importance of the pyruvate node in respiration and its impact on acetate overflow during aerobic growth.