应用代谢网络模型解析工业微生物胞内代谢

为了快速、高效地理解工业微生物胞内代谢特征,寻找潜在的代谢工程改造靶点,基因组规模代谢网络模型(GSMM)作为一种系统生物学工具越来越受到人们的关注。文中在回顾GSMM 20年发展历程的基础上,分析了当前GSMM的研究现状,总结了GSMM的构建及分析方法,从预测细胞表型和指导代谢工程两个方面阐述了GSMM在解析工业微生物胞内代谢中的应用,并展望了GSMM未来的发展趋势。     

Relationship between metabolic status and behavior in dairy cows in week 4 of lactation

Blood metabolite and hormone concentrations are indicative of metabolic status, but blood sampling and analysis is invasive and time-consuming. Monitoring behavior can be done automatically, and behaviors may also be used as indicators of metabolic status. The aim of this study was to analyze the relationships between metabolic status and feeding behavior, lying behavior, motion index and steps of dairy cows in week 4 postpartum. Behavioral data from 81 Holstein-Friesian cows were collected using computerized feeders and accelerometers, and blood samples were collected for analysis of free-fatty acid (FFA), β-hydroxybutyrate (BHB), glucose, insulin, IGF-1 and growth hormone (GH) concentrations. First, cluster analysis was performed to categorize cows as having poor, average, good or very good metabolic status based on their plasma FFA, BHB, glucose, insulin, IGF-1 and GH concentration. Subsequently, the performance and behavior of cows in clusters with poor, average and good metabolic status were compared using GLM. Cows with a poor or average metabolic status tended to have greater fat-and-protein-corrected milk yield than cows with good metabolic status. Furthermore, cows with a poor metabolic status had a lower energy balance and dry matter intake (DMI) than cows with an average or good metabolic status and had a lower number of meals than cows with good metabolic status. Daily number of visits to the feeder and lying time tended to be positively related with metabolic status. Feeding rate (kg/min), daily meal time (min/day), number of lying bouts per day, steps and motion index were not related with metabolic status. In conclusion, better metabolic status in dairy cows in early lactation was associated with a greater DMI, increased feeding activity and a tendency to more time spent lying, compared with poor metabolic status. These results suggest that compromised metabolic status is reflected in altered cow’s behavior in week 4 of lactation.     

Convergence of trophic interaction strengths in grassland food webs through metabolic scaling of herbivore biomass

1. Food web theory hypothesizes that trophic interaction strengths of consumers should vary with consumer metabolic body mass (mass(0·75) ) rather than simply with consumer body mass (mass(1·0) ) owing to constraints on consumption imposed by metabolic demand for and metabolic capacity to process nutrients and energy. Accordingly, species with similar metabolic body masses should have similar trophic interaction strengths. 2. We experimentally tested this hypothesis by assembling food webs comprised of species of arthropod predators, small sap-feeding and large leaf-chewing insect herbivores and herbaceous plants in a New England, USA meadow grassland. The experiment comprised of a density-matching treatment where herbivore species were stocked into field mesocosms at equal densities to quantify baseline species identity and metabolic body mass effects. The experiment also comprised of a metabolic biomass-matching treatment where smaller sap-feeding herbivore (SH) species were stocked into mesocosms such that the product of their density and metabolic body mass (metabolic biomass) was equal to the large herbivore (LH) species. We compared the magnitude of the direct effects of herbivore species on plants in the different treatments. We also compared the magnitude of indirect effects between predators and plants mediated by herbivores in the different treatments. 3. Consistent with the hypothesis, we found that increasing metabolic biomass translated into a 9-14-fold increase in magnitude of herbivore direct effects and up to a fivefold increase in indirect effects on plants. Moreover, metabolic biomass matching caused interaction strengths among herbivore species to converge. This result came about through increases in the herbivore mean effects as well as decreases in variation in effects among treatment replicates as herbivore metabolic biomass increased. 4. We found, however, that herbivore feeding mode rather than herbivore metabolic biomass explained differences in the sign of indirect effects in the different food webs. 5. We conclude that increasing herbivore metabolic biomass not only strengthened the direct and indirect effects on plants but also made those effects more consistent across space. Nevertheless, metabolic biomass alone could not completely explain variation in the nature of indirect effects in the food web, suggesting that additional consideration of consumer traits like feeding mode will provide a more nuanced understanding of trophic interaction strengths in food webs.     

Clustering of hemodynamic and metabolic abnormalities and of anthropometric characteristics in men and women, aged 21-60 years.

The associations between fat pattern and metabolic profile were evaluated, using cluster analysis, in 214 males and 244 females (aged 21-60 years). The subjects were randomly selected from the patients of one general practice in Castel D'Azzano (Italy). The metabolic status was indexed by blood pressure, blood glucose, uric acid, serum triglycerides, total cholesterol, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol (both total and percentage). Fat pattern was evaluated using six skinfolds and three circumferences. The analyses were performed separately on anthropometric and metabolic variables for each sex. The analyses were repeated five times to evaluate the stability of the cluster solution. Anthropometric rather than metabolic variables provided a more stable solution for cluster analysis. Anthropometric clusters showed significantly different metabolic patterns. Most of the differences disappeared when a body mass index (BMI) effect was taken into account but not when an adjustment for waist to hip ratio (WHR) was made. On the other hand, neither BMI nor WHR was able to fully account for the differences in metabolic profiles of metabolic clusters. Cross-classification results of anthropometric and metabolic cluster membership showed a significant, although moderate, degree of association between the two classification sets. These results indicate that in both sexes anthropometric characteristics contribute to a limited degree to the metabolic profile and that the associations probably reflect a complex mechanism.     

Sources and significance of variation in basal,summit and maximal metabolic rates in birds

The rates at which birds use energy may have profound effects on fitness, thereby influencing physiology, behavior, ecology and evolution. Comparisons of standardized metabolic rates (e.g., lower and upper limits of metabolic power output) present a method for elucidating the effects of ecological and evolutionary factors on the interface between physiology and life history in birds. In this paper we review variation in avian metabolic rates [basal metabolic rate (BMR; minimum normothermic metabolic rate), ...     

Chemical basis of metabolic network organization

Although the metabolic networks of the three domains of life consist of different constituents and metabolic pathways, they exhibit the same scale-free organization. This phenomenon has been hypothetically explained by preferential attachment principle that the new-recruited metabolites attach preferentially to those that are already well connected. However, since metabolites are usually small molecules and metabolic processes are basically chemical reactions, we speculate that the metabolic network organization may have a chemical basis. In this paper, chemoinformatic analyses on metabolic networks of Kyoto Encyclopedia of Genes and Genomes (KEGG), Escherichia coli and Saccharomyces cerevisiae were performed. It was found that there exist qualitative and quantitative correlations between network topology and chemical properties of metabolites. The metabolites with larger degrees of connectivity (hubs) are of relatively stronger polarity. This suggests that metabolic networks are chemically organized to a certain extent, which was further elucidated in terms of high concentrations required by metabolic hubs to drive a variety of reactions. This finding not only provides a chemical explanation to the preferential attachment principle for metabolic network expansion, but also has important implications for metabolic network design and metabolite concentration prediction.     

Effects of phorbol myristate acetate,phorbol dibutyrate,ethanol, dimethylsulfoxide,phenol, and seven metabolities of phenol on metabolic cooperation between chinese hamster v79 lung fibroblasts

The effect of phorbol myristate acetate, phorbol dibutyrate, ethanol, dimethylsulfoxide, phenol, and seven metabolites of phenol on metabolic cooperation were assessed as a function of mutant cell recovery from populations of cocultivated hypoxanthine-guanine phosphoribosyl transferase-deficient mutant (HGPRT–) and wild-type (HGPRT+) Chinese hamster V79 lung fibroblasts. Phorbol myristate acetate and phorbol diputyrate, two established tumor promoters, were potent inhibitors of metabolic cooperation. Ethanol and dimethylsulfoxide, solvents commonly used to prepare chemicals for testing, weakly inhibited metabolic cooperation. Phenol and phenylglucuronide had no effect on metabolic cooperation. Four oxidative metabolites (1,4-benzoquinone, catechol, hydroxyquinol and quinol) inhibited metabolic cooperation. Phenylsulfate weakly inhibited metabolic cooperation. Conversely, 2-methoxyphenol, a methylated derivative of catechol, appeared to enhance metabolic cooperation. These results generallyAbbreviations CAS Chemical Abstracts Service - DMSO dimethylsulfoxide - ETOH ethanol - HGPRT hypoxanthine-guanine phosphoribosyl transferase - HGPRT+ HGPRT-competent - HGPRT– HGPRT-te]deficient - MC metabolic cooperation - MC+ metabolic cooperation-competent - MC– metabolic cooperation-deficient - MEM minimum essential medium - PDBu phorbol dibutyrate - PMA phorbol myristate acetate - 6TG 6-thioguanine - 6TG^r 6-thioguanine-resistant - 6TG^s 6-thioguanine-sensitive - V79/MC assay Chinese hamster V79 lung fibroblast assay for metabolic cooperation     

Physiology of microbial cell and metabolic engineering

This review is devoted to the problems of the physiology and cell biology of microorganisms in relation to metabolic engineering. The latter is considered as a branch of fundamental and applied biotechnology aimed at controlling microbial metabolism by methods of genetic engineering and classical genetics and based on intimate knowledge of cell metabolism. Attention is also given to the problems associated with the metabolic limitation of microbial biosyntheses, analysis and control of metabolic fluxes, rigidity of metabolic pathways, the role of pleiotropic (global) regulatory systems in the control of metabolic fluxes, and prospects of physiological and evolutionary approaches in metabolic engineering.     

Flux analysis and metabolomics for systematic metabolic engineering of microorganisms

Rational engineering of metabolism is important for bio-production using microorganisms. Metabolic design based on in silico simulations and experimental validation of the metabolic state in the engineered strain helps in accomplishing systematic metabolic engineering. Flux balance analysis (FBA) is a method for the prediction of metabolic phenotype, and many applications have been developed using FBA to design metabolic networks. Elementary mode analysis (EMA) and ensemble modeling techniques are also useful tools for in silico strain design. The metabolome and flux distribution of the metabolic pathways enable us to evaluate the metabolic state and provide useful clues to improve target productivity. Here, we reviewed several computational applications for metabolic engineering by using genome-scale metabolic models of microorganisms. We also discussed the recent progress made in the field of metabolomics and ¹³C-metabolic flux analysis techniques, and reviewed these applications pertaining to bio-production development. Because these in silico or experimental approaches have their respective advantages and disadvantages, the combined usage of these methods is complementary and effective for metabolic engineering.     

Analysis of pharmacokinetic parameters for assessment of dextromethorphan metabolic phenotypes

In this study, the metabolic ratios of dextromethorphan to dextrorphan (DM/DX) in plasma were calculated at steady state after administering 2 dosage forms (Medicon) and Detusiv) of DM with different release rates. The urinary metabolic ratio for each subject was also determined based on the total drug concentration in the urine. An analysis of pharmacokinetic parameters for determining the DM metabolic phenotype was conducted. Results demonstrate that double logarithmic correlations between the metabolic ratios based on pharmacokinetic parameters of either AUC(0-tau,ss), C(max,ss), C(min,ss), or C(ave,ss) for Medicon and Detusiv and the urinary metabolic ratios were all significant. Probit plots of the metabolic ratios based on these pharmacokinetic parameters revealed 2 clusters of distribution, representing extensive and intermediate metabolizers. An antimode of 2.0 for total drug based on these pharmacokinetic parameters was determined and correspondingly referred to an antimode of 0.02 for the urinary metabolic ratio to delineate extensive and intermediate metabolizers. This model was also verified to be appropriate when using total plasma concentrations of DM and DX at any time during the period of the dosing interval at steady state to calculate the metabolic ratio for identifying extensive and intermediate metabolizers. Therefore, the metabolic ratio based on the pharmacokinetic parameters of either AUC(0-tau,ss), C(max,ss), C(min,ss), or C(ave,ss) and plasma concentrations of DM and DX in a single blood sample at steady state are proposed as an alternative way to identify phenotypes of CYP2D6.     

Unraveling the mystery of cancer metabolism in the genesis of tumor-initiating cells and development of cancer

Robust anaerobic metabolism plays a causative role in the origin of cancer cells; however, the oncogenic metabolic genes, factors, pathways, and networks in genesis of tumor-initiating cells (TICs) have not yet been systematically summarized. In addition, the mechanisms of oncogenic metabolism in the genesis of TICs are enigmatic. In this review, we discussed multiple cancer metabolism-related genes (MRGs) that are overexpressed in TICs and are responsible for inducing pluripotent stem cells. Moreover, we summarized that oncogenic metabolic genes and onco-metabolites induce metabolic reprogramming, which switches normal mitochondrial oxidative phosphorylation to cancer anaerobic metabolism, triggers epigenetic, genetic, and environmental alterations, drives the generation of TICs, and boosts the development of cancer. Importantly, cancer metabolism is controlled by positive and negative metabolic regulators. Positive oncogenic metabolic regulators, including key oncogenic metabolic genes, onco-metabolites, hypoxia, and an acidic environment, promote oncogenic metabolic reprogramming and anaerobic metabolism. However, dysfunction of negative metabolic regulators, including defects in p53, PTEN, and LKB1-AMPK-mTOR pathways, enhances cancer metabolism. Loss of the metabolic balance results in oncogenic metabolic reprogramming, genesis of TICs, and tumorigenesis. Collectively, this review provides new insight into the role and mechanism of these oncogenic metabolisms in the genesis of TICs and tumorigenesis. Accordingly, targeting key oncogenic genes, onco-metabolites, pathways, networks, and the acidic cancer microenvironment appears to be an attractive strategy for novel anti-tumor treatment.     

Physiology of microbial cells and metabolic engineering

This review is devoted to the problems of the physiology and cell biology of microorganisms in relation to metabolic engineering. The latter is considered as a branch of fundamental and applied biotechnology aimed at controlling microbial metabolism by methods of genetic engineering and classical genetics and based on intimate knowledge of cell metabolism. Attention is also given to the problems associated with the metabolic limitation of microbial biosyntheses, analysis and control of metabolic fluxes, rigidity of metabolic pathways, the role of pleiotropic (global) regulatory systems in the control of metabolic fluxes, and prospects of physiological and evolutionary approaches in metabolic engineering.     

基元模式分析在生物网络和途径分析中的应用

基元模式分析是应用最广泛的代谢途径分析方法。基元模式分析的研究对象从代谢网络发展到信号传导网络;研究尺度从细胞到生物反应器,甚至生态系统;数学描述从稳态分解到动态解析;研究领域从微生物代谢到人类疾病。以下综述了基元模式分析的算法和软件开发现状,以及其在代谢途径与鲁棒性、代谢通量分解、稳态代谢通量分析、动态模型与生物过程模拟、网络结构与调控、菌株设计和信号传导网络等方面的应用。开发新的算法解决组合爆炸问题,探索基元模式与代谢调控的关系以及提高菌株设计算法效率是今后基元模式的重要发展方向。     

乳酸乳球菌NZ9000基因组规模代谢网络模型的构建与验证

随着后基因组时代的到来,工业微生物的代谢工程改造在工业生产上发挥着越来越重要的作用。而基因组规模代谢网络模型(Genome-scalemetabolicmodel,GSMM)将生物体体内所有已知代谢信息进行整合,为全局理解生物体的代谢状态、理性指导代谢工程改造提供了最佳的平台。乳酸乳球菌NZ9000(Lactococcuslactis NZ9000)作为工业发酵领域的重要菌株之一,由于其遗传背景清晰且几乎不分泌蛋白,是基因工程改造和外源蛋白表达的理想模式菌株。文中基于基因组功能注释和比较基因组学构建了L.lactisNZ9000的首个基因组规模代谢网络模型iWK557,包含557个基因、668个代谢物、840个反应,并进一步在定性和定量两个层次验证了iWK557的准确性,以期为理性指导L. lactis NZ9000代谢工程改造提供良好工具。     

Enzymatic System of Metabolism and Detoxication of Xenobiotics as a Basis of Metabolic Portraiting during Prognostication of Risk of Pathological Processes

We studied intraspecific features of the main enzymes of metabolism and detoxication of xenobiotics on mice (eight inbred lines) and rats (five lines) for estimation of possible variants of complete or incomplete metabolic equality. Significant genetically determined intraspecific differences for activities of the enzymes of metabolism and detoxication of xenobiotics were described. Generalized criteria for comparison of the metabolic status were proposed on the basis of activities of the main enzymes: cytochrome P-450 (hydroxylation and epoxidation), epoxyhydrolase, glutathione-S-transferase, UDP-glucuronosyl transferase, and sulfotransferase. The proposed criteria for estimation of the metabolic parameters of an individual can serve as a basis of metabolic portraiting.     

Role of acidosis-induced increases in calcium on PTH secretion in acute metabolic and respiratory acidosis in the dog

Recently, we showed that both acute metabolic acidosis and respiratory acidosis stimulate parathyroid hormone (PTH) secretion in the dog. To evaluate the specific effect of acidosis, ionized calcium (iCa) was clamped at a normal value. Because iCa values normally increase during acute acidosis, we now have studied the PTH response to acute metabolic and respiratory acidosis in dogs in which the iCa concentration was allowed to increase (nonclamped) compared with dogs with a normal iCa concentration (clamped). Five groups of dogs were studied: control, metabolic (clamped and nonclamped), and respiratory (clamped and nonclamped) acidosis. Metabolic (HCl infusion) and respiratory (hypoventilation) acidosis was progressively induced during 60 min. In the two clamped groups, iCa was maintained at a normal value with an EDTA infusion. Both metabolic and respiratory acidosis increased (P < 0.05) iCa values in nonclamped groups. In metabolic acidosis, the increase in iCa was progressive and greater (P < 0.05) than in respiratory acidosis, in which iCa increased by 0.04 mM and then remained constant despite further pH reductions. The increase in PTH values was greater (P < 0.05) in clamped than in nonclamped groups (metabolic and respiratory acidosis). In the nonclamped metabolic acidosis group, PTH values first increased and then decreased from peak values when iCa increased by > 0.1 mM. In the nonclamped respiratory acidosis group, PTH values exceeded (P < 0.05) baseline values only after iCa values stopped increasing at a pH of 7.30. For the same increase in iCa in the nonclamped groups, PTH values increased more in metabolic acidosis. In conclusion, 1) both metabolic acidosis and respiratory acidosis stimulate PTH secretion; 2) the physiological increase in the iCa concentration during the induction of metabolic and respiratory acidosis reduces the magnitude of the PTH increase; 3) in metabolic acidosis, the increase in the iCa concentration can be of sufficient magnitude to reverse the increase in PTH values; and 4) for the same degree of acidosis-induced hypercalcemia, the increase in PTH values is greater in metabolic than in respiratory acidosis.     

Metabolic activity of CHO fibroblasts in HEMA-MMA microcapsules

Chinese hamster ovary (CHO) fibroblast cells were microencapsulated in polyacrylate membranes (HEMA-MMA: 75% HEMA) via an interfacial precipitation process. The CHO cells were observed to grow in large aggregates, attached to each other instead of to the capsule wall. When CHO cells were encapsulated at high density (4 x 10(6) cells/mL), the initial metabolic activity in microcapsules, as determined by the MTT assay, correlated with the polymer-cell extrusion ratio, presumably because of the dependence of encapsulation efficiency on the relative flow rates. However, there was a large variation in the metabolic activity among individual microcapsules throughout the present study. Capsules with low encapsulation efficiency (at a "seeding" density of 4 x 10(6) cells/mL) exhibited a rapid increase in the metabolic activity during the following week. When CHO cells were encapsulated at low density (4 x 10(5) cells/mL), there was only a small increase in the metabolic activity. Only a small fraction ( approximately 5%) of the capsules exhibited a high level of metabolic activity and 40% of the capsules exhibited undetectable metabolic activity even after 2 weeks. We conclude that CHO cells, which served as model cells, survive the encapsulation process and retain an active metabolic state once enclosed by the HEMA-MMA membranes. However, the resultant microcapsules are extremely heterogeneous in the amount of retained metabolic activity.     

Metabolic response of Platynota stultana pupae to controlled atmospheres and its relation to insect mortality response

The metabolic responses of Platynota stultana pupae to reduced O(2), elevated CO(2), and their combinations were investigated using microcalorimetry, and mortality of pupae under elevated CO(2) atmospheres was correlated with metabolic responses. The metabolic heat rate decreased slightly with decreasing O(2) concentration until a critical O(2) concentration (P(c)) below which the heat rate decreased rapidly. The P(c) increased with temperature. The percentage decreases of metabolic heat rate were comparable to the percentage decreases of O(2) consumption rate (RO(2)) at 10, 8, 6, and 4% O(2), but were smaller at 2 and 1% O(2). The metabolic heat rate decreased rapidly at 20% CO(2) relative to 0% CO(2), with little to no further decrease between 20 and 79% CO(2). The percentage decreases of RO(2) under 20 and 79% CO(2) at 20 degrees C were comparable to the percentage decreases of metabolic heat rates. The additive effects of subatmospheric O(2) and elevated CO(2) levels on reducing metabolic heat rate were generally fully realized at combinations of /=4% O(2), but became increasingly overlapped as the O(2) concentration decreased and the CO(2) concentration increased. The high susceptibility of pupae to elevated CO(2) at high temperature was correlated with high metabolic heat rate. The metabolic responses of pupae to reduced O(2) concentrations included metabolic arrest and anaerobic metabolism. The net effect of elevated CO(2) on the pupal respiratory metabolism was similar to that of reduced O(2); however, mechanisms other than the decrease of metabolism were also contributing to the toxicity of CO(2).     

Cardiovascular Disease Risk of Abdominal Obesity vs. Metabolic Abnormalities

It remains unclear whether abdominal obesity increases cardiovascular disease (CVD) risk independent of the metabolic abnormalities that often accompany it. Therefore, the objective of this study was to evaluate the independent effects of abdominal obesity vs. metabolic syndrome and diabetes on the risk for incident coronary heart disease (CHD) and stroke. The Framingham Offspring, Atherosclerosis Risk in Communities, and Cardiovascular Health studies were pooled to assess the independent effects of abdominal obesity (waist circumference >102 cm for men and >88 cm for women) vs. metabolic syndrome (excluding the waist circumference criterion) and diabetes on risk for incident CHD and stroke in 20,298 men and women aged ≥45 years. The average follow‐up was 8.3 (s.d. 1.9) years. There were 1,766 CVD events. After adjustment for demographic factors, smoking, alcohol intake, number of metabolic syndrome components, and diabetes, abdominal obesity was not significantly associated with an increased risk of CVD (hazard ratio (HR) (95% confidence interval): 1.09 (0.98, 1.20)). However, after adjustment for demographics, smoking, alcohol intake, and abdominal obesity, having 1–2 metabolic syndrome components, the metabolic syndrome and diabetes were each associated with a significantly increased risk of CVD (2.12 (1.80, 2.50), 2.82 (1.92, 4.12), and 5.33 (3.37, 8.41), respectively). Although abdominal obesity is an important clinical tool for identification of individuals likely to possess metabolic abnormalities, these data suggest that the metabolic syndrome and diabetes are considerably more important prognostic indicators of CVD risk.     

The effect of sub-lethal doses of dieldrin on resting and active metabolism in two species of shrimps

The effects of dieldrin on the active (VaO2) and resting (VrO2) oxygen consumption rates of the shrimps Macrobrachium faustinum (De Sassure) and Macrobrachium amazonicum (Heller) were studied during exposure for 4 days at 0.01 p.p.b. and 7 days at 0.0002 p.p.b., respectively. The VrO2 of M. faustinum increased significantly (P less than 0.01) by 48% but the VaO2 decreased by 13%. The VrO2 and VaO2 decreased by 43 and 70%, respectively, in M. amazonicum. Thus, in both species the aerobic metabolic scope for activity decreased. The increased resting metabolic rate of the indigenous M. faustinum is ascribed to energy consuming responses which allow compensation for the effects of the stressor. The stressor may be said to have moved this species into a metabolic "zone of compensation". The decreased resting metabolic rate of the pond-cultured M. amazonicum is ascribed to greater susceptibility, more extensive metabolic breakdown and failure of compensatory responses. This species might be said to have been forced by the stressor into a metabolic "zone of collapse".