柠檬酸钠对L-组氨酸发酵代谢流分布的影响

目的：建立谷氨酸棒杆菌TL1105生物合成L-组氨酸的代谢网络模型,并进行代谢网络计量分析。方法：通过所构建的L-组氨酸代谢网络模型,利用MATLAB软件计算出添加柠檬酸钠和不添加柠檬酸钠发酵中后期代谢网络的代谢流分布。结果：在L-组氨酸分批发酵过程中,在发酵初期未添加柠檬酸钠的条件下流向戊糖磷酸途径（HMP）的代谢流为9.59,合成组氨酸的代谢流为8.91;在发酵初期添加2g/L柠檬酸钠的条件下流向HMP的代谢流为12.74,合成组氨酸的代谢流为9.61。结论：在发酵初期添加柠檬酸钠能够改变L-组氨酸生物合成途径的关键节点6-磷酸葡萄糖、丙酮酸及乙酰辅酶A的代谢流分布,保持糖酵解途径、三羧酸循环与HMP之间代谢流量平衡,有利于提高L-组氨酸生物合成途径的代谢流量,最终使流向组氨酸的代谢流增加了7.86%。     

Metabolic Flux Responses to Pyruvate Kinase Knockout in Escherichia coli

The intracellular carbon flux distribution in wild-type and pyruvate kinase-deficient Escherichia coli was estimated using biosynthetically directed fractional 13C labeling experiments with [U-13C6]glucose in glucose- or ammonia-limited chemostats, two-dimensional nuclear magnetic resonance (NMR) spectroscopy of cellular amino acids, and a comprehensive isotopomer model. The general response to disruption of both pyruvate kinase isoenzymes in E. coli was a local flux rerouting via the combined reactions of phosphoenolpyruvate (PEP) carboxylase and malic enzyme. Responses in the pentose phosphate pathway and the tricarboxylic acid cycle were strongly dependent on the environmental conditions. In addition, high futile cycling activity via the gluconeogenic PEP carboxykinase was identified at a low dilution rate in glucose-limited chemostat culture of pyruvate kinase-deficient E. coli, with a turnover that is comparable to the specific glucose uptake rate. Furthermore, flux analysis in mutant cultures indicates that glucose uptake in E. coli is not catalyzed exclusively by the phosphotransferase system in glucose-limited cultures at a low dilution rate. Reliability of the flux estimates thus obtained was verified by statistical error analysis and by comparison to intracellular carbon flux ratios that were independently calculated from the same NMR data by metabolic flux ratio analysis.     

Mutations in Global Regulators Lead to Metabolic Selection during Adaptation to Complex Environments

Adaptation to ecologically complex environments can provide insights into the evolutionary dynamics and functional constraints encountered by organisms during natural selection. Adaptation to a new environment with abundant and varied resources can be difficult to achieve by small incremental changes if many mutations are required to achieve even modest gains in fitness. Since changing complex environments are quite common in nature, we investigated how such an epistatic bottleneck can be avoided to allow rapid adaptation. We show that adaptive mutations arise repeatedly in independently evolved populations in the context of greatly increased genetic and phenotypic diversity. We go on to show that weak selection requiring substantial metabolic reprogramming can be readily achieved by mutations in the global response regulator arcA and the stress response regulator rpoS. We identified 46 unique single-nucleotide variants of arcA and 18 mutations in rpoS, nine of which resulted in stop codons or large deletions, suggesting that subtle modulations of ArcA function and knockouts of rpoS are largely responsible for the metabolic shifts leading to adaptation. These mutations allow a higher order metabolic selection that eliminates epistatic bottlenecks, which could occur when many changes would be required. Proteomic and carbohydrate analysis of adapting E. coli populations revealed an up-regulation of enzymes associated with the TCA cycle and amino acid metabolism, and an increase in the secretion of putrescine. The overall effect of adaptation across populations is to redirect and efficiently utilize uptake and catabolism of abundant amino acids. Concomitantly, there is a pronounced spread of more ecologically limited strains that results from specialization through metabolic erosion. Remarkably, the global regulators arcA and rpoS can provide a “one-step” mechanism of adaptation to a novel environment, which highlights the importance of global resource management as a powerful strategy to adaptation.     

13C Metabolic Flux Analysis of acetate conversion to lipids by Yarrowia lipolytica

Volatile fatty acids (VFAs) are an inexpensive and renewable carbon source that can be generated from gas fermentation and anaerobic digestion of fermentable wastes. The oleaginous yeast Yarrowia lipolytica is a promising biocatalyst that can utilize VFAs and convert them into triacylglycerides (TAGs). However, currently there is limited knowledge on the metabolism of Y. lipolytica when cultured on VFAs. To develop a better understanding, we used acetate as the sole carbon source to culture two strains, a control strain and a previously engineered strain for lipid overaccumulation. For both strains, metabolism during the growth phase and lipid production phase were investigated by metabolic flux analysis using two parallel sodium acetate tracers. The resolved flux distributions demonstrate that the glyoxylate shunt pathway is constantly active and the flux through gluconeogenesis varies depending on strain and phase. In particular, by regulating the activities of malate transport and pyruvate kinase, the cells divert only a portion of the glyoxylate shunt flux required to satisfy the needs for anaplerotic reactions and NADPH production through gluconeogenesis and the oxidative pentose phosphate pathway (PPP). Excess flux flows back to the tricarboxylic acid (TCA) cycle for energy production. As with the case of glucose as the substrate, the primary source for lipogenic NADPH is derived from the oxidative PPP.     

Removing Constraints on the Biomass Production of Freshwater Macroalgae by Manipulating Water Exchange to Manage Nutrient Flux

Freshwater macroalgae represent a largely overlooked group of phototrophic organisms that could play an important role within an industrial ecology context in both utilising waste nutrients and water and supplying biomass for animal feeds and renewable chemicals and fuels. This study used water from the intensive aquaculture of freshwater fish (Barramundi) to examine how the biomass production rate and protein content of the freshwater macroalga Oedogonium responds to increasing the flux of nutrients and carbon, by either increasing water exchange rates or through the addition of supplementary nitrogen and CO₂. Biomass production rates were highest at low flow rates (0.1–1 vol.day⁻¹) using raw pond water. The addition of CO₂ to cultures increased biomass production rates by between 2 and 25% with this effect strongest at low water exchange rates. Paradoxically, the addition of nitrogen to cultures decreased productivity, especially at low water exchange rates. The optimal culture of Oedogonium occurred at flow rates of between 0.5–1 vol.day⁻¹, where uptake rates peaked at 1.09 g.m⁻².day⁻¹ for nitrogen and 0.13 g.m⁻².day⁻¹ for phosphorous. At these flow rates Oedogonium biomass had uptake efficiencies of 75.2% for nitrogen and 22.1% for phosphorous. In this study a nitrogen flux of 1.45 g.m⁻².day⁻¹ and a phosphorous flux of 0.6 g.m⁻².day⁻¹ was the minimum required to maintain the growth of Oedogonium at 16–17 g DW.m⁻².day⁻¹ and a crude protein content of 25%. A simple model of minimum inputs shows that for every gram of dry weight biomass production (g DW.m⁻².day⁻¹), Oedogonium requires 0.09 g.m⁻².day⁻¹ of nitrogen and 0.04 g.m⁻².day⁻¹ of phosphorous to maintain growth without nutrient limitation whilst simultaneously maintaining a high-nutrient uptake rate and efficiency. As such the integrated culture of freshwater macroalgae with aquaculture for the purposes of nutrient recovery is a feasible solution for the bioremediation of wastewater and the supply of a protein resource.     

Viral Adaptation to an Antiviral Protein Enhances the Fitness Level to Above That of the Uninhibited Wild Type

Viruses often evolve resistance to antiviral agents. While resistant strains are able to replicate in the presence of the agent, they generally exhibit lower fitness than the wild-type strain in the absence of the inhibitor. In some cases, resistant strains become dependent on the antiviral agent. However, the agent rarely, if ever, elevates dependent strain fitness above the uninhibited wild-type level. This would require an adaptive mechanism to convert the antiviral agent into a beneficial growth factor. Using an inhibitory scaffolding protein that specifically blocks φX174 capsid assembly, we demonstrate that such mechanisms are possible. To obtain the quintuple-mutant resistant strain, the wild-type virus was propagated for approximately 150 viral life cycles in the presence of increasing concentrations of the inhibitory protein. The expression of the inhibitory protein elevated the strain''s fitness significantly above the uninhibited wild-type level. Thus, selecting for resistance coselected for dependency, which was characterized and found to operate on the level of capsid nucleation. To the best of our knowledge, this is the first report of a virus evolving a mechanism to productively utilize an antiviral agent to stimulate its fitness above the uninhibited wild-type level. The results of this study may be predictive of the types of resistant phenotypes that could be selected by antiviral agents that specifically target capsid assembly.While viruses often acquire resistance to antiviral agents, resistance mutants generally exhibit lower fitness than the wild-type strain in the absence of the inhibitor (6, 16, 17, 25) and can develop a dependency on the antiviral agent (1, 19). However, the molecular mechanism of dependency rarely, if ever, involves the productive use of the antiviral agent to elevate fitness above the uninhibited wild-type level. Many studies are conducted with animal viruses, often in clinical settings, which can impose restraints on the experimental durations. Thus, prolonged exposure to antiviral agents may be required for the emergence of a multiply mutant strain that has evolved mechanisms to productively utilize inhibitors.Due to its rapid replication, bacteriophage φX174 has become an attractive model system for evolutionary studies (2, 3, 23, 24). Selective pressures can be applied for hundreds of infection cycles in a relatively short period of time. Using the atomic structure of assembly intermediates as a guide (8, 9, 15), viral scaffolding proteins that inhibit virion assembly have been designed (4). The molecular mechanism of inhibition was characterized, and resistance mutants were isolated via one-step genetic selections (4). In this study we report the isolation of a more robust resistant mutant. The quintuple mutant was generated by propagating φX174 for approximately 150 life cycles in the presence of increasing concentrations of the inhibitory protein, which was derived from the external scaffolding D protein. This protein forms asymmetric dimers that direct procapsid assembly. A conformational switch at glycine residue 61 (G61) in α-helix 3 is critical for productive dimer formation. In one subunit, α-helix 3 is bent 30°, whereas it assumes a straight conformation in the other subunit. All amino acid substitutions for G61 inhibit the ability to undergo the requisite conformational switch. The severity of the conferred dominant lethal phenotypes directly correlates with the side chain sizes of the substituted amino acids (4, 5).The inhibitory proteins most likely remove assembly intermediates by lowering the thermodynamic barriers that normally prevent off-pathway reactions (4, 5). Both off-pathway reactions and proper assembly involve D-D protein interactions across what will become the twofold axes of symmetry in the virion (8, 9). In the procapsid crystal structure, α-helix 3 of the D₂, D₃, and D₄ subunits mediates these interactions. Mutants resistant to the dominant lethal proteins were isolated in one-step genetic selections, and mutations mapped to either the coat or internal scaffolding proteins. These mutations may indirectly reinstate the avidity of the D protein electrostatic bonding partners required for productive morphogenesis (4, 5). However, the resistance phenotype is weak. To isolate a more robust phenotype, wild-type φX174 was continually cultured through exponential phase cells expressing an inhibitory D protein. Results from this analysis indicate that the selection for resistance coselected for a level of dependence. The inhibitory protein stimulates resistant strain fitness significantly above the uninhibited wild-type level and appears to be required for efficient capsid nucleation. These results suggest that the virus evolved a mechanism to convert this potent antiviral agent into a beneficial factor and may be predictive of the types of resistant phenotypes that could be selected by antiviral agents that specifically target capsid assembly.     

Basic FGF Stimulates MMP-13 via FGFR1-dependent Activation of MAPK and NFκB That Converge to Activate ELK-1 in Cartilage

This article has no abstract.     

Analysis of the Rice ADP-Glucose Transporter (OsBT1) Indicates the Presence of Regulatory Processes in the Amyloplast Stroma That Control ADP-Glucose Flux into Starch

Previous studies showed that efforts to further elevate starch synthesis in rice (Oryza sativa) seeds overproducing ADP-glucose (ADPglc) were prevented by processes downstream of ADPglc synthesis. Here, we identified the major ADPglc transporter by studying the shrunken3 locus of the EM1093 rice line, which harbors a mutation in the BRITTLE1 (BT1) adenylate transporter (OsBt1) gene. Despite containing elevated ADPglc levels (approximately 10-fold) compared with the wild-type, EM1093 grains are small and shriveled due to the reduction in the amounts and size of starch granules. Increases in ADPglc levels in EM1093 were due to their poor uptake of ADP-[¹⁴C]glc by amyloplasts. To assess the potential role of BT1 as a rate-determining step in starch biosynthesis, the maize ZmBt1 gene was overexpressed in the wild-type and the GlgC (CS8) transgenic line expressing a bacterial glgC-TM gene. ADPglc transport assays indicated that transgenic lines expressing ZmBT1 alone or combined with GlgC exhibited higher rates of transport (approximately 2-fold), with the GlgC (CS8) and GlgC/ZmBT1 (CS8/AT5) lines showing elevated ADPglc levels in amyloplasts. These increases, however, did not lead to further enhancement in seed weights even when these plant lines were grown under elevated CO₂. Overall, our results indicate that rice lines with enhanced ADPglc synthesis and import into amyloplasts reveal additional barriers within the stroma that restrict maximum carbon flow into starch.Cereal grains contribute a significant portion of worldwide starch production. Unlike other plant tissue, starch biosynthesis in the endosperm storage organ of cereal grains is unique in its dependence on two ADP-Glc pyrophosphorylase (AGPase) isoforms (Denyer et al., 1996; Thorbjørnsen et al., 1996; Sikka et al., 2001), a major cytosolic enzyme and a minor plastidial one, to generate ADP-glucose (ADPglc), the sugar nucleotide utilized by starch synthases in the amyloplast (Cakir et al., 2015). The majority of ADPglc in cereal endosperm is generated in the cytosol from AGPase (Tuncel and Okita, 2013) as well as by Suc synthase (Tuncel and Okita, 2013; Bahaji et al., 2014) and subsequently transported into amyloplasts by the BRITTLE-1 (BT1) protein located at the plastid envelope (Cao et al., 1995; Shannon et al., 1998).The Bt1 gene, first identified in maize (Zea mays; Mangelsdorf, 1926) and isolated by Sullivan et al. (1991), encodes a major amyloplast membrane protein ranging from 39 to 44 kD (Cao et al., 1995). The BT1 protein and its homologs belong to the mitochondrial carrier family (Sullivan et al., 1991; Haferkamp, 2007), which has a diverse range of substrates (Patron et al., 2004; Leroch et al., 2005; Kirchberger et al., 2008). The assignment of BT1 protein as the ADPglc transporter in cereal endosperms was first proposed by Sullivan et al. (1991), and then it was characterized based on the increased ADPglc levels and reduced ADPglc import rate in endosperms of BT1-deficient maize and barley (Hordeum vulgare) mutants (Tobias et al., 1992; Shannon et al., 1996, 1998; Patron et al., 2004). Biochemical transport studies of the maize BT1 showed that it imported ADPglc by counter exchanging with ADP (Kirchberger et al., 2007). The wheat (Triticum aestivum) BT1 homolog also transports ADPglc but has similar affinities for ADP and AMP as the counter-exchange substrate (Bowsher et al., 2007).Evidence from previous studies by our laboratory (Sakulsingharoj et al., 2004; Nagai et al., 2009) suggested the potential role of BT1 as well as other downstream processes as a rate-limiting step in starch biosynthesis in the transgenic rice (Oryza sativa) GlgC (CS8) lines overexpressing an up-regulated AGPase (Escherichia coli glgC-TM). In GlgC (CS8) rice lines, grain weights (starch) are elevated up to 15% compared with wild-type plants, indicating that the AGPase-catalyzed reaction is a rate-limiting step in starch biosynthesis under normal conditions. When transgenic GlgC (CS8) plants were grown under elevated CO₂ levels, no further increases in grain weight were evident compared with those grown at ambient CO₂. As Suc levels are elevated in leaf blades, leaf sheaths, culms (Rowland-Bamford et al., 1990), and peduncle exudates (Chen et al., 1994) in rice plants grown under elevated CO₂, developing GlgC (CS8) grains were unable to convert the increased levels of sugars into starch. This lack of increase indicated that the AGPase-catalyzed reaction (ADPglc synthesis) was no longer rate limiting and that one or more downstream processes regulated carbon flux from source tissues in developing GlgC (CS8) endosperm (Sakulsingharoj et al., 2004). This view is also supported by a subsequent metabolite study in which several GlgC (CS8) lines were found to contain up to 46% higher ADPglc levels than wild-type plants (Nagai et al., 2009). As this increase in ADPglc levels was nearly 3-fold higher than the increase in grain weight, starch biosynthesis is saturated with respect to ADPglc levels and carbon flow into starch is restricted by one or more downstream steps. Potential events that may limit the utilization of ADPglc in starch in GlgC (CS8) lines are the import of this sugar nucleotide via the BT1 transporter into amyloplasts and/or the utilization of ADPglc by starch synthases. Mutant analysis of the two major starch synthases indicated no significant impact on grain weight when one of these starch synthases was nonfunctional, suggesting that this enzyme activity, contributed by multiple enzyme isoforms, is present at excessive levels (Fujita et al., 2006, 2007). Therefore, we suspected that BT1 is the likely candidate limiting carbon flow into starch in GlgC (CS8) endosperms.The aim of this study was to investigate the role of BT1 in mediating the transport of ADPglc into amyloplast and to determine whether this transport activity is rate limiting in rice endosperm. In order to address these questions, we show that BT1 is the major transporter of ADPglc by analysis of the EM1093 rice line, which contains a mutation at the shrunken3 (shr3) locus and, specifically, in the OsBt1-1 gene. Second, we assessed the impact of the expression of the maize ZmBt1 gene in wild-type and GlgC (CS8) seeds to determine the potential limiting role of BT1 transport activity on starch biosynthesis. Our results indicate that BT1 is essential for starch synthesis but is not rate limiting and that one or more stroma-localized processes limit maximum carbon flow into starch.     

Metabolic responses of Neisseria gonorrhoeae to human serum and myeloid cells. Adaptation to host defenses?

The interaction of gonococci with host defenses including serum and phagocytic cells has been extensively studied. We have shown that a small molecular weight factor in serum stimulates gonococcal metabolism. This factor has now been isolated by column chromatography and may be released from mammalian cells including phagocytes. Exposure of gonococci to serum decreases membrane fluidity as demonstrated by EPR, seems to reduce OMP shedding, and reduces uptake by PMNS. Serum stimulated gonococci consume O₂ to an extent adequate to interfere with PMN formation of reactive oxygen intermediates. We propose that all of these responses are adaptive and favor survival of this pathogen.     

Survival Response to Increased Ceramide Involves Metabolic Adaptation through Novel Regulators of Glycolysis and Lipolysis

The sphingolipid ceramide elicits several stress responses, however, organisms survive despite increased ceramide but how they do so is poorly understood. We demonstrate here that the AKT/FOXO pathway regulates survival in increased ceramide environment by metabolic adaptation involving changes in glycolysis and lipolysis through novel downstream targets. We show that ceramide kinase mutants accumulate ceramide and this leads to reduction in energy levels due to compromised oxidative phosphorylation. Mutants show increased activation of Akt and a consequent decrease in FOXO levels. These changes lead to enhanced glycolysis by upregulating the activity of phosphoglyceromutase, enolase, pyruvate kinase, and lactate dehydrogenase to provide energy. A second major consequence of AKT/FOXO reprogramming in the mutants is the increased mobilization of lipid from the gut through novel lipase targets, CG8093 and CG6277 for energy contribution. Ubiquitous reduction of these targets by knockdown experiments results in semi or total lethality of the mutants, demonstrating the importance of activating them. The efficiency of these adaptive mechanisms decreases with age and leads to reduction in adult life span of the mutants. In particular, mutants develop cardiac dysfunction with age, likely reflecting the high energy requirement of a well-functioning heart. The lipases also regulate physiological triacylglycerol homeostasis and are important for energy metabolism since midgut specific reduction of them in wild type flies results in increased sensitivity to starvation and accumulation of triglycerides leading to cardiac defects. The central findings of increased AKT activation, decreased FOXO level and activation of phosphoglyceromutase and pyruvate kinase are also observed in mice heterozygous for ceramide transfer protein suggesting a conserved role of this pathway in mammals. These data reveal novel glycolytic and non-autonomous lipolytic pathways in response to increased ceramide for sustenance of high energy demanding organ functions like the heart.     

The Factor Inhibiting HIF Asparaginyl Hydroxylase Regulates Oxidative Metabolism and Accelerates Metabolic Adaptation to Hypoxia

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CD47 Receptor Globally Regulates Metabolic Pathways That Control Resistance to Ionizing Radiation

Modulating tissue responses to stress is an important therapeutic objective. Oxidative and genotoxic stresses caused by ionizing radiation are detrimental to healthy tissues but beneficial for treatment of cancer. CD47 is a signaling receptor for thrombospondin-1 and an attractive therapeutic target because blocking CD47 signaling protects normal tissues while sensitizing tumors to ionizing radiation. Here we utilized a metabolomic approach to define molecular mechanisms underlying this radioprotective activity. CD47-deficient cells and cd47-null mice exhibited global advantages in preserving metabolite levels after irradiation. Metabolic pathways required for controlling oxidative stress and mediating DNA repair were enhanced. Some cellular energetics pathways differed basally in CD47-deficient cells, and the global declines in the glycolytic and tricarboxylic acid cycle metabolites characteristic of normal cell and tissue responses to irradiation were prevented in the absence of CD47. Thus, CD47 mediates signaling from the extracellular matrix that coordinately regulates basal metabolism and cytoprotective responses to radiation injury.