Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals

Coral reef health depends on an intricate relationship among the coral animal, photosynthetic algae, and a complex microbial community. The holobiont can impact the nutrient balance of their hosts amid an otherwise oligotrophic environment, including by cycling physiologically important nitrogen compounds. Here we use ¹⁵N-tracer experiments to produce the first simultaneous measurements of ammonium oxidation, nitrate reduction, and nitrous oxide (N₂O) production among five iconic species of reef-building corals (Acropora palmata, Diploria labyrinthiformis, Orbicella faveolata, Porites astreoides, and Porites porites) in the highly protected Jardines de la Reina reefs of Cuba. Nitrate reduction is present in most species, but ammonium oxidation is low potentially due to photoinhibition and assimilatory competition. Coral-associated rates of N₂O production indicate a widespread potential for denitrification, especially among D. labyrinthiformis, at rates of ~1 nmol cm⁻² d⁻¹. In contrast, A. palmata displays minimal active nitrogen metabolism. Enhanced rates of nitrate reduction and N₂O production are observed coincident with dark net respiration periods. Genomes of bacterial cultures isolated from multiple coral species confirm that microorganisms with the ability to respire nitrate anaerobically to either dinitrogen gas or ammonium exist within the holobiont. This confirmation of anaerobic nitrogen metabolisms by coral-associated microorganisms sheds new light on coral and reef productivity.Subject terms: Biogeochemistry, Biogeochemistry     

Elucidating and reprogramming Escherichia coli metabolisms for obligate anaerobic n-butanol and isobutanol production

Elementary mode (EM) analysis based on the constraint-based metabolic network modeling was applied to elucidate and compare complex fermentative metabolisms of Escherichia coli for obligate anaerobic production of n-butanol and isobutanol. The result shows that the n-butanol fermentative metabolism was NADH-deficient, while the isobutanol fermentative metabolism was NADH redundant. E. coli could grow and produce n-butanol anaerobically as the sole fermentative product but not achieve the maximum theoretical n-butanol yield. In contrast, for the isobutanol fermentative metabolism, E. coli was required to couple with either ethanol- or succinate-producing pathway to recycle NADH. To overcome these "defective" metabolisms, EM analysis was implemented to reprogram the native fermentative metabolism of E. coli for optimized anaerobic production of n-butanol and isobutanol through multiple gene deletion (~8-9 genes), addition (~6-7 genes), up- and downexpression (~6-7 genes), and cofactor engineering (e.g., NADH, NADPH). The designed strains were forced to couple both growth and anaerobic production of n-butanol and isobutanol, which is a useful characteristic to enhance biofuel production and tolerance through metabolic pathway evolution. Even though the n-butanol and isobutanol fermentative metabolisms were quite different, the designed strains could be engineered to have identical metabolic flux distribution in "core" metabolic pathways mainly supporting cell growth and maintenance. Finally, the model prediction in elucidating and reprogramming the native fermentative metabolism of E. coli for obligate anaerobic production of n-butanol and isobutanol was validated with published experimental data.     

Stoichiometric analysis of self-maintaining metabolisms

This paper presents an extension of stoichiometric analysis in systems where the catalytic compounds (enzymes) are also intermediates of the metabolic network (dual property), so they are produced and degraded by the reaction network itself. To take this property into account, we introduce the definition of enzyme-maintaining mode, a set of reactions that produces its own catalyst and can operate at stationary state. Moreover, an enzyme-maintaining mode is defined as elementary with respect to a given reaction if the removal of any of the remaining reactions causes the cessation of any steady state flux through this reference reaction. These concepts are applied to determine the network structure of a simple self-maintaining system.     

Bioenergetic challenges of microbial iron metabolisms

Before cyanobacteria invented oxygenic photosynthesis and O(2) and H(2)O began to cycle between respiration and photosynthesis, redox cycles between other elements were used to sustain microbial metabolism on a global scale. Today these cycles continue to occur in more specialized niches. In this review we focus on the bioenergetic aspects of one of these cycles - the iron cycle - because iron presents unique and fascinating challenges for cells that use it for energy. Although iron is an important nutrient for nearly all life forms, we restrict our discussion to energy-yielding pathways that use ferrous iron [Fe(II)] as an electron donor or ferric iron [Fe(III)] as an electron acceptor. We briefly review general concepts in bioenergetics, focusing on what is known about the mechanisms of electron transfer in Fe(II)-oxidizing and Fe(III)-reducing bacteria, and highlight aspects of their bioenergetic pathways that are poorly understood.     

Co-dependence of bone and energy metabolisms

The growing number of genetically modified mouse models available but also of the possibility to delete one or several genes at will in a defined time frame or in a specific cell type or tissue(s) has open new possibilities for the study of whole animal physiology. This in vivo approach has been especially successful in uncovering a regulatory loop linking the control of energy metabolism and the regulation of bone remodeling. This review is intended to summarize the key events that led to the identification and the characterization of the different steps and molecules constituting this regulatory network.     

Organic sulfur metabolisms in hydrothermal environments

Sulfur is central to the metabolisms of many organisms that inhabit extreme environments. While biotic and abiotic cycling of organic sulfur compounds has been well documented in low‐temperature anaerobic environments, cycling of organic sulfur in hydrothermal environments has received less attention. Recently published thermodynamic data have been used to estimate aqueous alkyl thiol and sulfide activities in deep‐sea hydrothermal systems. Here we use geochemical mixing models to predict fluid compositions that result from mixing end‐member hydrothermal fluid from the East Pacific Rise with bottom seawater. These fluid compositions are combined with estimates of methanethiol and dimethylsulfide activities to evaluate energy yields for potential organic sulfur‐based metabolisms under hydrothermal conditions. Aerobic respiration has the highest energy yields (over ?240 kJ/mol e^?) at lower temperature; however, oxygen is unlikely to persist at high temperatures, restricting aerobic respiration to mesophilic communities. Nitrite reduction to N₂ has the highest energy yields at higher temperatures (greater than ～40 °C). Nitrate and nitrite reduction to ammonium also yield significant energy (up to ?70 kJ/mol e^?). Much lower, but still feasible energy yields are calculated for sulfate reduction, disproportionation, and reduction with H₂. Organic compound family and the activity of methanethiol and dimethylsulfide were less important than metabolic strategy in determining overall energy yields. All metabolic strategies considered were exergonic within some portion of the mixing regime suggesting that organic sulfur‐based metabolisms may be prevalent within deep‐sea hydrothermal vent microbial communities.     

Extremely thermophilic energy metabolisms: biotechnological prospects

1. Download : Download high-res image (171KB)
2. Download : Download full-size image

     

Compared energetics of primordial and biological metabolisms

In model experiments of chemical evolution, the accumulation of redox energy has been achieved up to now only within gaseous phase. Such experiments lead to atmospheric precursors and involve an accumulation of large quantities of free enthalpy. A part of this energy can be released after dissolution of the precursors in aqueous media, either by simple multiple bond hydration, or by addition of heteroatomic reagents more nucleophilic than water, or by addition of carbonaceous nucleophiles. Energy balances of such processes are discussed.The non-enzymic photochemical accumulation of redox energy in aqueous phase appears later on feasible, but the main unsolved problem lies in the understanding of the primordial processes which made the conversion of redox energy into energy available from hydrolysis possible in aqueous media in the earliest stage of chemical evolution.In this respect, chemiosmotic or configurational interpretations of oxidative phosphorylations cannot be taken into consideration because they require complex structures which cannot be allowed for at this early stage.On the contrary, a discussion of the energetics and kinetics of electron transfers to and from substrates makes understandable the basic principles involved in the energy storage processes by means of the chemical hypothesis, as well as their likely occurrence, even in a non-enzymic form, from the very earliest stages of chemical evolution.     

On maintenance and metabolisms in soil microbial communities

Plant and Soil - Biochemistry is an essential yet undervalued aspect of soil ecology, especially when analyzing soil C cycling. We assume, based on tradition, intuition or hope, that the complexity...     

抗酶抑制因子结构、功能与代谢的研究进展

抗酶抑制因子是一种热不稳定蛋白,与鸟氨酸脱羧酶同源,但不具有鸟氨酸脱羧酶活性,经泛素依赖途径被降解.抗酶抑制因子与抗酶高度亲和,抑制抗酶功能,恢复鸟氨酸脱羧酶活性.研究发现,抗酶抑制因子还能够调节多胺转运,抑制细胞周期蛋白D1的降解,以及加速中心粒复制,从而促进细胞增殖及肿瘤发生.     

Fermentation trip: amazing microbes,amazing metabolisms

Fermentation has been applied to many areas of human life, including industrial production, sewage treatment, and environment management. By understanding the process and mechanism of fermentation, more comprehensive and profound cognition of the fermentation may be established to lay a foundation for our further research. In this review, we present a brief summary of recent research about fermentation and microorganisms in different territories, including foods, environment, and human health. According to the growth characteristics of different stages of microorganisms, we introduced a series of metabolic changes, fermentation mechanism, and regulation methods and how the enzymes were transported out of the cell. With further understanding and utilization of microorganisms, food can produce better flavor, nutrition, and functional metabolites through fermentation. Fermentation is also used in other industries, such as wastewater and garbage disposal, environment, and soil management. The human gut flora, in particular, has begun to receive more attention. The profound influence of microorganism on human health cannot to be underestimated. It has become a hot research area in recent years. We can get the metabolites we want by controlling the rate of fermentation and regulate the direction of fermentation. As one of the important components of modern biotechnology, fermentation engineering has been widely used in areas including food, pharmaceutical, energy, chemical industries, and environmental protection. The development of genetic engineering has brought new vitality to fermentation engineering. The application of modernization, automation and artificial intelligence technology also opens up new space for fermentation engineering. In addition, research on the understanding and regulation of metabolic mechanism has further developed the fermentation function of microorganisms.     

AMPK在机体糖脂代谢中的作用

AMP激活的蛋白激酶(AMPK)是一种广泛参与调节细胞代谢的激酶,被称为"能量感受器".一旦胞浆中AMP/ATP比例升高,或其它因素激活AMPK时,AMPK可增强葡萄糖摄取和利用,以及脂肪酸氧化,产生更多能量;同时抑制葡萄糖异生、脂质合成及糖原合成等通路,减少能量消耗,从而使细胞能量代谢保持平衡.AMPK参与调节包括胰岛β细胞、肝脏、骨骼肌和脂肪在内的多种外周组织的糖脂代谢过程.本文旨在总结并讨论AMPK在机体主要糖脂代谢器官中的作用,并重点分析其在治疗胰岛素抵抗和2型糖尿病中的潜在作用.     

Properties, metabolisms, and applications of l-proline analogues

Due to the unique role of l-proline in the folding and structure of protein, a variety of synthetic proline analogues have been developed. l-Proline analogues have been proven to be valuable reagents for studying cellular metabolism and the regulation of macromolecule synthesis in both prokaryotic and eukaryotic cells. In addition to these fundamental researches, they are useful compounds for industrial use. For instance, microorganisms that overproduce l-proline have been obtained by isolating mutants resistant to l-proline analogues. They are also promising candidates for tuning the biological, pharmaceutical, or physicochemical properties of naturally occurring or de novo designed peptides. Among l-proline analogues, l-azetidine-2-carboxylic acid (l-AZC) is a toxic non-proteinogenic amino acid originally found in lily of the valley plants and trans-4-hydroxy-l-proline (4-l-THOP) is the most abundant component of mammalian collagen. Many hydroxyprolines (HOPs), such as 4-l-THOP and cis-4-hydroxy-l-proline (4-l-CHOP), are useful chiral building blocks for the organic synthesis of pharmaceuticals. In addition, l-AZC and 4-l-CHOP, which are potent inhibitors of cell growth, have been tested for their antitumor activity in tissue culture and in vivo. In this review, we describe the recent discoveries regarding the physiological properties and microbial production and metabolism of l-proline analogues, particularly l-AZC and HOPs. Their applications in fundamental research and industrial use are also discussed.     

基于能值理论的中国城市新陈代谢

运用城市新陈代谢能值指标方法,分析了2000和2010年31个典型中国城市的新陈代谢系统构成及发展特征.结果表明: 研究期间,中国城市新陈代谢系统的资源消耗型、沿海外贸型特征明显.内陆城市的非可再生资源能值占城市代谢系统能值总量的比例较高.北京、上海等大都市及东部沿海城市的进出口能值比重偏大,表现出显著的代谢外向型发展特征.在此基础上,明确了城市在实现可持续发展目标过程中的新陈代谢改进方向:发展可再生资源、能源产业;改善非可再生资源、能源利用效率;优化城市进出口服务、货物和燃料结构;弹性的城市新陈代谢管理机制.     

Advances in computational metabolomics and databases deepen the understanding of metabolisms

1. Download : Download high-res image (164KB)
2. Download : Download full-size image

     

Multiple effects of the inhibitory protein of ethylene production on cellular metabolisms

The effects of an inhibitory protein of ethylene productionisolated from etiolated mung bean hypocotyls (Planta 113: 115,1973) were investigated. Etiolated mung bean hypocotyl segmentsincubated with IAA for 3 hr (1st incubation) to induce ethylene-producingactivity were incubated for 1 hr with IAA in the presence ofthe inhibitory protein and a radioactive material to measuremetabolic activity. Under the conditions where ethylene productionwas inhibited 80% or more by the protein, RNA synthesis, proteinsynthesis and phosphate uptake were suppressed 55–60,65–80, and 60–75%, respectively. Conversion of 1-¹⁴C-acetateto CO₂, lipid, basic and neutral fractions was also inhibited,but the degrees of inhibition were much less than those forthe other processes. When the segments pretreated with the inhibitoryprotein during the 1st incubation period were washed free ofthe protein and assayed for their metabolic activities, theinhibition of RNA and protein syntheses and of phosphate uptakewas partially restored, while ethylene-producing activity wasfully restored to the control level. Similar reversible inhibitoryeffects were also observed for those metabolic activities inthe tissue segments not treated with IAA, thus not producinginduced ethylene. Oxygen uptake and conversion of U-¹⁴C-glucoseto CO₂ were not affected by the inhibitory protein. The possibilitythat the inhibitory protein acts on cell surface membranes andthe modified membranes affect the regulatory mechanism of cellularmetabolism is discussed. ¹ This investigation was supported in part by grants from theMinistries of Education (B-248009), and of Agriculture and Forestryof Japan. (Received November 4, 1977; )