Organization Of Metabolic Pathways Research Articles

DeepRF: A deep learning method for predicting metabolic pathways in organisms based on annotated genomes

The rapid increase of metabolomics has led to an increasing focus on metabolic pathway modeling and reconstruction. In particular, reconstructing an organism's metabolic network based on its genome sequence is a key challenge in systems biology. The method used to address this problem predicts the presence or absence of metabolic pathways from known pathways in a reference database. However, this method is based on manual metabolic pathway construction and cannot be used for large genome sequencing data. To address such problems, we apply a supervised machine learning approach consisting of deep neural networks to learn feature representations of metabolic pathways and feed these representations into random forests to predict metabolic pathways. The supervised learning model, DeepRF, predicts all known and unknown metabolic pathways in an organism. Evaluation of DeepRF on over 318,016 instances shows that the model can predict metabolic pathways with high-performance metrics accuracy (>97%), recall (>95%), and precision (>99%). Comparing DeepRF with other methods in the literature shows that DeepRF produces more reliable results than other methods.

Low Temperature Affects Fatty Acids Profiling and Key Synthesis Genes Expression Patterns in Zanthoxylum bungeanum Maxim.

Zanthoxylum bungeanum is one of the most important medicinal and edible homologous plants because of its potential health benefits and unique flavors. The chemical components in compositions and contents vary with plant genotype variations and various environmental stress conditions. Fatty acids participate in various important metabolic pathways in organisms to resist biotic and abiotic stresses. To determine the variations in metabolic profiling and genotypes, the fatty acid profiling and key differential genes under low temperature stress in two Z. bungeanum varieties, cold-tolerant (FG) and sensitive (FX), were investigated. Twelve main fatty acids were found in two Z. bungeanum varieties under cold stress. Results showed that the contents of total fatty acids and unsaturated fatty acids in FG were higher than those in FX, which made FG more resistant to low temperature. Based on the result of orthogonal partial least squares discriminant analysis, palmitic acid, isostearic acid, linolenic acid and eicosenoic acid were the important differential fatty acids in FG under cold stress, while isomyristic acid, palmitic acid, isostearic acid, stearic acid, oleic acid, linolenic acid and eicosenoic acid were the important differential fatty acids in FX. Furthermore, fatty acid synthesis pathway genes fatty acyl-ACP thioesterase A (FATA), Delta (8)-fatty-acid desaturase 2 (SLD2), protein ECERIFERUM 3 (CER3), fatty acid desaturase 3 (FAD3) and fatty acid desaturase 5 (FAD5) played key roles in FG, and SLD2, FAD5, 3-oxoacyl-[acyl-carrier-protein] synthase I (KAS I), fatty acyl-ACP thioesterase B (FATB) and acetyl-CoA carboxylase (ACC) were the key genes responding to low temperature in FX. The variation and strategies of fatty acids in two varieties of Z. bungeanum were revealed at the metabolic and molecular level. This work provides a reference for the study of chemical components in plant stress resistance.

Development of a Ratiometric Fluorescent Glucose Sensor Using an Oxygen-Sensing Membrane Immobilized with Glucose Oxidase for the Detection of Glucose in Tears.

Glucose concentration is an important parameter in biomedicine since glucose is involved in many metabolic pathways in organisms. Many methods for glucose detection have been developed for use in various applications, particularly in the field of healthcare in diabetics. In this study, ratiometric fluorescent glucose-sensing membranes were fabricated based on the oxygen levels consumed in the glucose oxidation reaction under the catalysis of glucose oxidase (GOD). The oxygen concentration was measured through the fluorescence quenching effect of an oxygen-sensitive fluorescent dye like platinum meso-tetra (pentafluorophenyl) porphyrin (PtP) by oxygen molecules. Coumarin 6 (C6) was used as a reference dye in the ratiometric fluorescence measurements. The glucose-sensing membrane consisted of two layers: The first layer was the oxygen-sensing membrane containing polystyrene particles (PS) doped with PtP and C6 (e.g., PS@C6^PtP) in a sol–gel matrix of aminopropyltrimethoxysilane and glycidoxypropyltrimethoxysilane (GA). The second layer was made by immobilizing GOD onto one of three supporting polymers over the first layer. These glucose-sensing membranes were characterized in terms of their response, reversibility, interferences, and stability. They showed a wide detection range to glucose concentration in the range of 0.1 to 10 mM, but high sensitivity with a linear detection range of 0.1 to 2 mM glucose. This stable and sensitive ratiometric fluorescent glucose biosensor provides a reliable way to determine low glucose concentrations in blood serum by measuring tear glucose.

Activation Studies of the γ-Carbonic Anhydrases from the Antarctic Marine Bacteria Pseudoalteromonas haloplanktis and Colwellia psychrerythraea with Amino Acids and Amines

The γ-carbonic anhydrases (CAs, EC 4.2.1.1) present in the Antarctic marine bacteria Pseudoalteromonas haloplanktis and Colwellia psychrerythraea, herein referred to as PhaCA and CpsCA, respectively, were investigated for their activation with a panel of 24 amino acids and amines. Both bacteria are considered Antarctic models for the investigation of photosynthetic and metabolic pathways in organisms adapted to live in cold seawater. PhaCA was much more sensitive to activation by these compounds compared to the genetically related enzyme CpsCA. The most effective PhaCA activators were d-Phe, l-/d-DOPA, l-Tyr and 2-pyridyl-methylamine, with the activation constant KA values of 0.72–3.27 µM. d-His, l-Trp, d-Tyr, histamine, dopamine, serotonin anddicarboxylic amino acids were also effective activators of PhaCA, with KA values of 6.48–9.85 µM. CpsCA was activated by d-Phe, d-DOPA, l-Trp, l-/d-Tyr, 4-amino-l-Phe, histamine, 2-pyridyl-methylamine and l-/d-Glu with KA values of 11.2–24.4 µM. The most effective CpsCA activator was l-DOPA (KA of 4.79 µM). Given that modulators of CAs from Antarctic bacteria have not been identified and investigated in detail for their metabolic roles to date, this research sheds some light on these poorly understood processes.

Water-Related Mechanisms Proposed for Storing and Transmitting Homeopathic Information: Putative Links with Biological Responses.

There are two critical pillars of homeopathy that contrast with the dominant scientific approach: the similitude principle and the potentization of serial dilutions. Three main hypotheses about the mechanisms of action are in discussion: nanobubbles-related hormesis; vehicle-related electric resonance; and quantum non-locality. The aim of this paper is to review and discuss some key points of such properties: the imprint of supramolecular structures based on the nanoparticle-allostatic, cross-adaptation-sensitization (NPCAS) model; the theory of non-molecular electromagnetic transfer of information, based on the coherent water domains model, and relying (like the NPCAS model) on the idea of local interactions; and the hypothesis of quantum entanglement, based on the concept of non-locality. The nanoparticles hypothesis has been considered since 2010, after the demonstration of suspended metal nanoparticles even in very highly diluted remedies: their actual action on biological structures is still under scrutiny. The second hypothesis considers the idea of electric resonance mechanisms between living systems (including intracellular water) and homeopathic medicines: recent findings about potency-related physical properties corroborate it. Finally, quantum theory of 'non-local' phenomena inspires the idea of an 'entanglement' process among patient, practitioner and the remedy: that quantic phenomena could occur in supra-atomic structures remains speculative however. Further studies are needed to ascertain whether and which of these hypotheses may be related to potential cellular effects of homeopathic preparations, such as organization of metabolic pathways or selective gene expression.

Model-based metabolism design: constraints for kinetic and stoichiometric models.

The implementation of model-based designs in metabolic engineering and synthetic biology may fail. One of the reasons for this failure is that only a part of the real-world complexity is included in models. Still, some knowledge can be simplified and taken into account in the form of optimization constraints to improve the feasibility of model-based designs of metabolic pathways in organisms. Some constraints (mass balance, energy balance, and steady-state assumption) serve as a basis for many modelling approaches. There are others (total enzyme activity constraint and homeostatic constraint) proposed decades ago, but which are frequently ignored in design development. Several new approaches of cellular analysis have made possible the application of constraints like cell size, surface, and resource balance. Constraints for kinetic and stoichiometric models are grouped according to their applicability preconditions in (1) general constraints, (2) organism-level constraints, and (3) experiment-level constraints. General constraints are universal and are applicable for any system. Organism-level constraints are applicable for biological systems and usually are organism-specific, but these constraints can be applied without information about experimental conditions. To apply experimental-level constraints, peculiarities of the organism and the experimental set-up have to be taken into account to calculate the values of constraints. The limitations of applicability of particular constraints for kinetic and stoichiometric models are addressed.

Translating Enzymology into Metabolic Regulation: The Case of the 2- Oxoglutarate Dehydrogenase Multienzyme Complex

Enzymes are catalysts designed to function in the metabolic networks of biological systems. This review shows mechanisms underlying chemical contribution to the biological system performance and adaptations in permanently changing environment. The catalyst is exemplified by the 2-oxoglutarate dehydrogenase complex irreversibly degrading a branch point metabolite 2-oxoglutarate at the crossroad of carbon, nitrogen and fat metabolism. According to the key metabolic position and multienzyme structure, the complex exhibits rich regulation, demonstrating main principles governing the catalysis within metabolic network. First, the catalyst kinetics is changed through the enzyme-ligand interactions affecting the catalyst structure. The ligands include both small molecules and proteins, affecting catalysis by binding either to active (coenzymes, substrates, products or inhibitors) or allosteric sites. Allostery enables enzymatic sensitivity to general cellular signals, transmitted, in particular, by second messengers (Ca2+), adenine nucleotide phosphorylation status or redox potential. Regulation of catalysis by heterologous protein-protein interactions helps organization of metabolic pathways. Secondly, different regulators may interact through the protein structure effecting synergistic or antagonistic relationships through combined conformational stabilization or competitive binding. The latter is supported by common structural elements, e.g. adenine moiety, present in a number of biologically essential molecules. Thirdly, cellular systems may control the enzymatic catalysis by posttranslational modifications which may either effect or disable catalysis. The inactivation may protect catalyst itself and/or surrounding medium under conditions of metabolic impairment. Thus, enzymology enables our predictive capacity regarding both the enzyme impact on general metabolism and response to the metabolic changes within cellular network. This paves the way to the knowledge-based design of pharmacological tools to perform metabolic regulation required for solving medical and bioengineering problems. Keywords: lipoic acid, multienzyme complex, neurodegeneration, 2-oxoglutarate dehydrogenase, phosphorylation potential, redox regulation, thiamine deficiency, tricarboxylic acid cycle

Metabonomics and its role in amino acid nutrition research

Metabonomics combines metabolic profiling and multivariate data analysis to facilitate the high-throughput analysis of metabolites in biological samples. This technique has been developed as a powerful analytical tool and hence has found successful widespread applications in many areas of bioscience. Metabonomics has also become an important part of systems biology. As a sensitive and powerful method, metabonomics can quantitatively measure subtle dynamic perturbations of metabolic pathways in organisms due to changes in pathophysiological, nutritional, and epigenetic states. Therefore, metabonomics holds great promise to enhance our understanding of the complex relationship between amino acids and metabolism to define the roles for dietary amino acids in maintaining health and the development of disease. Such a technique also aids in the studies of functions, metabolic regulation, safety, and individualized requirements of amino acids. Here, we highlight the common workflow of metabonomics and some of the applications to amino acid nutrition research to illustrate the great potential of this exciting new frontier in bioscience.

Evolutionary significance of self‐acylation property in acyl carrier proteins

Acyl carrier protein is an integral component of many cellular metabolic processes. A number of studies have reported self-acylation behavior in acyl carrier proteins. Although ACPs exhibit high levels of similarity in their primary and tertiary structures, self-acylation behavior is restricted to only some ACPs that can be classified into two major families based on their function. The first family of ACPs is involved in polyketide biosynthesis, whereas the second family participates in fatty acid synthesis. Facilitated by the growing number of genome sequences available for analyses, large-scale phylogenetic studies were used in these studies to uncover as to how self-acylation behavior of acyl carrier proteins is linked with the evolution of metabolic pathways in organisms. These studies show that self-acylation behavior in acyl carrier proteins was lost during the course of evolution, with certain organisms and organelles viz. plastids, retaining it for specified functions.

Organization of metabolic pathways in vastus lateralis of patients with chronic obstructive pulmonary disease

The objective of this study was to determine whether patients with chronic obstructive lung disease (COPD) display differences in organization of the metabolic pathways and segments involved in energy supply compared with healthy control subjects. Metabolic pathway potential, based on the measurement of the maximal activity (V(max)) of representative enzymes, was assessed in tissue extracted from the vastus lateralis in seven patients with COPD (age 67 +/- 4 yr; FEV(1)/FVC = 44 +/- 3%, where FEV(1) is forced expiratory volume in 1 s and FVC is forced vital capacity; means +/- SE) and nine healthy age-matched controls (age 68 +/- 2 yr; FEV(1)/FVC = 75 +/- 2%). Compared with control, the COPD patients displayed lower (P < 0.05) V(max) (mol.kg protein(-1).h(-1)) for cytochrome c oxidase (COX; 21.2 +/- 2.0 vs. 28.7 +/- 2.2) and 3-hydroxyacyl-CoA dehydrogenase (HADH; 2.54 +/- 0.14 vs. 3.74 +/- 0.12) but not citrate synthase (CS; 2.20 +/- 0.16 vs. 3.19 +/- 0.5). While no differences between groups were observed in V(max) for creatine phosphokinase, phosphorylase (PHOSPH), phosphofructokinase (PFK), pyruvate kinase, and lactate dehydrogenase, hexokinase (HEX) was elevated in COPD (P < 0.05). Enzyme activity ratios were higher (P < 0.05) for HEX/CS, HEX/COX, PHOSPH/HADH and PFK/HADH in COPD compared with control. It is concluded that COPD patients exhibit a reduced potential for both the electron transport system and fat oxidation and an increased potential for glucose phosphorylation while the potential for glycogenolysis and glycolysis remains normal. A comparison of enzyme ratios indicated greater potentials for glucose phosphorylation relative to the citric acid cycle and the electron transport chain and glycogenolysis and glycolysis relative to beta-oxidation.

Metabolic compartmentation - a system level property of muscle cells: real problems of diffusion in living cells.

Problems of quantitative investigation of intracellular diffusion and compartmentation of metabolites are analyzed. Principal controversies in recently published analyses of these problems for the living cells are discussed. It is shown that the formal theoretical analysis of diffusion of metabolites based on Fick's equation and using fixed diffusion coefficients for diluted homogenous aqueous solutions, but applied for biological systems in vivo without any comparison with experimental results, may lead to misleading conclusions, which are contradictory to most biological observations. However, if the same theoretical methods are used for analysis of actual experimental data, the apparent diffusion constants obtained are orders of magnitude lower than those in diluted aqueous solutions. Thus, it can be concluded that local restrictions of diffusion of metabolites in a cell are a system-level properties caused by complex structural organization of the cells, macromolecular crowding, cytoskeletal networks and organization of metabolic pathways into multienzyme complexes and metabolons. This results in microcompartmentation of metabolites, their channeling between enzymes and in modular organization of cellular metabolic networks. The perspectives of further studies of these complex intracellular interactions in the framework of Systems Biology are discussed.

Organization of metabolic pathways and molecular-genetic mechanisms of xenobiotic degradation in microorganisms: A review

Contemporary data on the mechanism of biodegradation of aromatic hydrocarbons and biodegradation genes (genomic organization and pathways of evolution) in diverse groups of microorganisms have been reviewed. Studies of this problem are topical, in view of the need in identification and construction of new strains degrading xenobiotics, particularly those halogenated. For this reason, emphasis is placed on specific features of explored metabolic pathways that can be used for constructing new enzymatic systems not present in nature. Sections on the mechanisms of genomic rearrangements involving biodegradation determinants are presented from the same standpoint. Part of the review is devoted to analyzing methods used for studying the population dynamics of bacterial communities involved in xenobiotic degradation in natural biotopes or industrial waste disposal plants. Particular attention is given to methods of gene systematics.

Effect of Thiol‐Containing Molecule Cysteamine on the Induction of Inducible Nitric Oxide Synthase in Hepatocytes

Cysteamine, which is a known antioxidant and anti-inflammatory agent, is believed to be a key regulator of essential metabolic pathways in organisms. Cysteamine has beneficial effects in liver damaged by a variety of insults. During liver injury, inducible nitric oxide synthase (iNOS) is induced by lipopolysaccharide or proinflammatory cytokines, leading to excessive nitric oxide (NO) production. Accumulated evidence indicates that NO is an important factor associated with hepatic dysfunction. We examined whether cysteamine influences the induction of iNOS in hepatocytes. Primary cultured rat hepatocytes were treated with interleukin (IL)-1beta in the presence and absence of cysteamine. NO production, iNOS induction, and iNOS signal were analyzed. IL-1beta stimulated the inhibitory protein kappaB (IkappaB)/nuclear factor kappaB (NFkappaB) pathway, resulting in the activation of NFkappaB (nuclear translocation and DNA binding), which was followed by the induction of iNOS and NO production. The addition of IL-1beta and cysteamine (1-4 mmol/L) markedly inhibited NO production, with a maximal effect at 4 mmol/L (80%-90% inhibition). Cysteamine also decreased the levels of iNOS protein and mRNA. Transfection experiments revealed that cysteamine decreased the transactivation activity of the iNOS promoter. An electrophoretic mobility shift assay demonstrated that cysteamine inhibited the activation of NFkappaB. Furthermore, cysteamine decreased the mRNA levels of the NFkappaB subunit p65 but increased those of the inhibitory protein IkappaB. These findings suggest that cysteamine inhibits iNOS induction at the step of NFkappaB activation. Further study is necessary to define the molecular basis of this effect of cysteamine on the regulation of NFkappaB and its pharmacologic implications.