A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks

A set of linear pathways often does not capture the full range of behaviors of a metabolic network. The concept of 'elementary flux modes' provides a mathematical tool to define and comprehensively describe all metabolic routes that are both stoichiometrically and thermodynamically feasible for a group of enzymes. We have used this concept to analyze the interplay between the pentose phosphate pathway (PPP) and glycolysis. The set of elementary modes for this system involves conventional glycolysis, a futile cycle, all the modes of PPP function described in biochemistry textbooks, and additional modes that are a priori equally entitled to pathway status. Applications include maximizing product yield in amino acid and antibiotic synthesis, reconstruction and consistency checks of metabolism from genome data, analysis of enzyme deficiencies, and drug target identification in metabolic networks.     

Increasing the flux in metabolic pathways: A metabolic control analysis perspective

The problems of engineering increased flux in metabolic pathways are analyzed in terms of the understanding provided by metabolic control analysis. Over-expression of a single enzyme is unlikely to be effective unless it is known to have a high flux control coefficient, which can be used as an approximate predictive tool. This is likely to rule out enzymes subject to feedback inhibition, because it transfers control downstream from the inhibited enzyme to the enzymes utilizing the feedback metabolite. Although abolishing feedback inhibition can restore flux control to an enzyme, it is also likely to cause large increases in the concentrations of metabolic intermediates. Simultaneous and coordinated over-expression of most of the enzymes in a pathway can, in principle, produce substantial flux increases without changes in metabolite levels, though technically it may be difficult to achieve. It is, however, closer to the method used by cells to change flux levels, where coordinated changes in the level of activity of pathway enzymes are the norm. Another option is to increase the demand for the pathway product, perhaps by increasing its rate of excretion or removal. Copyright 1998 John Wiley & Sons, Inc.     

可降解新烟碱类杀虫剂微生物及其代谢途径的研究进展

新烟碱类化合物基于烟碱结构改造修饰制备,相较菊酯、含磷类等杀虫剂,因其选择性毒力被认为是一类对人类和生态无害的农药。然而,近年来由于新烟碱类杀虫剂(neonicotinoid insecticides)过度施用,其残余或转化的物质通过在土壤与水体中累积,影响昆虫甚至哺乳动物及其生理与行为,导致了一系列生态环境问题和继发危害。本文聚焦新烟碱类杀虫剂的产业现状,面向生物降解新烟碱类杀虫剂这一迫切需求,围绕新烟碱类杀虫剂的微生物菌株资源,重点阐述微生物降解新烟碱类杀虫剂的代谢机制及其多样性。通过梳理新烟碱类杀虫剂生物降解及其应用转化的关键问题和前沿进展,旨在为借助合成生物学和宏基因组学手段建立或筛选安全可控的新烟碱类杀虫剂的高效转化体系提供参考。     

Photorespiration: metabolic pathways and their role in stress protection

Photorespiration results from the oxygenase reaction catalysed by ribulose-1,5-bisphosphate carboxylase/oxygenase. In this reaction glycollate-2-phosphate is produced and subsequently metabolized in the photorespiratory pathway to form the Calvin cycle intermediate glycerate-3-phosphate. During this metabolic process, CO2 and NH3 are produced and ATP and reducing equivalents are consumed, thus making photorespiration a wasteful process. However, precisely because of this inefficiency, photorespiration could serve as an energy sink preventing the overreduction of the photosynthetic electron transport chain and photoinhibition, especially under stress conditions that lead to reduced rates of photosynthetic CO2 assimilation. Furthermore, photorespiration provides metabolites for other metabolic processes, e.g. glycine for the synthesis of glutathione, which is also involved in stress protection. In this review we describe the use of photorespiratory mutants to study the control and regulation of photorespiratory pathways. In addition, we discuss the possible role of photorespiration under stress conditions, such as drought, high salt concentrations and high light intensities encountered by alpine plants.     

Somatic embryogenesis of Panax ginseng in liquid cultures: a role for polyamines and their metabolic pathways

A callus with embryogenic capacity was generated fromroot sections of Panax ginseng and used as aninoculum source for embryogenic liquid cultures in athree-step process: – a suspension culture of cellaggregates in the presence of an auxin/cytokininmixture, – an induction medium containing auxin only(for 5 to 30 days), – a regeneration medium containingcytokinin only (for one month). Up to 25 embryos wererecovered per 2.5 g of aggregates in these conditions.Incorporation of polyamines or their precursorsarginine and ornithine into either the induction orregeneration media increased the number of embryosproduced by up to 4 times. Inhibitors of bothbiosynthesis and biodegradation of polyamines reducedthe number of embryos. These results support earlierfindings of the role of polyamines in the process ofsomatic embryogenesis. The success of these liquidcultures opens up the possibility of producing somaticembryos of Panax ginseng in bioreactors.     

甲基营养微生物的甲醛代谢途径及其在环境生物技术中的应用

甲醛是一种毒性很高的一碳化合物,甲基营养菌是一类能在有高浓度甲醛的环境中生存的微生物,它们体内有多种降解甲醛的氧化途径和将甲醛转化为细胞组分的同化途径。丝氨酸途径和酮糖单磷酸途径是同时存在于甲基营养型细菌中的两种甲醛同化途径,木酮糖单磷酸途径是甲基营养型酵母菌中独有的甲醛同化途径。为了充分挖掘甲基营养型微生物在环境生物技术中的潜在应用价值,最近有很多研究尝试利用甲基营养微生物的细胞及其甲醛代谢途径关键酶开发甲醛污染检测方法和生物治理技术,对这方面的研究进展进行综述。     

On the use of qualitative reasoning to simulate and identify metabolic pathways

MOTIVATION: Perhaps the greatest challenge of modern biology is to develop accurate in silico models of cells. To do this we require computational formalisms for both simulation (how according to the model the state of the cell evolves over time) and identification (learning a model cell from observation of states). We propose the use of qualitative reasoning (QR) as a unified formalism for both tasks. The two most commonly used alternative methods of modelling biochemical pathways are ordinary differential equations (ODEs), and logical/graph-based (LG) models. RESULTS: The QR formalism we use is an abstraction of ODEs. It enables the behaviour of many ODEs, with different functional forms and parameters, to be captured in a single QR model. QR has the advantage over LG models of explicitly including dynamics. To simulate biochemical pathways we have developed 'enzyme' and 'metabolite' QR building blocks that fit together to form models. These models are finite, directly executable, easy to interpret and robust. To identify QR models we have developed heuristic chemoinformatics graph analysis and machine learning procedures. The graph analysis procedure is a series of constraints and heuristics that limit the number of ways metabolites can combine to form pathways. The machine learning procedure is generate-and-test inductive logic programming. We illustrate the use of QR for modelling and simulation using the example of glycolysis. AVAILABILITY: All data and programs used are available on request.     

Rodent and nonrodent malaria parasites differ in their phospholipid metabolic pathways

Malaria, a disease affecting humans and other animals, is caused by a protist of the genus Plasmodium. At the intraerythrocytic stage, the parasite synthesizes a high amount of phospholipids through a bewildering number of pathways. In the human Plasmodium falciparum species, a plant-like pathway that relies on serine decarboxylase and phosphoethanolamine N-methyltransferase activities diverts host serine to provide additional phosphatidylcholine and phosphatidylethanolamine to the parasite. This feature of parasitic dependence toward its host was investigated in other Plasmodium species. In silico analyses led to the identification of phosphoethanolamine N-methyltransferase gene orthologs in primate and bird parasite genomes. However, the gene was not detected in the rodent P. berghei, P. yoelii, and P. chabaudi species. Biochemical experiments with labeled choline, ethanolamine, and serine showed marked differences in biosynthetic pathways when comparing rodent P. berghei and P. vinckei, and human P. falciparum species. Notably, in both rodent parasites, ethanolamine and serine were not significantly incorporated into phosphatidylcholine, indicating the absence of phosphoethanolamine N-methyltransferase activity. To our knowledge, this is the first study to highlight a crucial difference in phospholipid metabolism between Plasmodium species. The findings should facilitate efforts to develop more rational approaches to identify and evaluate new targets for antimalarial therapy.     

Elucidation of salt-tolerance metabolic pathways in contrasting rice genotypes and their segregating progenies

Key message

Differentially expressed antioxidant enzymes, amino acids and proteins in contrasting rice genotypes, and co-location of their genes in the QTLs mapped using bi-parental population, indicated their role in salt tolerance.

Abstract

Soil salinity is a major environmental constraint limiting rice productivity. Salt-tolerant ‘CSR27’, salt-sensitive ‘MI48’and their extreme tolerant and sensitive recombinant inbred line (RIL) progenies were used for the elucidation of salt stress tolerance metabolic pathways. Salt stress-mediated biochemical and molecular changes were analyzed in the two parents along with bulked-tolerant (BT) and bulked-sensitive (BS) extreme RILs. The tolerant parent and BT RILs suffered much lower reduction in the chlorophyll as compared to their sensitive counterparts. Activities of antioxidant enzymes superoxide dismutase (SOD) and peroxidase (POD) and non-enzymatic antioxidant ascorbic acid were much higher in salt-stressed CSR27 and BT RILs than MI48 and BS RILs. Further, the tolerant lines showed significant enhancement in the levels of amino acids methionine and proline in response to salt stress in comparison to the sensitive lines. Similarly, the tolerant genotypes showed minimal reduction in cysteine content whereas sensitive genotypes showed a sharp reduction. Real time PCR analysis confirmed the induction of methionine biosynthetic pathway (MBP) enzymes cystathionine-β synthase (CbS), S-adenosyl methionine synthase (SAMS), S-adenosyl methionine decarboxylase (SAMDC) and serine hydroxymethyl transferase (SHMT) genes in tolerant lines, suggesting potential role of the MBP in conferring salt tolerance in rice variety CSR27. Proteome profiling also confirmed higher expression of SOD, POD and plastidic CbS and other proteins in the tolerant lines, whose genes were co-located in the QTL intervals for salt tolerance mapped in the RIL population. The study signifies integrated biochemical-molecular approach for identifying salt tolerance genes for genetic improvement for stress tolerant rice varieties.

     

The metabolic pathway collection from EMP: the enzymes and metabolic pathways database.

The Enzymes and Metabolic Pathways database (EMP) is an encoding of the contents of over 10 000 original publications on the topics of enzymology and metabolism. This large body of information has been transformed into a queryable database. An extraction of over 1800 pictorial representations of metabolic pathways from this collection is freely available on the World Wide Web. We believe that this collection will play an important role in the interpretation of genetic sequence data, as well as offering a meaningful framework for the integration of many other forms of biological data.     

Butanol production from renewable biomass: rediscovery of metabolic pathways and metabolic engineering

Biofuel from renewable biomass is one of the answers to help solve the problems associated with limited fossil resources and climate change. Butanol has superior liquid-fuel characteristics, with similar properties to gasoline, and thus, has the potential to be used as a substitute for gasoline. Clostridia are recognized as a good butanol producers and are employed in the industrial-scale production of solvents. Due to the difficulty of performing genetic manipulations on clostridia, however, strain improvement has been rather slow. Furthermore, complex metabolic characteristics of acidogenesis followed by solventogenesis in this strain have hampered the development of engineered clostridia strains with highly efficient and selective butanol-production capabilities. In recent years, the butanol-producing characteristics in clostridia have been further characterized and alternative pathways discovered. More recently, systems-level metabolic engineering approaches were taken to develop superior strains. Herein, we review recent discoveries of metabolic pathways for butanol production and the metabolic engineering strategies being developed.     

Reconstruction of metabolic pathways for the cattle genome

Background  

Metabolic reconstruction of microbial, plant and animal genomes is a necessary step toward understanding the evolutionary origins of metabolism and species-specific adaptive traits. The aims of this study were to reconstruct conserved metabolic pathways in the cattle genome and to identify metabolic pathways with missing genes and proteins. The MetaCyc database and PathwayTools software suite were chosen for this work because they are widely used and easy to implement.     

Regulatory cross-talk of mouse liver polyamine and methionine metabolic pathways: a systemic approach to its physiopathological consequences

Both polyamines and methionine derivatives are nitrogen compounds directly related to the regulation of gene expression. In silico predictions and experimental evidence suggest a cross-talk between polyamine and methionine metabolism in mammalian tissues. Since liver is the major organ that controls nitrogen metabolism of the whole organism, it is the best tissue to further test this hypothesis in vivo. In this work, we studied the effects of the chronic administration of a methionine-supplemented diet (0.5% Met in drinking water for 5 months) on the liver of mice (designated as MET-mice). Metabolic and proteomic approaches were performed and the data obtained were subjected to biocomputational analysis. Results showed that a supplemental methionine intake can indeed regulate biogenic amine metabolism in an in vivo model by multiple mechanisms including metabolic regulation and specific gene demethylation. Furthermore, putative systemic effects were investigated by molecular and cellular biology methods. Among other results, altered expression levels of multiple inflammation and cell proliferation/death balance markers were found and macrophage activation was observed. Overall, the results presented here will be of interest across a variety of biomedical disciplines, including nutrition, orphan diseases, immunology and oncology.     

Plant surface lipid biosynthetic pathways and their utility for metabolic engineering of waxes and hydrocarbon biofuels

Due to their unique physical properties, waxes are high-value materials that are used in a variety of industrial applications. They are generated by chemical synthesis, extracted from fossil sources, or harvested from a small number of plant and animal species. As a result, the diversity of chemical structures in commercial waxes is low and so are their yields. These limitations can be overcome by engineering of wax biosynthetic pathways in the seeds of high-yielding oil crops to produce designer waxes for specific industrial end uses. In this review, we first summarize the current knowledge regarding the genes and enzymes generating the chemical diversity of cuticular waxes that accumulate at the surfaces of primary plant organs. We then consider the potential of cuticle biosynthetic genes for biotechnological wax production, focusing on selected examples of wax ester chain lengths and isomers. Finally, we discuss the genes/enzymes of cuticular alkane biosynthesis and their potential in future metabolic engineering of plants for the production of renewable hydrocarbon fuels.     

Deriving phylogenetic trees from the similarity analysis of metabolic pathways

MOTIVATION: Comparative analysis of metabolic pathways in different genomes can give insights into the understanding of evolutionary and organizational relationships among species. This type of analysis allows one to measure the evolution of complete processes (with different functional roles) rather than the individual elements of a conventional analysis. We present a new technique for the phylogenetic analysis of metabolic pathways based on the topology of the underlying graphs. A distance measure between graphs is defined using the similarity between nodes of the graphs and the structural relationship between them. This distance measure is applied to the enzyme-enzyme relational graphs derived from metabolic pathways. Using this approach, pathways and group of pathways of different organisms are compared to each other and the resulting distance matrix is used to obtain a phylogenetic tree. RESULTS: We apply the method to the Citric Acid Cycle and the Glycolysis pathways of different groups of organisms, as well as to the Carbohydrate metabolic networks. Phylogenetic trees obtained from the experiments were close to existing phylogenies and revealed interesting relationships among organisms.     

NADP-malic enzyme from plants: a ubiquitous enzyme involved in different metabolic pathways

NADP-malic enzyme (NADP-ME) is a widely distributed enzyme that catalyzes the oxidative decarboxylation of L-malate. Photosynthetic NADP-MEs are found in C4 bundle sheath chloroplasts and in the cytosol of CAM plants, while non-photosynthetic NADP-MEs are either plastidic or cytosolic in various plants. We propose a classification of plant NADP-MEs based on their physiological function and localization and we describe recent advances in the characterization of each isoform. Based on the alignment of amino acid sequences of plant NADP-MEs, we identify putative binding sites for the substrates and analyze the phylogenetic origin of each isoform, revealing several features of the molecular evolution of this ubiquitous enzyme.     

Regulation of respiration in plants: a role for alternative metabolic pathways

Respiratory metabolism includes the reactions of glycolysis, the tricarboxylic acid cycle and the mitochondrial electron transport chain, but is also directly linked with many other metabolic pathways such as protein and lipid biosynthesis and photosynthesis via photorespiration. Furthermore, any change in respiratory activity can impact the redox status of the cell and the production of reactive oxygen species. In this review, it is discussed how respiration is regulated and what alternative pathways are known that increase the metabolic flexibility of this vital metabolic process. By looking at the adaptive responses of respiration to hypoxia or changes in the oxygen availability of a cell, the integration of regulatory responses of various pathways is illustrated.