Metabolic tree

METEOR Rule-based Metabolite prediction software Predicts the metabolic fate of chemicals Displays results as a metabolic tree. User can filter results for likely metabolites. Links directly to MetaboLynx for analysis of mass spectrometry data www.lhasalimited.org... 

MetabolExperF Rule-based Metabolite prediction software Predicts the most common metabolic pathways in animals, plants or through photodegradation. Results are presented in metabolic tree format. Graphical interface for editing and adding rules www.compudrug.com... 

Darvas et al. (1999) and Tarjanyi et al. 1998 presented an illustration of the predictions of MetabolExpert for the drug (-)-diprenyl. A metabolic tree was shown including 4 generations and 36 different metabolites. For 25 of these metabolites experimental retention times were reported. It is not clear whether all these 25 metabolites were observed in experimental metabolism studies. Most metabolic studies report relatively few metabolites minor ones may not be detected or identified and their observation may be dependent on the experimental conditions used in the analysis. An important predicted metabolite of deprenyl, benzyl methyl ketone, was reported to be observed only when an appropriate HPLC extraction system was used (Darvas et al., 1999). Bencze et al. (2000) have illustrated the use of the system in conjunction with the related HazardExpert system in a hazard assessment of ethylene oxide. 

To support metabolic studies, there is an option to restrict the growth of reaction sequences to products containing a specified, radio labeled atom. There is also an option to construct a very large metabolic tree initially and then to prune it automatically to show only branches that lead to structures with specified molecular formulas coming from mass spectrometric studies. 

Another program available form Lhasa Ltd. is Meteor, software that allows predicting metabolic pathways of xenobiotic compounds [13-15], Again, the program uses expert knowledge in form of rules to predict the metabolic pathway of compounds. The predictions are presented in metabolic trees, similar to a synthesis tree, and may be filtered according to the likelihood of metabolites. 

R. Bentley (1990). The shikimate pathway - A metabolic tree with many branches. Crit. Rev. Biochem. Mol. Biol, 25, 307-384. 

Expert systems and their databases (MetabolExpert, METEOR,. .. ) nature of metabolites, metabolic trees, reactive/adduct-fonning metabolites, relative importance of these metabolites depending on biological factors. 

Goal 2 Same as above, organized in a metabolic tree... 

The benzoquinones and naphthoquinones are derived from the shikimate pathway (Figure 2), which has been described as a metabolic tree with many branches. Most of the information concerning the biosynthesis of MK and Q was obtained with E. coli hy using isotopic tracers, by the isolation of mutants, and by the accumulation of intermediates and enzyme assays. Due to space limitations, only a general account is given here for more information, several comprehensive reviews should be consulted. ... 

Figure 11.5 Meteor on-screen results display showing the metabolic tree and the summary table.

The unripened fruit of the akee tree contains hypoglycin, a rare amino acid (Figure 24.14). Metabolism of hypoglycin yields methylenecydopropylacetyl-CoA (MCPA-CoA). Acyl-CoA dehydrogenase will accept MCPA-CoA as a substrate,... 

Damage to epicuticular waxes Altered photosynthesis Increased water loss Accumulation of acidic anions Leaching of ions, sugars, etc. Mineral imbalances Altered metabolism Increased susceptibility to winter freezing injury Death of fine roots Destabilization of trees Reduced water/mineral uptake Reduced water uptake Cations leached below roots Accumulation of acidic anions Altered structure/texture Altered microflora Reduced litter decomposition Altered N transformations Solubilization of metal ions... 

Burken JG, JL Schnoor (1997) Uptake and metabolism of atrazine by poplar trees. Environ Sci Technol 31 1399-1406. 

Most of the TCE that is taken up by the poplars is expected to volatilize slowly to the atmosphere. A portion will be metabolized by the leaves and woody tissue of the trees. 

CAM plants Abbreviation for crassulacean acid metabolism plants. cambium The layer of cells between the phloem and the wood of a tree, cameo A small relief carving on a different colored background, made from either onyx or two-color layered glass. 

Natural resins are substances with a high viscosity, semisolids or solid and insoluble in water. They are formed in the so-called resiniferous canals of several trees. Many varieties of plants spontaneously exude resins as a product of their metabolism, to protect themselves against excessive loss of water and attack from micro-organisms. 

Polyphenol oxidase occurs within certain mammalian tissues as well as both lower (46,47) and higher (48-55) plants. In mammalian systems, the enzyme as tyrosinase (56) plays a significant role in melanin synthesis. The PPO complex of higher plants consists of a cresolase, a cate-cholase and a laccase. These copper metalloproteins catalyze the one and two electron oxidations of phenols to quinones at the expense of 02. Polyphenol oxidase also occurs in certain fungi where it is involved in the metabolism of certain tree-synthesized phenolic compounds that have been implicated in disease resistance, wound healing, and anti-nutrative modification of plant proteins to discourage herbivory (53,55). This protocol presents the Triton X-114-mediated solubilization of Vida faba chloroplast polyphenol oxidase as performed by Hutcheson and Buchanan (57). 

Eckenrode et al. demonstrated that copper oxidases could oxidize vindoline through the same sequence of intermediates found in the metabolism of the alkaloid by Streptomyces griseus. Laccase from Polyporus anceps, laccase from the lacquer tree, and the mammalian (human serum) equivalent copper oxidase... 

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