Network construction and analysis method for oxidized bacterium gluconicum genome scale metabolism

A technology for oxidizing glucose and genome scale, applied in data visualization, special data processing applications, instruments, etc.

Inactive Publication Date: 2012-09-12
TIANJIN UNIV
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Problems solved by technology

There is no report on the genome-scale metabolic network of Gluconobacter oxidans. Therefore, constructing the genome-scale metabolic network of Gluconobacter oxid

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  • Network construction and analysis method for oxidized bacterium gluconicum genome scale metabolism
  • Network construction and analysis method for oxidized bacterium gluconicum genome scale metabolism

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Embodiment 1

[0038] The genome-scale metabolic network of Gluconobacter oxidans was constructed according to the KEGG database and other related databases and literature reports. The metabolic network consists of 1007 metabolites, 860 reactions, 433 genes, and 403 enzymes, classified into 72 sub-metabolic pathways or subsystems, which include intracellular and extracellular small molecule metabolic reactions, biomass synthesis reactions, and transport reactions .

[0039] To use Pajek to draw a metabolic network diagram, the metabolic network needs to be modified and converted into a format recognizable by Pajek. The modification is as follows: ATP, ADP, NADH, NAD+, NADPH, NADP+, THF, and other circulating metabolites are deleted, because although they participate in a large number of metabolic reactions, they do not directly participate in the conversion process of substrates to products. Delete polymerization reactions and reactions involving macromolecules, such as synthesis of protein...

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Abstract

The invention discloses a network construction and analysis method for oxidized bacterium gluconicum genome scale metabolism. The method comprises the steps of utilizing annotation information of oxidized bacterium gluconicum and biochemistry information of corresponding enzymes in the KEGG database to construct a reaction list sketch; modifying the sketch; adding reactions of biomass synthesis, transport and exchangeto form a metabolism network; converting the metabolism network to an SBML format, utilizing Matlab and Bobara Toolbox to debug the metabolism network, analyzing gaps and ineffective cycles and making correction according to the result of debugging; inthe light of the metabolism network, drawing a metabolism diagram by using Pagek and analyzing the network topology structure; and according to the metabolism network, analyzing one or more of the robustness, gene essentiality and flux changeability by utilizing the Matlab and Cobra Toolbox. The metabolism network can be used for analyzing the different metabolism states of oxidized bacterium gluconicum when the oxidized bacterium gluconicum produces dihydroxy acetone, vitamin C and glucose acid.

Description

technical field [0001] The invention relates to a network construction and analysis method. In particular, it relates to a genome-scale metabolic network construction and analysis method for Gluconobacter oxidans. Background technique [0002] Gluconobacter oxydans belongs to the family Acetobacteriaceae and is Gram-negative. Can incompletely oxidize various alcohols, polyols and carbohydrates to the corresponding ketones and sugar acids. For example, oxidation of glycerol to dihydroxyacetone, glucose to gluconic acid, sorbitol to 2-keto-gulonic acid, etc. [0003] Due to its unique and efficient incomplete oxidation ability, Gluconobacter oxydans has been widely used in industry. The products produced by it have good application value in the field of drug or drug synthesis precursor. The research on Gluconobacter oxydans has been paid more and more attention. Since the genome of Gluconobacter oxydans was sequenced and most of its genes were annotated in 2005, the under...

Claims

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Application Information

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IPC IPC(8): G06F19/26G16B45/00
Inventor 卢文玉吴欣森
Owner TIANJIN UNIV
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