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Construction and application technology of Torulopsis glabrata genome metabolism model

A technology of T. glabrata and genome, applied in the field of systems biology, can solve the problems of uneven model quality and so on

Inactive Publication Date: 2012-08-01
JIANGNAN UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Variations in model quality due to differences in resources available to specific organisms and differences in model building methods

Method used

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  • Construction and application technology of Torulopsis glabrata genome metabolism model
  • Construction and application technology of Torulopsis glabrata genome metabolism model
  • Construction and application technology of Torulopsis glabrata genome metabolism model

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0011] Example 1 A model framework is built using KEGG converter.

[0012] Download the KGML format file of the metabolic pathway of Torulopsis glabrata from the KEGG database, and use KEGG converter software to integrate all metabolic pathways into a metabolic network model in Systems Biology Markup Language (SBML) format.

Embodiment 2

[0013] Example 2 Annotation of the genome sequence of Toruula glabrata based on protein sequence homology

[0014] The comparison strains were selected among microorganisms for which genome-scale metabolic network models had been constructed. First, starting from the phylogenetic tree, select microorganisms that belong to the same family with close kinship. Saccharomyces cerevisiae and Pichia pastoris were selected here as close relatives of Toruula glabrata. To ensure the comprehensiveness of gene annotation, model microorganisms such as Aspergillus niger, Escherichia coli, and Bacillus subtilis were also used as comparison strains.

[0015] Download the FASTA format of the protein sequences of the above microorganisms from UniprotKB, and perform BLASTp with the protein sequences of Torulopsis glabrata. The comparison results meet the similarity greater than 35% and the E value is less than 10 -30 , and the ratio of similar length to any sequence length is greater than 70%...

Embodiment 3

[0018] Example 3 Metabolic network model combined with bibliographic studies of Toruula glabrata

[0019] Using (Candida glabrata or Torulopsis glabrata) and (metabolism or physiology) as keywords, the literature related to the physiological and biochemical metabolism of Torulopsis glabrata was excavated in PubMed and Web of Science. According to literature reports, 254 reactions were confirmed to exist in Torulopsis glabrata, and 82 putative proteins were functionally annotated (this annotation does not coincide with the gene annotations of KEGG and comparative genomics). Partial annotation information is shown in Table 2.

[0020] Table 2 Partial information of gene annotation based on bibliographic omics

[0021]

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PUM

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Abstract

The invention discloses a construction method and an application technology of a Torulopsis glabrata genome-scale metabolism network model, belonging to the field of systems biology. The construction method of the model is an all-round semi-automatic construction method of combining comparative genomics annotation and bacteria-specific information of Torulopsis glabrata protein homology based on an automatic model. The invention provides a method for characterizing auxotroph characteristics in a Torulopsis glabrata metabolism network by adding necessary nutrient substances, lacked in bacteria, to a biomass equation. Alcohol dehydrogenase is knocked out by using single genes in the Torulopsis glabrata metabolism network model, and flow equilibrium analysis is applied, so that the output of pyruvic acid is increased. The construction method and the application technology of the Torulopsis glabrata genome-scale metabolism network model provide a high-efficient platform for fully understanding and reforming physiological and biochemical metabolisms of the Torulopsis glabrata.

Description

technical field [0001] The present invention relates to a method for constructing a genome-scale metabolic network (Genome Scale Metabolic Model, GSMM) of an auxotrophic yeast, Candida glabrata, and a strategy for obtaining bacterial transformation through model simulation analysis, which belongs to system biology field of study. Background technique [0002] Industrial systems biology includes the collection, analysis, and integration of genome-scale high-throughput omics data to obtain quantitative phenotypic descriptions of target biological systems. The continuously updated systems biology toolbox is widely used for genome-scale simulations of metabolic networks to guide the production of metabolic intermediates in industrial microorganisms. Typical examples are: Saccharomyces cerevisia uses xylose to produce alcohol, Escherichia coli produces 1,3-propanediol metabolite flow analysis (Metabolic Flux Analysis, MFA), Mannheimia succiniciproducens in Production of succini...

Claims

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Application Information

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IPC IPC(8): G06F19/18
Inventor 刘立明徐楠刘婷
Owner JIANGNAN UNIV
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