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. 2009;10(6):R69.
doi: 10.1186/gb-2009-10-6-r69. Epub 2009 Jun 25.

"VSports在线直播" iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

Christopher S Henry  1 , Jenifer F Zinner, Matthew P Cohoon, Rick L Stevens
Affiliations

"V体育官网入口" iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

Christopher S Henry et al. Genome Biol. 2009.

Abstract

Background: Bacillus subtilis is an organism of interest because of its extensive industrial applications, its similarity to pathogenic organisms, and its role as the model organism for Gram-positive, sporulating bacteria. In this work, we introduce a new genome-scale metabolic model of B VSports手机版. subtilis 168 called iBsu1103. This new model is based on the annotated B. subtilis 168 genome generated by the SEED, one of the most up-to-date and accurate annotations of B. subtilis 168 available. .

Results: The iBsu1103 model includes 1,437 reactions associated with 1,103 genes, making it the most complete model of B. subtilis available V体育安卓版. The model also includes Gibbs free energy change (DeltarG' degrees ) values for 1,403 (97%) of the model reactions estimated by using the group contribution method. These data were used with an improved reaction reversibility prediction method to identify 653 (45%) irreversible reactions in the model. The model was validated against an experimental dataset consisting of 1,500 distinct conditions and was optimized by using an improved model optimization method to increase model accuracy from 89. 7% to 93. 1%. .

Conclusions: Basing the iBsu1103 model on the annotations generated by the SEED significantly improved the model completeness and accuracy compared with the most recent previously published model. The enhanced accuracy of the iBsu1103 model also demonstrates the efficacy of the improved reaction directionality prediction method in accurately identifying irreversible reactions in the B V体育ios版. subtilis metabolism. The proposed improved model optimization methodology was also demonstrated to be effective in minimally adjusting model content to improve model accuracy. .

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Figures

Figure 1
Figure 1
Distribution of reactions conforming to reversibility rules. (a) The distribution of reactions in the iBsu1103 model conforming to every possible state in the proposed set of rules for assigning reaction directionality and reversibility is shown. This distribution indicates that most of the irreversible reactions in the model were determined to be irreversible because the ΔrG' max value calculated for the reaction was negative. (b) The distribution of reactions in the iBsu1103 model involving the compounds used in the reversibility score calculation is also shown. These compounds are prevalent in the reactions of the iBsu1103 model, with 64% of the reactions in the model involving at least one of these compounds.
Figure 2
Figure 2
Model optimization procedure results. The results are shown from the application of each step of the model optimization procedure to fit the iBsu1103 model to the 1,500 available experimental data-points. KO, knock out.
Figure 3
Figure 3
Classification of model reactions by function and behavior. (a) Reactions in the optimized iBsu1103 model are categorized into ten regions of the B. subtilis metabolism. Regions of metabolism involving a diverse set of substrates typically involve the greatest number of reactions. (b) The iBsu1103 reactions were also categorized according to their essentiality during minimal growth on Luria-Bertani (LB) media.
Figure 4
Figure 4
Comparison of iBsu1103 model to the Oh et al. model. (a) A detailed comparison of the iBsu1103 model and the Oh et al. model was performed to determine overlap of reactions, genes, annotations, and gene complexes between the two models. In the annotation comparison, only annotations involving the 818 overlapping reactions in the two models were compared; and each annotation consisted of a single reaction paired with a single gene. If two genes were mapped to a single reaction, this was treated as two separate annotations in this comparison. (b) The distribution of the 628 reactions that are exclusive to the iBsu1103 model among the metabolic pathways of the cell. Almost half of the exclusive reactions in the iBsu1103 model are involved in the Fatty Acids and Lipids pathway due to the unlumping of these reaction pathways in the iBsu1103 model.
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