Highlighting Metabolic Strategies Using Network Analysis over Strain Optimization Results
The field of Metabolic Engineering has been growing, supported by the increase in the number of annotated genomes and genome-scale metabolic models. In silico strain optimization methods allow to create mutant strains able to overproduce certain metabolites of interest in Biotechnology. Thus, it is possible to reach (near-) optimal solutions, i.e. strains that provide the desired phenotype in computational phenotype simulations. However, the validation of the results involves understanding the strategies followed by these mutant strains to achieve the desired phenotype, studying the different use of reactions/ pathways by the mutants. This is quite complex given the size of the networks and the interactions between (sometimes distant) components. The manual verification and comparison of phenotypes is typically impossible.
Here, automatic methods are proposed to analyse large sets of mutant strains, by taking the phenotypes of a large number of possible solutions and identifying shared patterns, using methods from network topology analysis. The topological comparison between the networks provided by the wild type and mutant strains highlights the major changes that lead to successful mutants. The methods are applied to a case study considering E. coli and aiming at the production of succinate, optimizing the set of gene knockouts to apply to the wild type. Solutions provided by the use of Simulated Annealing and Evolutionary Algorithms are analyzed. The results show that these methods can help in the identification of the strategies leading to the overproduction of succinate.
KeywordsMetabolic Engineering Strain optimization Metabolic networks Network visualization
- 5.Lee, S.Y., Hong, S.H., Moon, S.Y.: In silico metabolic pathway analysis and design: succinic acid production by metabolically engineered escherichia coli as an example. Genome Informatics 13, 214–223 (2002)Google Scholar
- 6.Patil, K., Rocha, I., Forster, J., Nielsen, J.: Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 6(308) (2005)Google Scholar
- 7.Reed, J.L., Vo, T.D., Schilling, C.H., Palsson, B.O.: An expanded genome-scale model of escherichia coli k-12 (ijr904 gsm/gpr). Genome Biology 4(9), R54.1–R54.12 (2003)Google Scholar
- 8.Rocha, I., Maia, P., Evangelista, P., Vilaça, P., Soares, S., Pinto, J.P., Nielsen, J., Patil, K.R., Ferreira, E.C., Rocha, M.: Optflux: an open-source software platform for in silico metabolic engineering. BMC Systems Biology 4(45) (2010)Google Scholar
- 9.Rocha, M., Maia, P., Mendes, R., Pinto, J.P., Ferreira, E.C., Nielsen, J., Patil, K.R., Rocha, I.: Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinformatics 9 (2008)Google Scholar