Thermodynamic Framework for Mutant Phenotype Prediction
- Conference: Conference on Constraint-Based Reconstruction and Analysis (COBRA)
- Year: 2018
- Proceeding: 5th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2018)
- Group: General Submissions
Tuesday, October 16, 2018 - 4:25pm-4:50pm
Previous mutant prediction algorithms have essentially two components: (1) a metric to characterize the cellâs desired metabolic state (for example flux or gene expression profiles) and (2) a metric to describe the distance from the desired state (for example, Euclidean distance). The mutant flux profile is then computed as the closest possible to the wild type state subject to the constraints of genetic or environmental perturbations. Different algorithms have reported significant gains in accuracy by tweaking the definitions of the two metrics.
To further improve the fidelity of knockout predictions and subsequent computational strain design, we developed a thermodynamics-based method, RElative MEtabolite Patterns (REMEP). REMEP hypothesizes that the optimum metabolic state is reflected in the energetic requirements to sustain flux through each metabolite node, and thus cell fluxomes adapt to perturbations from a reference state by preserving relative pattern of metabolite energy flows. REMEP performs better than comparable algorithms across different experimental datasets for E. coli and S. cerevisiae (in terms of lower root mean square errors and higher Pearsonâs correlation coefficients). These improvements support the REMEP assumption that cellular mechanisms of response to genetic and environmental perturbations leaves signatures that can be inferred from thermodynamics-derived metabolite patterns. The findings provide a new paradigm for genotype to phenotype mapping and insights into microbial flux network plasticity.