(547g) Comparative Modeling of Metabolism Across the Shewanella Genus

Shewanella is a genus of facultatively anaerobic, Gram-negative bacteria that have highly adaptable metabolism which allows them to thrive in diverse environments. This quality makes them attractive target bacteria for research in bioremediation, biofuel production, and microbial fuel cell applications. Constraint-based modeling is a useful tool for helping researchers gain insights into the metabolic capabilities of these bacteria. While the genomes for 22 Shewanella species have been sequenced, Shewanella oneidensis (MR-1) is the only species with a genome-scale metabolic model constructed [1]. In this work, we updated the MR-1 model based on experimental evidence of certain pathways. We also constructed metabolic models for three other species, namely Shewanella sp. MR-4, Shewanella sp. W3-18-1, and Shewanella denitrificans (Sden) which span the genus based on the number of shared genes. We also constructed a core Shewanella model which consists only of the genes shared by all 22 sequenced species. Model comparisons between the five constructed models were done at two levels – for wildtype strains under different growth conditions and for knockout mutants under the same growth condition. In the first level, growth/no-growth phenotypes were predicted by the models on various carbon sources and electron acceptors. Cluster analysis of these results revealed that MR-1 is most similar to W3-18-1, followed by MR-4 and Sden when considering growth phenotypes. However, a cluster analysis done based on gene content revealed that MR-1 is more similar to MR-4, followed by W3-18-1 and Sden. As a second level of comparison, we identified differences in reactions and gene content which give rise to different functional predictions of single gene knockout mutants using CONGA [2]. Here, we showed how CONGA can be used to find metabolic reaction and gene differences between models. In conclusion, we have developed four species-specific models and a general core model that can be used to do various in silico studies of Shewanella metabolism. The developed models provide a platform for a systematic investigation of Shewanella metabolism to aid researchers using Shewanella in various applications.

1.  Pinchuk GE, Hill EA, Geydebrekht OV, De Ingeniis J, Zhang X, et al. (2010) Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: A Tool for Data Analysis and Hypothesis Generation. PLoS Comput Biol 6(6): e1000822. doi:10.1371/journal.pcbi.1000822

2.  Hamilton JJ, Reed JL (2012) Identification of Functional Differences in Metabolic Networks Using Comparative Genomics and Constraint-Based Models. PLoS ONE 7(4): e34670. doi:10.1371/journal.pone.0034670