Comparisons of Shewanella strains based on genome annotations, modeling, and experiments
Ong, Wai Kit
Vu, Trang T.
Lovendahl, Klaus N.
Llull, Jenna M.
Serres, Margrethe H.
Romine, Margaret F.
Reed, Jennifer L.
MetadataShow full item record
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 an attractive bacterial target for research in bioremediation and microbial fuel cell applications. Constraint-based modeling is a useful tool for helping researchers gain insights into the metabolic capabilities of these bacteria. However, Shewanella oneidensis MR-1 is the only strain with a genome-scale metabolic model constructed out of 21 sequenced Shewanella strains. In this work, we updated the model for Shewanella oneidensis MR-1 and constructed metabolic models for three other strains, namely Shewanella sp. MR-4, Shewanella sp. W3-18-1, and Shewanella denitrificans OS217 which span the genus based on the number of genes lost in comparison to MR-1. We also constructed a Shewanella core model that contains the genes shared by all 21 sequenced strains and a few non-conserved genes associated with essential reactions. 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 the MR-1 model is most similar to the W3-18-1 model, followed by the MR-4 and OS217 models when considering predicted growth phenotypes. However, a cluster analysis done based on metabolic gene content revealed that the MR-4 and W3-18-1 models are the most similar, with the MR-1 and OS217 models being more distinct from these latter two strains. As a second level of comparison, we identified differences in reaction and gene content which give rise to different functional predictions of single and double gene knockout mutants using Comparison of Networks by Gene Alignment (CONGA). Here, we showed how CONGA can be used to find biomass, metabolic, and genetic differences between models. We developed four strain-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 biotechnology applications.
© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Systems Biology 8 (2014): 31, doi:10.1186/1752-0509-8-31.
Suggested CitationArticle: Ong, Wai Kit, Vu, Trang T., Lovendahl, Klaus N., Llull, Jenna M., Serres, Margrethe H., Romine, Margaret F., Reed, Jennifer L., "Comparisons of Shewanella strains based on genome annotations, modeling, and experiments", BMC Systems Biology 8 (2014): 31, DOI:10.1186/1752-0509-8-31, https://hdl.handle.net/1912/6685
The following license files are associated with this item:
Showing items related by title, author, creator and subject.
Cohesive and mixed sediment in the Regional Ocean Modeling System (ROMS v3.6) implemented in the Coupled Ocean–Atmosphere–Wave–Sediment Transport Modeling System (COAWST r1234) Sherwood, Christopher R.; Aretxabaleta, Alfredo L.; Harris, Courtney K.; Rinehimer, J. Paul; Verney, Romaric; Ferré, Bénédicte (Copernicus Publications on behalf of the European Geosciences Union, 2018-05-14)We describe and demonstrate algorithms for treating cohesive and mixed sediment that have been added to the Regional Ocean Modeling System (ROMS version 3.6), as implemented in the Coupled Ocean–Atmosphere–Wave–Sediment ...
Sediment transport model including short-lived radioisotopes: Model description and idealized test cases Birchler, Justin J.; Harris, Courtney K.; Sherwood, Christopher R.; Kniskern, Tara A. (American Meteorological Society, 2018-11-27)Geochronologies derived from sediment cores in coastal locations are often used to infer event bed characteristics such as deposit thicknesses and accumulation rates. Such studies commonly use naturally occurring, short-lived ...
Model behavior and sensitivity in an application of the Cohesive Bed Component of the Community Sediment Transport Modeling System for the York River estuary, VA, USA Fall, Kelsey A.; Harris, Courtney K.; Friedrichs, Carl T.; Rinehimer, J. Paul; Sherwood, Christopher R. (MDPI AG, 2014-05-19)The Community Sediment Transport Modeling System (CSTMS) cohesive bed sub-model that accounts for erosion, deposition, consolidation, and swelling was implemented in a three-dimensional domain to represent the York River ...