Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

doi:10.1186/1752-0509-3-38

BMC Systems Biology

Volume 3

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Research article

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

Anu Raghunathan¹^* , Jennifer Reed²^* , Sookil Shin¹ , Bernhard Palsson³ and Simon Daefler¹

¹Department of Infectious Diseases, Mount Sinai School of Medicine, New York, USA

²Department of Chemical and Biological Engineering, University of Wisconsin, Madison, USA

³Department of Bioengineering, University of California San Diego, San Diego, USA

author email corresponding author email* Contributed equally

BMC Systems Biology 2009, 3:38doi:10.1186/1752-0509-3-38


Published:	8 April 2009

Additional files

Additional file 1:

Salmonella metabolic network iRR1083. Gene-Protein-Reaction associations in the final version of the reconstruction iRR1083.

Format: XLS Size: 366KB Download file

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Additional file 2:

Cellular composition of S. typhimurium. Experimentally determined values for Salmonella cellular content of amino acids, carbohydrates, DNA, RNA, selected organic and inorganic compounds, and fatty acid composition of membrane and cell wall components.

Format: XLS Size: 27KB Download file

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Additional file 3:

Flux Variability Analysis. In silico reactome as determined by flux variability analysis (FVA).

Format: XLS Size: 217KB Download file

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Additional file 4:

Comparison of qualitative phenotyping (experimental vs in silico). Predictions for 163 possible carbon sources and 98 possible nitrogen sources were compared with experimental data.

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Additional file 5:

Gene essentiality comparison between E. coli and S. typhimurium. List of discrepancies in gene essentiality predictions between orthologs which are present in genome-scale models of S. typhimurium (iRR1083) and E. coli (iAF1261).

Format: XLS Size: 41KB Download file

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Additional file 6:

Media compositions used in silico for M9, LB and host cell environment. Carbohydrates, amino acids, vitamins, minerals, inorganic molecules, nucleotides, and amines used for in silico analysis.

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Additional file 7:

Salmonella serovars typhimurium, typhi, paratyphi, and enteritidis. List of genes present in serovar typhimurium and absent or non functional (pseudogenes) in serovars typhi, paratyphi and enteritidis.

Format: XLS Size: 24KB Download file

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Additional file 8:

Selected metabolic gene expression during infection of macrophages by Salmonella. Selected metabolic genes used for measuring gene expression or mRNA transcript levels in S. typhimurium extracted from macrophages post infection.

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Additional file 9:

Reconstruction of Salmonella metabolic network. Flow chart for reiterative model building for Salmonella network iRR1083.

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Additional file 10:

Primer Sequences. Primer Sequences used to measure gene expression or mRNA transcript levels of the chosen metabolic gene set described in S6 using GEXP.

Format: XLS Size: 50KB Download file

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