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Table 2 Computational and experimental minimal media

From: Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation

Computational

Experimental

 

proline OR arginine OR glutamate OR alanine OR

alanine

amino acids

aspartate OR glycine OR ornithine OR serine OR

glycine

 

threonine

isoleucine

 
 

arginine

 
 

valine

 
 

proline

 

cytidine OR cytosine OR uridine OR uracil

 

nucleotides

phosphate

phosphate

cofactors, ions, etc.

sulfate

sulfate

 

nicotinamide OR nicotinate

nicotinamide OR nicotinate

 

iron

iron? (disagreement in literature)

 

oxygen OR ((nitrate OR nitrite) AND protoheme)

oxygen assumed

 

thiamin

thiamin

 
 

biotin

 
 

calcium pantothenate

 
 

ammonium

 

glucose

glucose

carbon source

  1. The computed and experimentally determined minimal media for growth of S. aureus compare reasonably well. The most noticeable difference is the amino acid requirement, which can be attributed to regulation, as detailed in the text. The boolean statements (AND/OR) are standard; for example, there are three terminal electron acceptors that can be members of the computational minimal medium, o2, no3, and no2, but both no3 and no2 also require the presence of pheme. The absence of an explicit logic statement between lines is equivalent to using AND; for example, all 6 amino acids listed are required together in the experimental minimal medium.