Supplementary Table 2: Common issues encountered during metabolic network reconstruction

Adam M. Feist, Markus J. Herrgard, Ines Thiele, Jennie L. Reed, Bernhard Ø. Palsson "Reconstruction of Biochemical Networks in Microbial Organisms", Under Review

Supplementary Table 1 - Supplementary Table 1 Available predictive genome-scale metabolic network reconstructions

Issue Common Solutions Example
Reaction directionality is unknown Compute thermodynamic reversibility estimates Thermodynamic consistency analysis performed for E. coli reconstruction iAF1260(Feist, Henry et al. 2007).
Proton translocation stoichiometry information missing for an enzyme or pathway. Determine the translocation efficiencies for individual reactions or the overall pathway through primary literature search or experimental investigation. The apparent P/O ratio for E. coli and individual enzyme translocation efficiencies were determined by simultaneously examining oxygen and phosphate consumption rates of respirating cells(Noguchi, Nakai et al. 2004).
Missing conversion in a pathway between gene-associated reactions 1. Biochemically determine if the reaction occurs in the organism from either primary literature or experimental assay 
2. Utilize a gap-filling algorithm to find the most likely candidate reaction and/or encoding gene		 Network topology-based gap-filling algorithms(Kharchenko, Vitkup et al. 2004; Chen and Vitkup 2006; Kharchenko, Chen et al. 2006) were used to generate tentative ORF assignments that were further investigated through biochemical characterization studies utilizing genetic mutants to characterize and assign function to an encoding gene(Fuhrer, Chen et al. 2007).
Maintenance energies necessary to account for non-metabolic activity is unknown. Compute maintenance values through simulation by examining uptake, production, and growth rates under the desired growth condition. Maintenance costs (ATP equivalents) were determined for Lactobacillus plantarum from fermentation data at different growth rates(Teusink, Wiersma et al. 2006).
Cofactor specificity for an enzyme 1. Utilize cofactor specificity from a closely related organism 
2. Biochemically characterize the gene product in your strain through experimental analysis		 The first enzyme in the de novo biosynthesis of NAD uses oxygen or fumarate as a co-substrate in most bacteria and many archaea (a FAD-dependent enzyme, e.g., NadB in E. coli). In Thermotoga maritima and methanogenic archaea, this same step converting aspartate to imminoaspartate is replaced by a non-homologous NAD-dependent enzyme(Yang, Savchenko et al. 2003).

References

Chen, L. and D. Vitkup (2006). "Predicting genes for orphan metabolic activities using phylogenetic profiles." Genome Biol 7(2): R17.

Feist, A. M., C. S. Henry, et al. (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3(121).

Fuhrer, T., L. Chen, et al. (2007). "Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli." J Bacteriol.

Kharchenko, P., L. Chen, et al. (2006). "Identifying metabolic enzymes with multiple types of association evidence." BMC Bioinformatics 7(177).

Kharchenko, P., D. Vitkup, et al. (2004). "Filling gaps in a metabolic network using expression information." Bioinformatics 20 Suppl 1: I178-I185.

Noguchi, Y., Y. Nakai, et al. (2004). "The energetic conversion competence of Escherichia coli during aerobic respiration studied by 31P NMR using a circulating fermentation system." J Biochem (Tokyo) 136(4): 509-15.

Teusink, B., A. Wiersma, et al. (2006). "Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model." J Biol Chem 281(52): 40041-8.

Yang, Z., A. Savchenko, et al. (2003). "Aspartate dehydrogenase, a novel enzyme identified from structural and functional studies of TM1643." J Biol Chem 278(10): 8804-8.