Table 1

Examples of nonnative metabolites for which our algorithm detected heterologous reactions matching those of previous studies
Compound (synonym separated by a semicolon) KEGG ID Heterologous reaction(s) from the literature Reference Evaluation ofin silicodesign
Isoprene; 2-methyl-1,3-butadiene C16521 Introduced ispS gene from Populus nigra to Escherichia coli [47] Identical reaction found in E. coli and in Saccharomyces cerevisiae and Cerevisiae glutamicum as the host
α-Farnesene C09665 Introduced farnesene synthase from plant to E. coli [13] Identical reaction found in E. coli and in S. cerevisiae and C. glutamicum as the host
Poly-β-hydroxybutyrate; PHB C06143 Introduced phbC and phbB from Streptomyces aureofaciens to E. coli [48] Identical reaction found in E. coli and in S. cerevisiae and C. glutamicum as the host
Cadaverine; 1,5-pentanediamine; 1,5-diaminopentane C01672 Introduced ldcC from E. coli to C. glutamicum [35,49] Identical reaction found in C. glutamicum and in S. cerevisiae as the host
Amorpha-4,11-diene C16028 Introduced AMS1 from the plant Artemisia annua L. to E. coli [50,51] Identical reaction found in E. coli and S. cerevisiae and in C. glutamicum as the host
Propane-1,3-diol; 1,3propanediol; trimethylene glycol C02457 Introduced glycerol dehydratase and 1,3-propanediol oxidoreductase from Klebsiella pneumonia to E. coli. [52,53] Identical reaction found in E. coli and in S. cerevisiae as the host
Ethanol; ethyl alcohol; methylcarbinol C00469 Introduced pyruvate decarboxylase and alcohol dehydrogenase genes from Zymomonas mobilis to C. glutamicum [54] Identical reaction found in C. glutamicum as the host
(R,R)-Butane-2,3-diol; (R,R)-2,3-Butanediol; (R,R)-2,3-Butylene glycol C03044 Introduced acetolactate decarboxylase and butanediol dehydrogenase genes to E. coli [55] Identical reaction found in E. coli as the host
(R)-Propane-1,2-diol; (R)-1,2-propanediol; (R)-propylene glycol C02912 Introduced glycerol dehydrogenase gene from Klebsiella pneumonia and used aldehyde dehydrogenase to produce product in E. coli [56] Alternative pathway found to produce target by adding methylglyoxal reductase and lactaldehyde reductase to E. coli
Introduced glycerol dehydrogenase and methylglyoxal synthase genes from E. coli to S. cerevisiae [57] Alternative pathway found to produce target by adding methylglyoxal reductase and lactaldehyde reductase to S. cerevisiae
Itaconate; itaconic acid; methylenesuccinic acid C00490 No information NA EC 4.2.1.4-citrate dehydratase and EC 4.1.1.6-aconitate decarboxylase were found to be added to E. coli as the host.
cis,cis-Muconate;cis,cis-hexadienedioate;cis,cis-2,4-hexadienedioic acid C02480 Introduced aroZ, aroY, and catA to E. coli [58] Alternative pathways from antharnilate or 2,3-dihydroxybenzoate to produce catechol, which is a substrate for cis,cis-muconate production
Adipate; adipic acid; hexanedioate; hexan-1,6-dicarboxylate C06104 Introduced aroZ, aroY, and catA to E. coli for producing cis,cis- muconate and then convert to adipic acid by chemical synthesis [58] Alternative pathway found to produce the target by adding 5 heterologous reactions to E. coli or C. glutamicum as the hosts (see Additional files 5 and 6 for enzyme information)

Chatsurachai et al.

Chatsurachai et al. BMC Bioinformatics 2012 13:93   doi:10.1186/1471-2105-13-93

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