Ab Initio Whole Cell Kinetic Models of Escherichia coli BL21 (ebeTBSW25) and MG1655 (ecoMAL25) - mauriceling/mauriceling.github.io GitHub Wiki

Citation: Wong, TBS, Le, MA, Arivazhagan, M, Senthilkumar, A, Yeo, KY, Saisudhanbabu, T, Lukianto, VR, Ling, MHT. 2025. Ab Initio Whole Cell Kinetic Models of Escherichia coli BL21 (ebeTBSW25) and MG1655 (ecoMAL25). Scholastic Medical Sciences 3(2): 01-04.

Link to [PDF].

Here is the permanent [PDF] and ecoMAL25.zip and ebeTBSW25.zip links to my archive.

Escherichia coli is a well-studied organism and has been metabolic engineering for wide variety of chemical production. Mathematical models are useful tools in this endeavour as they can guide engineering approaches. Such models can be classified primarily into genome-scale models (GSMs) or kinetic models (KMs). Over the years, several GSMs have been developed but only 1 KM (ecoJC20) has been developed for E. coli. KM ecoJC20 is only about 19-24% the number of reactions compared to notable E. coli GSMs, as it is an adaptation of a generic cell KM of the same size. This study aims to construct larger whole cell kinetic models of E. coli MG1655 and BL21 using previously described ab initio approach via annotated genomes. The result is 2 simulatable whole cell kinetic models of E. coli – one for BL21 strain, ebeTBSW25, which consists of 1624 metabolites and 2340 enzymatic reactions; and another for MG1655 strain, ecoMAL25, which consists of 1801 metabolites and 3012 enzymatic reactions. The number of reactions and metabolites in both ebeTBSW25 and ecoMAL25 are substantially larger than ecoJC20 and within the range of existing GSMs.