Computer-assisted engineering of the synthetic pathway for biodegradation of a toxic persistent pollutant

Nagendra Prasad Kurumbang, Pavel Dvorak, Jaroslav Bendl, Jan Brezovsky, Zbynek Prokop, Jiri Damborsky

Research output: Contribution to journalArticlepeer-review

34 Scopus citations


Anthropogenic halogenated compounds were unknown to nature until the industrial revolution, and microorganisms have not had sufficient time to evolve enzymes for their degradation. The lack of efficient enzymes and natural pathways can be addressed through a combination of protein and metabolic engineering. We have assembled a synthetic route for conversion of the highly toxic and recalcitrant 1,2,3-trichloropropane to glycerol in Escherichia coli, and used it for a systematic study of pathway bottlenecks. Optimal ratios of enzymes for the maximal production of glycerol, and minimal toxicity of metabolites were predicted using a mathematical model. The strains containing the expected optimal ratios of enzymes were constructed and characterized for their viability and degradation efficiency. Excellent agreement between predicted and experimental data was observed. The validated model was used to quantitatively describe the kinetic limitations of currently available enzyme variants and predict improvements required for further pathway optimization. This highlights the potential of forward engineering of microorganisms for the degradation of toxic anthropogenic compounds.

Original languageEnglish
Pages (from-to)172-181
Number of pages10
JournalACS Synthetic Biology
Issue number3
StatePublished - 21 Mar 2014
Externally publishedYes


  • activity
  • enantioselectivity
  • kinetic modeling
  • protein and metabolic engineering
  • synthetic pathway
  • toxicity


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