Host Engineering

Microbes represent an inexhaustible source of beneficial chemicals but, in their native state, most microbes produce only small quantities of these molecules. This is an important constraint to be overcome in the production of biofuels and commodity chemicals. Researchers in the Host Engineering Group use genomics and synthetic biology to optimize the production of desired molecules in engineered microbes. Their goals are to develop microbes that can accumulate high levels of fuel products, tolerate inhibitory pretreatment byproducts and consume all forms of carbon in the biomass.


  • Bacterial hosts (P. putida, E. coli, C. glutamicum): Discovery and optimization of tolerance mechanisms for biomass-related inhibitors and final products to generate robust, scalable production platforms
  • Fungal hosts (R. toruloides, S. cerevisiae): Development of new tools and strategies to enable sophisticated strain engineering

Featured Media

Featured Publications

  • Jensen, H. M., Eng, T., Chubukov, V., Herbert, R. A. & Mukhopadhyay, A*. Improving membrane protein expression and function using genomic edits. Nature Scientific Reports 2017. open access
  • Chubukov V, Desmarais JJ, Wang G, Chan LJG, Baidoo EEK, Petzold CJ, Keasling JD, Mukhopadhyay A* Engineering glucose metabolism of Escherichia coli under nitrogen starvation. Nature Systems Biology and Applications 2017 open access
  • Reider Apel A, d’Espaux L, Wehrs M, Sachs D, Li R, Tong G, Garber M, Nnadi O, Zhuang W, Hillson N, Keasling JD, Mukhopadhyay, A* A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae NAR 2016 open access
  • Frederix M, Mingardon F, Sun N, Pray T, Singh S, Simmons BA, Keasling JD, Mukhopadhyay A* Development of an coli strain for one-pot biofuel production from ionic liquid pretreated cellulose and switchgrass. Green Chemistry 2016 open access
  • Chubukov V, Mukhopadhyay A, Petzold CJ, Keasling JD, Garcia-Martín HG * Synthetic and systems biology for microbial production of commodity chemicals, Nature Systems Biology and Applications 2016 open access
  • Reider-Apel, Ouellet M, Szmidt-Middleton H, Keasling JD, Mukhopadhyay A*, Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae Nature. Sci Rep 2016 open access
  • Chubukov V, Mingardon F, Schackwitz W, Baidoo EEK, Alonso-Gutierrez J, Hu Q, Lee TS, Keasling JD, MukhopadhyayA* Acute limonene toxicity in Escherichia coli is caused by limonene-hydroperoxide and alleviated by a point mutation in alkyl hydroperoxidase (AhpC) AEM 2015 online
  • Mingardon F, Clement C, Hirano K, Nhan M, Luning EG, Chanal A, Mukhopadhyay A* Improving olefin tolerance and production in E. coli using native and evolved AcrB. Biotechnology and Bioengineering. 2015 online
  • Foo JL, Jensen HM, Dahl RH, George K, Keasling JD, Lee TS,Leong SSJ, Mukhopadhyay A*. Improving microbial bio-gasoline production in Escherichia coli using tolerance engineering. mBio 2014 online
  • Engineering microbial biofuel tolerance and export using efflux pumps, Mol Syst Biol. (2011). online
  • Rutherford BJ, Dahl R, Price R, Szmidt HM,  Benke PI, Mukhopadhyay A*, and  Keasling JD. Functional Genomic Study of Exogenous n-Butanol Stress in Escherichia coli. Appl Environ Microbiol. 2010 online