Host Engineering

view profile for Aindrila Mukhopadhyay

Aindrila Mukhopadhyay

Vice President for Biofuels and Bioproducts, and Director of Host Engineering

view profile for Adam Feist

Adam Feist

Scientific Lead, Host Engineering

view profile for Deepanwita Banerjee

Deepanwita Banerjee

Post Doctoral Researcher

view profile for Thomas Eng

Thomas Eng

Research Scientist

view profile for Andrew Lau

Andrew Lau

Research Assistant

view profile for Anne Kakouridis

Anne Kakouridis

Post Doctoral Researcher

view profile for Ankita Kothari

Ankita Kothari

Project Scientist

view profile for Javier Menasalvas

Javier Menasalvas

Research Assistant

view profile for Aparajitha Srinivasan

Aparajitha Srinivasan

Post Doctoral Researcher

Microbes represent an inexhaustible source of beneficial chemicals and can use a range of carbon sources but, in their native state, most microbes only use a fraction of the carbon types and can 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 carbon utilization, 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 carbon utilization regimes, 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

  •  Dong J, Chen Y, Benites VT, Baidoo EE, Petzold CJ, Beller HR, Eudes A, Mukhopadhyay A, Singer SW* Methyl ketone production by Pseudomonas putida is enhanced by plant-derived amino acids, Biotech and Bioeng 2019 open access
  • Czamanski Nora L, Wehrs M, Kim J-H, Cheng J-F, Tarver A, Simmons BA, Magnuson J, Harmon-Smith M, Silva-Rocha R, Gladden JM, Mukhopadhyay A, Skerker JM*, Kirby J* A toolset of promoters for metabolic engineering of Rhodosporidium toruloides Microbial Cell Factories 2019 open access
  • Wehrs, M., Gladden JM, Liu Y, Platz L, Prahl J-P, Moon J, Papa G, Sundstrom E, Geiselman GM, Tanjore D, Keasling JD, Pray TR, Simmons BA Mukhopadhyay A* Sustainable bioproduction of the blue pigment indigoidine: Expanding the range of heterologous products in R. toruloides to include non-ribosomal peptides Green Chemistry 2019 open access
  • Wehrs M, Tanjore D, Eng T, Lievense J, Pray TR, Mukhopadhyay A* Engineering robust production microbes for large scale cultivation Trends in Microbiology 2019 open access
  • Sasaki Y, Eng T, Herbert RA, Trinh J, Chen Y, Rodriguez, A, Gladden, JM, Simmons BA, Petzold CJ, Mukhopadhyay, A* Engineering Corynebacterium glutamicum to produce the biogasoline isopentenol from plant biomass hydrolysates. Biotechnology for Biofuels. 2019 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