Aindrila Mukhopadhyay

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

Research Focus

Dr. Mukhopadhyay is a Senior Scientist in the Biological Systems and Engineering Division at the Lawrence Berkeley National Laboratory in Berkeley, CA.  At JBEI, Dr. Mukhopadhyay is the Vice President of the Biofuels and Bioproducts Division and the Director of the Host Engineering group. She received a Masters in Chemistry from the Indian Institute of Technology, Mumbai, and a PhD in Organic Chemistry from the University of Chicago 

Her group develops tools to examine and engineer a variety of microbial platforms including P. putida, C. glutamicum, E. coli, R. toruloides, S. cerevisiae, and other microbial strains. Her group specifically focuses on developing robust strains that show high tolerance and productivity during biofuel and chemical production, and the optimization required to achieve scalability. Visit the M-group website for more on her group’s work.


  • Bacterial and Fungal Host Engineering: Develop tools to engineer model and non-model microbial strains. Improve strain tolerance to  biofuels and chemicals, as well as to process conditions. Optimize gene and pathway expression in production strains, and understand the bottlenecks to scalability and develop robust production systems. 
  • Systems Biology: Functional genomics approaches to examine tolerance, response, signaling and to develop synthetic biology tools for microbial systems.

Featured Media

Participation at the Nation Lab Day at the University of Toledo

Discussion on California Wildfire mitigation with CCST

Host Engineering team participates LBNL Pitch Competition 2019 and the Lab led DOE’s Energy I-Corps Training

Sustainable Blue Pigment production in a fungal host

From Bioenergy to Bioproducts: The Digest’s 2019 Multi-Slide Guide to JBEI

New Cas9-based Toolkit Eases Obstacles in Genetic Engineering

Berkeley Lab Scientists Brew Jet Fuel in One-Pot Recipe

frederix_mukhopadhyay - 768

KQED Quest Career Spotlight: Microbiologist

Tolerance Engineering boosts biogasoline production in bacteria


Women @ Energy: Aindrila Mukhopadhyay


Aindrila’s Mission: JBEI Scientist Sketches Her SF Neighborhood

Select Publications

Complete list from Google Scholar

  • Wehrs M, Tanjore D, Eng T, Lievense J, Pray TR, Mukhopadhyay A* Engineering robust production microbes for large scale cultivation Trends in Microbiology 2019 online
  • 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 online
  • Herbert RA, Eng T, Martinez U, Wang B, Langley S, Wan K, Pidatala V, Hoffman E, Chen JC, Bissell MJ, Brown JB, Mukhopadhyay A* Mortimer JC* Rhizobacteria mediate the phytotoxicity of a range of biorefinery‐relevant compounds. Environmental Toxicology and Chemistry 2019 online
  • 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 online
  • Jensen, H. M., Eng, T., Chubukov, V., Herbert, R. A. & Mukhopadhyay, A*. Improving membrane protein expression and function using genomic edits. npj Scientific Reports 2017. online
  • Frederix M, Mingardon F, Sun N, Pray T, Singh S, Simmons BA, Keasling JD, Mukhopadhyay A* Development of an E. coli strain for one-pot biofuel production from ionic liquid pretreated cellulose and switchgrass. Green Chemistry 2016 online
  • 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
  • Dunlop MJ, Dossani ZY, Szmidt HL, Chu HC, Lee TS, Keasling JD, Hadi MZ, Mukhopadhyay A*. Engineering microbial biofuel tolerance and export using efflux pumps. Mol Syst Biol. 2011 online
  • Rutherford BJ, Dahl R, Price R, Szmidt HL, Benke PI, Mukhopadhyay A*, and Keasling JD. Functional Genomic Study of Exogenous n-Butanol Stress in Escherichia coli. Appl Environ Microbiol. 2010 online
  • Mukhopadhyay A, Redding AM, Rutherford BJ, Keasling JD. Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotechnol. 2008 online

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