Aindrila Mukhopadhyay

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.

Projects

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 extra-metabolic features to develop synthetic biology tools for microbial systems.

Featured Media

Biosensor-driven strain engineering reveals key cellular processes for maximizing isoprenol production in Pseudomonas putida

Mukhopadhyay Elected American Academy of Microbiology Fellow

The Future of Sustainable Biomanufacturing is Microscopic Factories

C&EN: Carbenes created in a cell

Discussion on California Wildfire mitigation with CCST

New Cas9-based Toolkit Eases Obstacles in Genetic Engineering

Berkeley Lab Scientists Brew Jet Fuel in One-Pot Recipe

KQED Quest Career Spotlight: Microbiologist

Tolerance Engineering boosts biogasoline production in bacteria

Aindrila’s Mission: JBEI Scientist Sketches Her SF Neighborhood

Select Publications

Complete list from Google Scholar

Menasalvas J, Kulakowski S, Chen Y, Gin JW, Akyuz Turumtay E, Baral NR, Apolonio MA, Rivier A, Yunus IS, Garber ME, Scown CD, Adams PD, Lee TS, Blaby IK, Baidoo EEK, Petzold CJ, Eng T, Mukhopadhyay* Biosensor-driven strain engineering reveals key cellular processes for maximizing isoprenol production in Pseudomonas putida. Science Advances 2025 online
de Siqueira GMV, Eng T, Mukhopadhyay A*, Guazzaroni M-E. Differences in GenBank and RefSeq annotations may affect genomics data interpretation for Pseudomonas putida KT2440. mSphere 2025 online
Baral NR, Banerjee D, Eng T, Simmons BA, Mukhopadhyay A*, Scown CD Microbial Pathways for Cost-Effective Low-Carbon Renewable Indigoidine. ACS Sustainable Chemistry & Engineering 2025 online
Eng T, Banerjee D, Menasalvas J, Chen Y, Gin J, Choudhary H, Baidoo E, Chen JH, Ekman A, Kakumanu R, Diercks YL, Codik A, Larabell C, Gladden J, Simmons BA, Keasling JD, Petzold CJ, Mukhopadhyay A* Maximizing microbial bioproduction from sustainable carbon sources using iterative systems engineering. Cell Reports 2023 online
Huang J, Quest A, Cruz-Morales P, Deng K, Pereira J, Van Cura D, Kakumanu R, Baidoo E, Dan Q, Chen Y, Petzold C, Northen T, Adams P, Clark D, Balskus E, Hartwig J, Mukhopadhyay A*, Keasling J Complete integration of carbene-transfer chemistry into biosynthesis. Nature 2023 online
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