I am a Ph.D. scholar working at the intersection of synthetic biology, enzyme engineering, and metabolic bioprocessing, with a vision to develop scalable and sustainable microbial systems for bioproduction and environmental biotechnology. Below are my focused areas of research:
As part of my Ph.D. research, I have designed and developed a synthetic microbial consortium consisting of two engineered bacterial strains with complementary metabolic functions. The first strain was engineered to secrete a cellulase enzyme cocktail capable of degrading lignocellulosic biomass into fermentable glucose. The second strain was metabolically engineered to overproduce tyrosine via an optimized biosynthetic pathway. This design enables cross-feeding between the strains, where the glucose released by the cellulolytic strain serves as a carbon source for the tyrosine-producing strain.
To enhance coordination between the two strains, I implemented and optimized a Lux quorum sensing (QS) system, allowing dynamic regulation of gene expression in response to cell density. This system facilitates inter-strain communication and enables conditional activation of metabolic pathways in co-culture settings. The overall goal of this strategy is to achieve carbon-source independence and dynamic control over pathway activation, improving the robustness and scalability of microbial production systems.
Gupta, M, et al. 'Synthetic microbial consortia: modular regulation for enhanced metabolic flexibility' (manuscript under preparation)
In my doctoral research, I have explored novel strategies for efficient enzyme secretion and biocatalyst optimization in E. coli. I identified and experimentally validated a set of previously uncharacterized secretion signal peptides from the E. coli genome, benchmarking their performance against well-established secretion tags reported in the literature. These novel tags enabled high-level extracellular secretion of enzymes, which was rigorously confirmed through immunodetection assays.
To support modular and rapid screening of secretion signals, I developed a secretion toolkit based on Golden Gate Assembly, allowing one-pot cloning of enzymes with various secretion tags. This toolkit enables the combinatorial assembly and parallel testing of multiple signal peptides in a single reaction setup, accelerating the discovery of optimal secretion configurations for different enzymes.
Gupta, M, et al. 'Reprogramming E. coli for secretion of thermophilic cellulase cocktail for seawater-compatible lignocellulosic bioprocessing.' (manuscript under preparation)
Gupta, M, et al. 'Modular Secretion Toolkit for Escherichia coli Using Golden Gate Assembly with sfGFP Negative Selection .' (manuscript under preparation)
Additionally, in a collaborative project focused on enzyme replacement therapy (ERT), I engineered bioconjugatable enzymes by incorporating specific mutations. These modified enzymes were designed for downstream conjugation with targeting ligands or delivery systems, broadening the applicability of enzyme-based therapeutics for rare metabolic disorders
Padhy, A; Gupta, M, et al. 'Lysosome Specific Delivery of β-glucosidase Enzyme using Protein-glycopolypeptide Conjugate via Protein Engineering and Bioconjugation.' Bioconjugate Chemistry https://doi.org/10.1021/acs.bioconjchem.4c00430
To enable real-time monitoring and better understanding of glucose metabolism and production in microbial systems, I developed a whole-cell glucose biosensor leveraging a CRISPR-dCas9-based transcriptional inverter. This biosensor employs a glucose-sensitive promoter, which is inverted using dCas9 to produce a measurable fluorescent or reporter output correlated directly with glucose levels.
I demonstrated the utility of this biosensor in both monoculture and co-culture systems, particularly in cellulose-degrading consortia, allowing dynamic tracking of glucose release and consumption in complex microbial communities. This tool provides a powerful platform for optimizing metabolic pathways and enhancing bioprocess control in synthetic biology applications.
Gupta, M, Das A, Datta S. et al. 'Engineering a Glucose-Responsive Whole-Cell Biosensor via CRISPR-dCas9-Mediated Modulation of the cap Promoter in E. coli .' (manuscript under preparation)
My research focuses on developing robust methods for enzyme immobilization on solid supports to enhance stability under ambient and harsh conditions, thereby enabling sustainable and recyclable biocatalysis. In collaboration with Prof. Rahul Banerjee’s group, we synthesized and characterized three distinct covalent organic frameworks (COFs), including a novel COF foam, specifically designed for enzyme immobilization. One of these materials facilitates direct purification of enzymes from crude cell lysates, streamlining downstream processing by combining purification and immobilization in a single step.
The other two COFs were engineered to improve enzyme stability and catalytic performance during repeated biotransformations. To elucidate the molecular interactions between the enzymes and the COF matrices, we employed advanced characterization techniques such as Fourier-transform infrared spectroscopy (FTIR), nanoscale FTIR (nanoFTIR), solid-state NMR (ssNMR) including ¹H double quantum–¹H single quantum (DQ–SQ) homonuclear NMR experiments, and scattering-type scanning near-field optical microscopy (s-SNOM). These high-resolution analytical methods, conducted in collaboration with researchers from the University of Oxford and JEOL (Japan), enabled spatial mapping and confirmation of enzyme distribution within the COF frameworks at the nanoscale.
Additionally, I developed a novel nanoparticle-based method for the direct purification of extracellular enzymes from culture media, which can be integrated seamlessly into heterogeneous biocatalysis workflows. This approach enhances enzyme recovery efficiency and facilitates enzyme reuse, advancing green and cost-effective bioprocess technologies.
Paul, S# ; Gupta, M# . et al. (2023), 'Covalent Organic Frameworks for the Purification of Recombinant Enzymes and Heterogeneous Biocatalysis,' Journal of the American Chemical Society (JACS), 146(1), pp. 858–867. https://doi.org/10.1021/jacs.3c11169. (# Contributed equally)
Paul, S., Gupta, M., Dey, K., et al. (2023), 'Hierarchical covalent organic framework-foam for multi-enzyme tandem catalysis,' Chemical Science, 14(24), pp. 6643–6653. https://doi.org/10.1039/d3sc01367g.
Gupta, M. et al., (2025), Heterogeneous biocatalysis by magnetic nanoparticle immobilized biomass-degrading enzymes derived from microbial cultures.' JMC B https://doi.org/10.1039/D4TB02011A
Paul, S#; Gupta M#. et al. 'Coprecipitation of Enzyme-Encapsulated Covalent Organic Framework for Biocatalysis.' Journal of the American Chemical Society (JACS) https://doi.org/10.1021/jacs.5c05496 (Just Accepted) (# Contributed equally)
Together, my research integrates cutting-edge synthetic biology, enzyme engineering, and advanced biocatalysis to develop innovative microbial systems and biotechnologies with real-world applications. By combining molecular design, dynamic control, and novel materials, I aim to contribute to sustainable solutions in biomanufacturing, environmental remediation, and healthcare. I am passionate about translating fundamental research into practical technologies that address global challenges.