About This Project
We will engineer synthetic enzymes, metabolic pathways, and microbial hosts capable of removing methane from various distributed sources, particularly in oxygen-limited environments.
Ask the Scientists
Join The DiscussionMotivating Factor
Global methane emissions exceed 600 million metric tons annually, posing a significant threat to climate stability. As a potent greenhouse gas with 83-fold greater warming capacity than CO2 over a 20-year period, methane demands urgent attention [1]. The challenge lies in its distributed emission pattern—remote oil and gas operations, agricultural activities, and landfills release methane at low concentrations without economic incentives for capture [2]. At just 2 ppm in the atmosphere, methane is too dilute for cost-effective direct air capture. This combination of distributed sources, low concentration, and lack of economic drivers has created a technological gap, with no effective strategies currently available to capture and valorize methane from either these remote point sources or the atmosphere itself.
Specific Bottleneck
Biological methane conversion holds promise for distributed, low-concentration sources, yet current enzymatic approaches face several limitations. Methane monooxygenase (MMO) requires oxygen as a co-substrate, rendering it ineffective in oxygen-limited, methane-rich environments such as landfills. Moreover, attempts at heterologous MMO expression have yielded minimal success due to its complex folding requirements and chaperone dependencies [3]. The oxygen-independent alternative, methyl-coenzyme M reductase (MCR), faces its own challenges: thermodynamic constraints require high methane pressure and lead to slow growth rates and poor yields. Additionally, MCR's reliance on specialized cofactors exclusive to methanogenic archaea creates significant barriers to heterologous expression [4].
Actionable Goals
Development of an effective solution requires an oxygen-independent methane-activating enzyme that functions efficiently at low methane concentrations, uses common cellular cofactors and substrates, and can be expressed functionally in diverse microbial hosts found in soil and marine environments. Methylsuccinate synthase (MSS) presents a promising oxygen-independent, new-to-nature approach for methane activation and removal. MSS activates methane via glycyl radical activation in a thermodynamically favorable reaction [5]. Functional expression of a closely related variant of this enzyme in Escherichia coli has been achieved without additional chaperone proteins [6]. Upon identification of MSS and downstream metabolic pathways for biomass and energy generation, these pathways can be deployed to various soil and ocean bacteria for effective greenhouse gas removal in natural environments.
Budget
It will cover expenses such as graduate student salary, consumables, and equipment.
Meet the Team
Affiliates
Team Bio
Allen and Ari first connected through a collaboration between the Gonzalez lab and Erb lab during their PhD. While pursuing different research angles on synthetic one-carbon utilization pathways, they developed distinct yet complementary areas of expertise. This project represents an exciting opportunity for them to combine their specialized knowledge, potentially yielding transformative discoveries in enzymatic methane removal and utilization technologies.
Seung Hwan "Allen" Lee
Seung Hwan "Allen" Lee is a Postdoctoral Associate in the Gregory Stephanopoulos Research Group at the Massachusetts Institute of Technology. His passion for engineering microorganisms to enable sustainable energy and chemical production began during his undergraduate research at UCLA under Prof. James Liao. After completing his undergraduate studies, he earned his Ph.D. in Chemical and Biomolecular Engineering from Rice University, where he worked under the guidance of Prof. Ramon Gonzalez. His undergraduate and doctoral research focused on the efficient biological utilization of one-carbon (C1) compounds through engineering native and synthetic metabolic pathways. As one of the co-inventors of the Formyl-CoA Elongation (FORCE) pathways, he helped develop a novel approach for converting C1 feedstock into value-added small molecules. In his postdoctoral work, he has expanded his research to include engineering non-model organisms, leveraging their inherent abilities to efficiently utilize C1 and C2 feedstocks. Beyond his research, Allen is actively engaged in biotechnology and climate technology communities, participating in organizations such as the Society for Industrial Microbiology and Biotechnology (SIMB), the Engineering Biology Research Consortium (EBRC), and the MIT Energy Conference.
Allen's previous publications (Google Scholar)
Ari Satanowski
Ari Satanowski is a Postdoctoral Fellow at The Francis Crick Institute in London, where he has joined the Biodesign Lab lead by Erika DeBenedictis. He works on developing phage-assisted continuous evolution (PACE) methods for metabolic enzymes and sustainable bioproduction.
Ari earned his PhD at the Max Planck Society in Germany under the guidance of Prof. Tobias Erb and Dr. Arren Bar-Even. His PhD research focussed on the design and demonstration of new-to-nature metabolic pathways for utilization of CO2 and one-carbon compounds. Ari remains interested in the question how to engineer such pathways most effectively inside living microbes, and aims to apply rapid, high-throughput evolution techniques to speed up this development.
The project we propose here for the "Garden Grants" will tie in well with ongoing work at the Biodesign Lab, taking advantage of recent methods developed by Ari and other team members, including the directed evolution of biosensors and metabolic enzymes. Ari will be able to tap into the pool of instruments, genetic resources, and technical expertise available in the group, most importantly for phage- and robotics-assisted evolution (PRANCE) on an automated liquid handling platform.
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