Enhanced carbon fixation in plants by engineering a novel carbon concentrating mechanism

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About This Project

To mitigate climate change, this proposal aims to enhance CO2 removal efficiency of C3 plants by engineering carbon concentrating mechanisms through a deep learning, molecular modeling, and experimental approach. The goal is to design proteins that optimize the efficacy of Rubisco and carbonic anhydrase enzymes. The project represents a new framework to design carbon concentrating mechanisms.

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What is the context of this research?

Successful climate change mitigation through net-zero carbon strategies requires gigatons of CO2 removed per year. To achieve this goal, a minimum of 100-fold increase in CO2 removal efficiency compared to present technologies is required. Plants are a natural, biological avenue for carbon capture and utilization as they remove CO2 through photosynthesis. Rubisco, the carbon fixing enzyme, is the most abundant protein on Earth; however, it is a slow and inefficient enzyme because 1 of every 4 turnovers uses O2 instead of CO2. Despite numerous attempts to engineer Rubisco itself to improve both the turnover rate (speed) and selectivity, it seems that humanity cannot outdo evolution. Other approaches to increase the productivity of Rubisco are needed to increase the rate of carbon fixation.

What is the significance of this project?

Photosynthetic organisms, including cyanobacteria and algae, have evolved to thrive under low-CO2 conditions through carbon concentrating mechanisms (CCMs). Prior efforts to improve the carbon utilization by plants have focused on transplanting the CCM machinery from either cyanobacteria or algae into plants. These studies have demonstrated that it is possible to express non-native CCM proteins, such as Rubisco from algae, but significant strides are still needed to improve carbon fixation efficacy. An alternate approach is to engineer CCM-inspired proteins that are adapted specifically to C3 plant Rubisco and carbonic anhydrase (CA), which is another critical enzyme involved in CCM. In doing so, it is likely that CCM can be synthetically induced in plants for improved CO2 fixation.

What are the goals of the project?

The vision is to reduce accidental fixation of O2 instead of CO2 by Rubisco, a process known as photorespiration, using protein engineering strategies inspired by aquatic single-cell organisms, such as algae and cyanobacteria, to concentrate CO2 near Rubisco. We hypothesize that deep learning methods for protein structure prediction can be leveraged with computational molecular modeling and experimental assays to create an efficient funneling pipeline to engineer CCM-inducing proteins in C3 plants. Through the introduction of our synthetic CCM machinery, the goal is to increase plant CO2 utilization by two-fold under ambient or low CO2 concentrations. This research will serve as a proof of concept for computationally-aided design of synthetic CCMs in plants.


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Detailed budget items are in the solution statement.

Project Timeline

Detailed timeline and milestones are in the solution statement.

Mar 31, 2024

Demonstrate co-localization of Rubisco and CA

Dec 31, 2024

Demonstrate 2-fold increase in plant growth

Meet the Team

Alex Pak
Alex Pak
Assistant Professor


Chemical and Biological Engineering, Quantitative Biosciences and Engineering, Materials Science, Colorado School of Mines
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Nanette Boyle
Nanette Boyle
Associate Professor


Chemical & Biological Engineering, Quantitative Biosciences & Engineering, Colorado School of Mines
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Team Bio

We are an interdisciplinary team with expertise across experimental (metabolic engineering, systems and synthetic biology with a focus on photosynthetic systems) and computational (i.e., multiscale modeling, systematic coarse-graining, statistical inference) domains with a joint interest in synthetic biology and microbial engineering for applications across sustainability.

Alex Pak

I am the principal investigator of the Laboratory for Multiscale Modeling of Macromolecular Assembly and Control (LMAC) at Colorado School of Mines. Our mission is to develop and apply multiscale computational methods to learn the fundamental principles of biomacromolecular self-organization and to design biological materials inspired by nature.

Nanette Boyle

Nanette Boyle is the interim department head and associate professor in chemical & biological engineering at Colorado School of Mines. The Boyle Laboratory focuses on the application of chemical engineering principles, systems biology and synthetic biology to interrogate biological systems with an emphasis on photosynthetic systems. She received her B.S.E. in chemical engineering from Arizona State University and her PhD in chemical engineering from Purdue University, where she was an NSF graduate research fellow. Nanette joined the faculty at Mines in 2013 after completing two postdoctoral fellowships at CU Boulder and UCLA. She is a DOE early career program awardee, a Scialog Fellow for Negative Emission Science and most recently, a Fulbright Scholar in The Netherlands.

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