Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

2023 Abstracts

Synthetic Membrane Biology of Microbial Cell Factories: Lipid Interactions that Shape the Inner Mitochondrial Membrane


Kailash Venkatraman1, Christopher Lee1, Guadalupe C. Garcia2, Arijit Mahapatra1, Mark Ellisman1, Padmini Rangamani1, and Itay Budin1* ([email protected])


1University of California–San Diego; and 2Salk Institute for Biological Studies


The goal of this Early Career Program project is to engineer the structure and properties of cell membranes to improve the performance of industrially relevant microbes. The project’s first objective is to enhance the rate and efficiency of the respiratory metabolism by engineering the organization of the Electron Transport Chain. Engineering efforts will define the limits of respiratory metabolism and seek to increase the production of energy-intensive next-generation biofuels. The second objective is to apply the emerging biochemistry of intracellular lipid trafficking pathways to develop new transporters for the capture of valuable biochemicals produced by the engineered yeast.


The inner mitochondrial membrane (IMM) is the site of bulk ATP generation for yeast cell factories and is thus essential for production of high-energy biofuels and bioproducts. The IMM is defined by highly curved cristae membranes (CM), whose lipidome is composed of unsaturated phospholipids and cardiolipin (CL). Recent efforts combined experimental lipidome dissection with multiscale modeling to investigate how lipid interactions shape CM morphology and metabolic function. When modulating fatty acid unsaturation in engineered yeast strains, the team observed that loss of di-unsaturated phospholipids (PLs) led to a surprising breakpoint in IMM topology and respiratory capacity. PL unsaturation modulates the organization of ATP synthases that shape cristae ridges, phenocopying the loss of CM shaping proteins. Based on molecular modeling of mitochondrial-specific membrane adaptations, the team hypothesized that conical lipids like CL buffer against the effects of saturation on the IMM. Loss of CL was found to collapse the IMM at intermediate levels of PL saturation, a function that is independent of ATP synthase oligomerization. To explain this interaction, researchers employed a continuum modeling approach, finding that lipid and protein-mediated curvatures act in concert to form curved membranes in the IMM. These results suggested that fermentation conditions that alter the fatty acid pool, such as oxygen availability or overproduction of saturated fatty acids in engineered strains, define the CL function. While loss of CL only has a minimal phenotype in highly aerated shake flasks, research shows that its synthesis is essential in microaerobic fermenters, which promote saturated lipidomes. Lipid and protein mediated mechanisms of curvature generation thus act together to support mitochondrial architecture in industrially relevant environments.

Funding Information

This research is supported by the DOE Office of Science, Biological and Environmental Research (BER) Program, grant no. DE-SC0022954.