Biology subjects

Safronova, N.

Publications and source records attributed to Safronova, N..

3 recordsLinked to original sources

bioRxiv2025

Metabolic heat flow from the minimal cell JCVI-Syn3B reveals the lipidome-dependence of growth and metabolism

The cell membrane facilitates interactions with the environment and serves as an organizational platform for coordinating cellular processes, with lipids playing a central role in determining membrane property and function. Yet, how lipidome composition influences cellular fitness remains poorly defined. Recent approaches to chemically tune and minimize the lipidomes of genomically minimized bacterial organisms such as JCVI-Syn3A/B offer a streamlined system to explore why cells need such diverse lipid chemistries. In this study, we use isothermal microcalorimetry to assess how changes in lipid composition affect heat dissipated by JCVI-Syn3B cells, a parameter reflecting both growth and metabolic efficiency. By transposing the Monod equation into a calorimetric equation and extending it to the full life times of batch cultures, we introduce a new approach to quantify the metabolic efficiency of JCVI-Syn3B. Remarkably, our results demonstrate that tuning lipidome composition results in considerable variations of energy dissipation at the expense of biomass production. As a consequence, the volume of these minimal cells becomes inversely coupled to the lipidome-dependent entropic cost of cell division. The corresponding change in heat flow per cell mass gives rise to a complex but systematic dependence of growth rates on lipid composition. Interestingly, the maximal rate correlates with maximal lipid diversity, suggesting that the ability to tune local cell membrane charge and curvature through lipid structural diversity is crucial for divisome function. Our observations highlight the critical role of lipidome composition in cell metabolism and growth, and provide a new tool for interrogating the relationship between membrane composition and cell fitness.

biophysics↗

bioRxiv2024

Chemically defined lipid diets reveal the versatility of lipidome remodeling in genomically minimal cells

All cells are encapsulated in a lipid membrane that provides a responsive interface between life and its environment. Although simple membranes can be built from a single type of lipid, cellular membranes contain 10s to 100s of unique lipid species. Deciphering the significance of lipidome complexity is a central challenge in understanding the design principles of living membranes. While functions of individual lipids have been extensively studied, understanding how lipidomes collectively contribute to membrane function and cell phenotypes is experimentally challenging in most organisms. To address this challenge, we turned to the simple pathogenic organism Mycoplasma mycoides and its genomically derived "Minimal Cell" JCVI-syn3B, to establish a living minimal membrane model system in which lipidome complexity can be experimentally manipulated. By complexing lipids with cyclodextrins, we introduce a chemically defined approach to deliver lipid diets with different chemistries to cells, resulting in cellular lipidomes with as few as seven to nearly 30 lipids species. We explored how lipidome size and composition influences cell growth, osmotic sensitivity, and membrane adaptability to changes in growth temperature. Our findings indicate that lipidome composition dictates membrane adaptation to temperature change. Moreover, we show that lipidome diversity enhances cellular robustness to hypoosmotic shock. We further show that impaired acyl chain remodeling in the minimal cell is associated with impaired membrane temperature adaptation. Finally, we demonstrate as a proof of principle, how cells with tuneable lipidomes can be used as experimental chassis for screening membrane active antimicrobial peptides. Our study introduces an experimental resource and foundation for deciphering the role of lipidome complexity in membrane function and cellular fitness.

synthetic biology↗

bioRxiv2023

From hot to cold: dissecting lipidome adaptation in the minimal organisms Mycoplasma mycoides and JCVI-Syn3B

Cell membranes insulate and mediate interactions between life and its environment, with lipids determining their properties and functions. However, the intricacies of how cells adjust their lipidome compositions to tune membrane properties remain relatively undefined. The complexity of most model organisms has made it challenging to characterize lipidomic adaptation. An ideal model system would be a relatively simple organism with a single membrane that can adapt to environmental changes, particularly temperature, which is known to affect membrane properties. To this end, we used quantitative shotgun lipidomics to analyze temperature adaptation in Mycoplasma mycoides and its minimal synthetic counterpart, JCVI-Syn3B. Comparing with lipidomes from eukaryotes and bacteria, we observed a universal logarithmic distribution of lipid abundances. Additionally, the extent of lipid remodeling needed for temperature adaptation appears relatively constrained, irrespective of lipidomic or organismal complexity. Through lipid features analysis, we demonstrate head group-specific acyl chain remodeling as characteristic of temperature-induced lipidome adaptation and its deficiency in Syn3B is associated with impaired homeoviscous adaptation. Temporal analysis uncovers a two-stage cold adaptation process: swift cholesterol and cardiolipin shifts followed by gradual acyl chain modifications. This work provides an in-depth analysis of lipidome adaptation in minimal cells, laying a foundation to probe the fundamental design principles of living membranes.

biochemistry↗