Proton gradients from light-harvesting E. coli control DNA assemblies for synthetic cells

Kevin Jahnke,Julius Fichtler,Joachim P Spatz,Rasmus R Schröder,Tobias Abele,Anna Nitschke,Götz Hofhaus,Kerstin Göpfrich,Noah Ritzmann,Ilia Platzman,Daniel J Müller,Yannik Dreher

doi:10.1038/s41467-021-24103-x

Abstract

Bottom-up and top-down approaches to synthetic biology each employ distinct methodologies with the common aim to harness living systems. Here, we realize a strategic merger of both approaches to convert light into proton gradients for the actuation of synthetic cellular systems. We genetically engineer E. coli to overexpress the light-driven inward-directed proton pump xenorhodopsin and encapsulate them in artificial cell-sized compartments. Exposing the compartments to light-dark cycles, we reversibly switch the pH by almost one pH unit and employ these pH gradients to trigger the attachment of DNA structures to the compartment periphery. For this purpose, a DNA triplex motif serves as a nanomechanical switch responding to the pH-trigger of the E. coli. When DNA origami plates are modified with the pH-sensitive triplex motif, the proton-pumping E. coli can trigger their attachment to giant unilamellar lipid vesicles (GUVs) upon illumination. A DNA cortex is formed upon DNA origami polymerization, which sculpts and deforms the GUVs. We foresee that the combination of bottom-up and top down approaches is an efficient way to engineer synthetic cells.

Highlights

Bottom-up and top-down approaches to synthetic biology each employ distinct methodologies with the common aim to harness living systems
Thereby, we can reversibly switch the pH upon illumination to trigger an optical or a mechanical response. The latter is based on the pH-sensitive membrane attachment of a triplex-forming DNA motif triggered by proton gradients from light-harvesting E. coli
We chose xenorhodopsin because it shows unique features compared to other proton pumps, such as bacteriorhodopsin or proteorhodopsin: First of all, xenorhodopsin exhibits a substantially faster photocycle, which can result in larger proton gradients[25]

Summary

Introduction

Bottom-up and top-down approaches to synthetic biology each employ distinct methodologies with the common aim to harness living systems. Exposing the compartments to light-dark cycles, we reversibly switch the pH by almost one pH unit and employ these pH gradients to trigger the attachment of DNA structures to the compartment periphery For this purpose, a DNA triplex motif serves as a nanomechanical switch responding to the pH-trigger of the E. coli. Merging the capacities of top-down and bottom-up approaches to synthetic biology can be a leap forward towards complex bottom-up assemblies and more versatile and well-defined top-down systems Leading to this direction, communication between natural and synthetic cells has been implemented[19,20,21] and bottom-up assembled vesicles were used as organelle mimics in living cells[22]. Thereby, we can reversibly switch the pH upon illumination to trigger an optical or a mechanical response The latter is based on the pH-sensitive membrane attachment of a triplex-forming DNA motif triggered by proton gradients from light-harvesting E. coli. We employ the pH-gradients to sculpt synthetic cellular compartments by attaching a DNA origami plate to the pH-sensitive DNA strand

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Conclusion