For life to emerge, the confinement of catalytic reactions within protocellular environments has been proposed to be a decisive aspect to regulate chemical activity in space1. Today, cells and organisms adapt to signals2,3,4,5,6 by processing them through reaction networks that ultimately provide downstream functional responses and structural morphogenesis7,8. Re-enacting such signal processing in de novo-designed protocells is a profound challenge, but of high importance for understanding the design of adaptive systems with life-like traits. We report on engineered all-DNA protocells9 harbouring an artificial metalloenzyme10 whose olefin metathesis activity leads to downstream morphogenetic protocellular responses with varying levels of complexity. The artificial metalloenzyme catalyses the uncaging of a pro-fluorescent signal molecule that generates a self-reporting fluorescent metabolite designed to weaken DNA duplex interactions. This leads to pronounced growth, intraparticular functional adaptation in the presence of a fluorescent DNA mechanosensor11 or interparticle protocell fusion. Such processes mimic chemically transduced processes found in cell adaptation and cell-to-cell adhesion. Our concept showcases new opportunities to study life-like behaviour via abiotic bioorthogonal chemical and mechanical transformations in synthetic protocells. Furthermore, it reveals a strategy for inducing complex behaviour in adaptive and communicating soft-matter microsystems, and it illustrates how dynamic properties can be upregulated and sustained in micro-compartmentalized media.
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Data for the catalysis experiments are available online. Any other data can be made available upon reasonable request to the corresponding authors. Source data are provided with this paper.
Oparin, A. I. Origin of Life (Dover, 1953).
Brangwynne, C. P. et al. Germline P granules are liquid droplets that localize by controlled dissolution/condensation. Science 324, 1729–1732 (2009).
Pawson, T. Specificity in signal transduction: from phosphotyrosine-SH2 domain interactions to complex cellular systems. Cell 116, 191–203 (2004).
Pawson, T. & Nash, P. Assembly of cell regulatory systems through protein interaction domains. Science 300, 445–452 (2003).
You, L., Cox, R. S., Weiss, R. & Arnold, F. H. Programmed population control by cell–cell communication and regulated killing. Nature 428, 868–871 (2004).
Bacchus, W. et al. Synthetic two-way communication between mammalian cells. Nat. Biotechnol. 30, 991–996 (2012).
Na, S. et al. Rapid signal transduction in living cells is a unique feature of mechanotransduction. Proc. Natl. Acad. Sci. USA 105, 6626–6631 (2008).
Trepat, X. et al. Universal physical responses to stretch in the living cell. Nature 447, 592–595 (2007).
Merindol, R., Loescher, S., Samanta, A. & Walther, A. Pathway-controlled formation of mesostructured all-DNA colloids and superstructures. Nat. Nanotechnol. 13, 730–738 (2018).
Jeschek, M. et al. Directed evolution of artificial metalloenzymes for in vivo metathesis. Nature 537, 661–665 (2016).
Merindol, R., Delechiave, G., Heinen, L., Catalani, L. H. & Walther, A. Modular design of programmable mechanofluorescent DNA hydrogels. Nat. Commun. 10, 528 (2019).
Martin, N. Dynamic synthetic cells based on liquid–liquid phase separation. ChemBioChem 20, 2553–2568 (2019).
Sokolova, E. et al. Enhanced transcription rates in membrane-free protocells formed by coacervation of cell lysate. Proc. Natl. Acad. Sci. USA 110, 11692–11697 (2013).
Zwicker, D., Seyboldt, R., Weber, C. A., Hyman, A. A. & Jülicher, F. Growth and division of active droplets provides a model for protocells. Nat. Phys. 13, 408–413 (2017).
Changeux, J.-P. & Christopoulos, A. Allosteric modulation as a unifying mechanism for receptor function and regulation. Cell 166, 1084–1102 (2016).
Strulson, C. A., Molden, R. C., Keating, C. D. & Bevilacqua, P. C. RNA catalysis through compartmentalization. Nat. Chem. 4, 941–946 (2012).
Booth, R., Qiao, Y., Li, M. & Mann, S. Spatial positioning and chemical coupling in coacervate-in-proteinosome protocells. Angew. Chem. Int. Ed. 58, 9120–9124 (2019).
Mansy, S. S. et al. Template-directed synthesis of a genetic polymer in a model protocell. Nature 454, 122–125 (2008).
Adamala, K. & Szostak, J. W. Nonenzymatic template-directed RNA synthesis inside model protocells. Science 342, 1098–1100 (2013).
Adamala, K. & Szostak, J. W. Competition between model protocells driven by an encapsulated catalyst. Nat. Chem. 5, 495–501 (2013).
Langton, M. J., Scriven, L. M., Williams, N. H. & Hunter, C. A. Triggered release from lipid bilayer vesicles by an artificial transmembrane signal transduction system. J. Am. Chem. Soc. 139, 15768–15773 (2017).
Fulton, A. B. How crowded is the cytoplasm? Cell 30, 345–347 (1982).
Gobbo, P. et al. Programmed assembly of synthetic protocells into thermoresponsive prototissues. Nat. Mater. 17, 1145–1153 (2018).
Joesaar, A. et al. DNA-based communication in populations of synthetic protocells. Nat. Nanotechnol. 14, 369–378 (2019).
Wilson, M. E. & Whitesides, G. M. Conversion of a protein to a homogeneous asymmetric hydrogenation catalyst by site-specific modification with a diphosphinerhodium(I) moiety. J. Am. Chem. Soc. 100, 306–307 (1978).
Schwizer, F. et al. Artificial metalloenzymes: reaction scope and optimization strategies. Chem. Rev. 118, 142–231 (2018).
Okamoto, Y. et al. A cell-penetrating artificial metalloenzyme regulates a gene switch in a designer mammalian cell. Nat. Commun. 9, 1943 (2018).
Fan, X. et al. Optimized tetrazine derivatives for rapid bioorthogonal decaging in living cells. Angew. Chem. Int. Ed. 55, 14046–14050 (2016).
Sabatino, V., Rebelein, J. G. & Ward, T. R. “Close-to-release”: spontaneous bioorthogonal uncaging resulting from ring-closing metathesis. J. Am. Chem. Soc. 141, 17048–17052 (2019).
Wilner, O. I. et al. Enzyme cascades activated on topologically programmed DNA scaffolds. Nat. Nanotechnol. 4, 249–254 (2009).
Ou, C.-N., Tsai, C.-H., Tapley, K. J. & Song, P.-S. Photobinding of 8-methoxypsoralen and 5,7-dimethoxycoumarin to DNA and its effect on template activity. Biochemistry 17, 1047–1053 (1978).
Banks, T. M., Clay, S. F., Glover, S. A. & Schumacher, R. R. Mutagenicity of N-acyloxy-N-alkoxyamides as an indicator of DNA intercalation part 1: evidence for naphthalene as a DNA intercalator. Org. Biomol. Chem. 14, 3699–3714 (2016).
Ellis, R. J. Macromolecular crowding: obvious but underappreciated. Trends Biochem. Sci. 26, 597–604 (2001).
We acknowledge the support by the European Research Council starting grant to A.W. (TimeProSAMat (agreement 677960)) and advanced grant to T.R.W. (DrEAM, agreement 694424), the DFG Cluster of Excellence livMatS “Living, Adaptive and Energy-Autonomous Materials Systems” and the NCCR Molecular Systems Engineering. A.S. acknowledges the support by the Alexander von Humboldt Foundation.
The authors declare no competing interests.
Peer review information Nature Nanotechnology thanks Tom de Greef and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
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Supplementary Figs. 1–11, Tables 1 and 2, Notes 1 and 2 and refs 1–4.
Fluorescence recovery after successive photobleaching in the case of pristine PCs.
Fluorescence recovery after photobleaching in the case of streptavidin-loaded protocells.
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Samanta, A., Sabatino, V., Ward, T.R. et al. Functional and morphological adaptation in DNA protocells via signal processing prompted by artificial metalloenzymes. Nat. Nanotechnol. 15, 914–921 (2020). https://doi.org/10.1038/s41565-020-0761-y