Synthetic cells with self-activating optogenetic proteins communicate with natural cells.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
28 04 2022
28 04 2022
Historique:
received:
17
06
2021
accepted:
04
04
2022
entrez:
28
4
2022
pubmed:
29
4
2022
medline:
3
5
2022
Statut:
epublish
Résumé
Development of regulated cellular processes and signaling methods in synthetic cells is essential for their integration with living materials. Light is an attractive tool to achieve this, but the limited penetration depth into tissue of visible light restricts its usability for in-vivo applications. Here, we describe the design and implementation of bioluminescent intercellular and intracellular signaling mechanisms in synthetic cells, dismissing the need for an external light source. First, we engineer light generating SCs with an optimized lipid membrane and internal composition, to maximize luciferase expression levels and enable high-intensity emission. Next, we show these cells' capacity to trigger bioprocesses in natural cells by initiating asexual sporulation of dark-grown mycelial cells of the fungus Trichoderma atroviride. Finally, we demonstrate regulated transcription and membrane recruitment in synthetic cells using bioluminescent intracellular signaling with self-activating fusion proteins. These functionalities pave the way for deploying synthetic cells as embeddable microscale light sources that are capable of controlling engineered processes inside tissues.
Identifiants
pubmed: 35484097
doi: 10.1038/s41467-022-29871-8
pii: 10.1038/s41467-022-29871-8
pmc: PMC9050678
doi:
Substances chimiques
Luciferases
EC 1.13.12.-
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2328Informations de copyright
© 2022. The Author(s).
Références
Göpfrich, K., Platzman, I. & Spatz, J. P. Mastering complexity: towards bottom-up construction of multifunctional eukaryotic synthetic cells. Trends Biotechnol. 36, 938–951 (2018).
Noireaux, V. & Libchaber, A. A vesicle bioreactor as a step toward an artificial cell assembly. Proc. Natl Acad. Sci. USA 101, 17669–17674 (2004).
pubmed: 15591347
pmcid: 539773
doi: 10.1073/pnas.0408236101
Fanalista, F. et al. Shape and size control of artificial cells for bottom-up biology. ACS Nano 13, 5439–5450 (2019).
pubmed: 31074603
pmcid: 6543616
doi: 10.1021/acsnano.9b00220
Elani, Y., Law, R. V. & Ces, O. Protein synthesis in artificial cells: using compartmentalisation for spatial organisation in vesicle bioreactors. Phys. Chem. Chem. Phys. 17, 15534–15537 (2015).
pubmed: 25932977
doi: 10.1039/C4CP05933F
Chen, Z. et al. Light‐gated synthetic protocells for plasmon‐enhanced chemiosmotic gradient generation and ATP synthesis. Angew. Chem. Int. Ed. 58, 4896–4900 (2019).
doi: 10.1002/anie.201813963
Van Nies, P. et al. Self-replication of DNA by its encoded proteins in liposome-based synthetic cells. Nat. Commun. 9, 1583 (2018).
pubmed: 29679002
pmcid: 5910420
doi: 10.1038/s41467-018-03926-1
Merkle, D., Kahya, N. & Schwille, P. Reconstitution and anchoring of cytoskeleton inside giant unilamellar vesicles. ChemBioChem 9, 2673–2681 (2008).
pubmed: 18830993
doi: 10.1002/cbic.200800340
Chen, Z. et al. Synthetic beta cells for fusion-mediated dynamic insulin secretion. Nat. Chem. Biol. 14, 86 (2018).
pubmed: 29083418
doi: 10.1038/nchembio.2511
Krinsky, N. et al. Synthetic cells synthesize therapeutic proteins inside tumors. Adv. Healthc. Mater. 7, 1701163 (2018).
doi: 10.1002/adhm.201701163
Blain, J. C. & Szostak, J. W. Progress toward synthetic cells. Annu. Rev. Biochem. 83, 615–640 (2014).
pubmed: 24606140
doi: 10.1146/annurev-biochem-080411-124036
Luisi, P. L., Ferri, F. & Stano, P. Approaches to semi-synthetic minimal cells: a review. Naturwissenschaften 93, 1–13 (2006).
pubmed: 16292523
doi: 10.1007/s00114-005-0056-z
Adamala, K. P., Martin-Alarcon, D. A., Guthrie-Honea, K. R. & Boyden, E. S. Engineering genetic circuit interactions within and between synthetic minimal cells. Nat. Chem. 9, 431 (2017).
pubmed: 28430194
doi: 10.1038/nchem.2644
Lentini, R. et al. Integrating artificial with natural cells to translate chemical messages that direct E. coli behaviour. Nat. Commun. 5, 4012 (2014).
pubmed: 24874202
doi: 10.1038/ncomms5012
Dupin, A. & Simmel, F. C. Signalling and differentiation in emulsion-based multi-compartmentalized in vitro gene circuits. Nat. Chem. 11, 32–39 (2019).
pubmed: 30478365
doi: 10.1038/s41557-018-0174-9
Tang, T. D. et al. Gene-mediated chemical communication in synthetic protocell communities. ACS Synth. Biol. 7, 339–346 (2018).
pubmed: 29091420
doi: 10.1021/acssynbio.7b00306
Schroeder, A. et al. Remotely activated protein-producing nanoparticles. Nano Lett. 12, 2685–2689 (2012).
pubmed: 22432731
pmcid: 3388722
doi: 10.1021/nl2036047
Booth, M. J., Schild, V. R., Graham, A. D., Olof, S. N. & Bayley, H. Light-activated communication in synthetic tissues. Sci. Adv. 2, e1600056 (2016).
pubmed: 27051884
pmcid: 4820383
doi: 10.1126/sciadv.1600056
Berhanu, S., Ueda, T. & Kuruma, Y. Artificial photosynthetic cell producing energy for protein synthesis. Nat. Commun. 10, 1–10 (2019).
doi: 10.1038/s41467-019-09147-4
Cardin, J. A. et al. Targeted optogenetic stimulation and recording of neurons in vivo using cell-type-specific expression of Channelrhodopsin-2. Nat. Protoc. 5, 247 (2010).
pubmed: 20134425
pmcid: 3655719
doi: 10.1038/nprot.2009.228
Nussinovitch, U. & Gepstein, L. Optogenetics for in vivo cardiac pacing and resynchronization therapies. Nat. Biotechnol. 33, 750 (2015).
pubmed: 26098449
doi: 10.1038/nbt.3268
Fan, F. & Wood, K. V. Bioluminescent assays for high-throughput screening. Assay. Drug Dev. Technol. 5, 127–136 (2007).
pubmed: 17355205
doi: 10.1089/adt.2006.053
Iwano, S. et al. Single-cell bioluminescence imaging of deep tissue in freely moving animals. Science 359, 935–939 (2018).
pubmed: 29472486
doi: 10.1126/science.aaq1067
Sureda-Vives, M. & Sarkisyan, K. S. Bioluminescence-driven optogenetics. Life 10, 318 (2020).
pmcid: 7760859
doi: 10.3390/life10120318
Kim, C. K., Cho, K. F., Kim, M. W. & Ting, A. Y. Luciferase-LOV BRET enables versatile and specific transcriptional readout of cellular protein-protein interactions. Elife 8, e43826 (2019).
pubmed: 30942168
pmcid: 6447360
doi: 10.7554/eLife.43826
Berglund, K. et al. Luminopsins integrate opto-and chemogenetics by using physical and biological light sources for opsin activation. Proc. Natl Acad. Sci. USA 113, E358–E367 (2016).
pubmed: 26733686
pmcid: 4725499
doi: 10.1073/pnas.1510899113
Li, T. et al. A synthetic BRET-based optogenetic device for pulsatile transgene expression enabling glucose homeostasis in mice. Nat. Commun. 12, 1–10 (2021).
Prakash, M. et al. Selective control of synaptically-connected circuit elements by all-optical synapses. Commun. Biol. 5, 1–13 (2022).
doi: 10.1038/s42003-021-02981-7
Zoltowski, B. D., Vaccaro, B. & Crane, B. R. Mechanism-based tuning of a LOV domain photoreceptor. Nat. Chem. Biol. 5, 827–834 (2009).
pubmed: 19718042
pmcid: 2865183
doi: 10.1038/nchembio.210
Tannous, B. A., Kim, D.-E., Fernandez, J. L., Weissleder, R. & Breakefield, X. O. Codon-optimized Gaussia luciferase cDNA for mammalian gene expression in culture and in vivo. Mol. Ther. 11, 435–443 (2005).
pubmed: 15727940
doi: 10.1016/j.ymthe.2004.10.016
Moga, A., Yandrapalli, N., Dimova, R. & Robinson, T. Optimization of the inverted emulsion method for high‐yield production of biomimetic giant unilamellar vesicles. ChemBioChem 20, 2674 (2019).
pubmed: 31529570
pmcid: 6856842
doi: 10.1002/cbic.201900529
Wheeler, O. H. & Mateos, J. L. The ultraviolet absorption of isolated double bonds1. J. Org. Chem. 21, 1110–1112 (1956).
doi: 10.1021/jo01116a014
Kripke, M. L., Cox, P. A., Alas, L. G. & Yarosh, D. B. Pyrimidine dimers in DNA initiate systemic immunosuppression in UV-irradiated mice. Proc. Natl Acad. Sci. USA 89, 7516–7520 (1992).
pubmed: 1502162
pmcid: 49741
doi: 10.1073/pnas.89.16.7516
Hart, R., Setlow, R. & Woodhead, A. Evidence that pyrimidine dimers in DNA can give rise to tumors. Proc. Natl Acad. Sci. 74, 5574–5578 (1977).
pubmed: 271984
pmcid: 431814
doi: 10.1073/pnas.74.12.5574
Ayala-Torres, S., Chen, Y., Svoboda, T., Rosenblatt, J. & Van Houten, B. Analysis of gene-specific DNA damage and repair using quantitative polymerase chain reaction. Methods 22, 135–147 (2000).
pubmed: 11020328
doi: 10.1006/meth.2000.1054
Welsh, J. P., Patel, K. G., Manthiram, K. & Swartz, J. R. Multiply mutated Gaussia luciferases provide prolonged and intense bioluminescence. Biochem. Biophys. Res. Commun. 389, 563–568 (2009).
pubmed: 19825431
doi: 10.1016/j.bbrc.2009.09.006
Lorenz, W. W., McCann, R. O., Longiaru, M. & Cormier, M. J. Isolation and expression of a cDNA encoding Renilla reniformis luciferase. Proc. Natl Acad. Sci. USA 88, 4438–4442 (1991).
pubmed: 1674607
pmcid: 51675
doi: 10.1073/pnas.88.10.4438
Tannous, B. A. Gaussia luciferase reporter assay for monitoring biological processes in culture and in vivo. Nat. Protoc. 4, 582 (2009).
pubmed: 19373229
pmcid: 2692611
doi: 10.1038/nprot.2009.28
Messens, J. & Collet, J.-F. Pathways of disulfide bond formation in Escherichia coli. Int. J. Biochem. Cell Biol. 38, 1050–1062 (2006).
pubmed: 16446111
doi: 10.1016/j.biocel.2005.12.011
Goerke, A. R., Loening, A. M., Gambhir, S. S. & Swartz, J. R. Cell-free metabolic engineering promotes high-level production of bioactive Gaussia princeps luciferase. Metab. Eng. 10, 187–200 (2008).
pubmed: 18555198
doi: 10.1016/j.ymben.2008.04.001
Horwitz, B. A., Perlman, A. & Gressel, J. Induction of Trichoderma sporulation by nanosecond laser pulses: evidence against cryptochrome cycling. Photochemistry Photobiol. 51, 99–104 (1990).
doi: 10.1111/j.1751-1097.1990.tb01689.x
Berrocal-Tito, G., Sametz-Baron, L., Eichenberg, K., Horwitz, B. A. & Herrera-Estrella, A. Rapid blue light regulation of a Trichoderma harzianum photolyase gene. J. Biol. Chem. 274, 14288–14294 (1999).
pubmed: 10318850
doi: 10.1074/jbc.274.20.14288
Casas-Flores, S., Rios-Momberg, M., Bibbins, M., Ponce-Noyola, P. & Herrera-Estrella, A. BLR-1 and BLR-2, key regulatory elements of photoconidiation and mycelial growth in Trichoderma atroviride. Microbiology 150, 3561–3569 (2004).
pubmed: 15528646
doi: 10.1099/mic.0.27346-0
Diggle, S. P., Crusz, S. A. & Cámara, M. Quorum sensing. Curr. Biol. 17, R907–R910 (2007).
pubmed: 17983563
doi: 10.1016/j.cub.2007.08.045
Miller, M. B. & Bassler, B. L. Quorum sensing in bacteria. Annu. Rev. Microbiol. 55, 165–199 (2001).
pubmed: 11544353
doi: 10.1146/annurev.micro.55.1.165
Motta-Mena, L. B. et al. An optogenetic gene expression system with rapid activation and deactivation kinetics. Nat. Chem. Biol. 10, 196–202 (2014).
pubmed: 24413462
pmcid: 3944926
doi: 10.1038/nchembio.1430
Jayaraman, P. et al. Cell-free optogenetic gene expression system. ACS Synth. Biol. 7, 986–994 (2018).
pubmed: 29596741
doi: 10.1021/acssynbio.7b00422
Guntas, G. et al. Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins. Proc. Natl Acad. Sci. USA 112, 112–117 (2015).
pubmed: 25535392
doi: 10.1073/pnas.1417910112
Göpfrich, K. et al. One-pot assembly of complex giant unilamellar vesicle-based synthetic cells. ACS Synth. Biol. 8, 937–947 (2019).
Bartelt, S. M. et al. Dynamic blue light-switchable protein patterns on giant unilamellar vesicles. Chem. Commun. 54, 948–951 (2018).
doi: 10.1039/C7CC08758F
Lentini, R., Martín, N. Y. & Mansy, S. S. Communicating artificial cells. Curr. Opin. Chem. Biol. 34, 53–61 (2016).
pubmed: 27352299
doi: 10.1016/j.cbpa.2016.06.013
Aufinger, L. & Simmel, F. C. Establishing communication between artificial cells. Chem.–A Eur. J. 25, 12659–12670 (2019).
doi: 10.1002/chem.201901726
Zhang, F. et al. Red-shifted optogenetic excitation: a tool for fast neural control derived from Volvox carteri. Nat. Neurosci. 11, 631–633 (2008).
pubmed: 18432196
pmcid: 2692303
doi: 10.1038/nn.2120
Inoue, K. et al. Red-shifting mutation of light-driven sodium-pump rhodopsin. Nat. Commun. 10, 1–11 (2019).
doi: 10.1038/s41467-019-10000-x
Chen, S. et al. Near-infrared deep brain stimulation via upconversion nanoparticle–mediated optogenetics. Science 359, 679–684 (2018).
pubmed: 29439241
doi: 10.1126/science.aaq1144
Cleaves, H. J. & Miller, S. L. Oceanic protection of prebiotic organic compounds from UV radiation. Proc. Natl Acad. Sci. USA 95, 7260–7263 (1998).
pubmed: 9636136
pmcid: 22584
doi: 10.1073/pnas.95.13.7260
De Gier, J., Mandersloot, J. & Van Deenen, L. Lipid composition and permeability of liposomes. Biochim. et. Biophys. Acta (BBA)-Biomembranes 150, 666–675 (1968).
doi: 10.1016/0005-2736(68)90056-4
Mattis, J. et al. Principles for applying optogenetic tools derived from direct comparative analysis of microbial opsins. Nat. Methods 9, 159 (2012).
doi: 10.1038/nmeth.1808
Gong, X. et al. An ultra-sensitive step-function opsin for minimally invasive optogenetic stimulation in mice and macaques. Neuron 107, 38–51 (2020). e38.
pubmed: 32353253
pmcid: 7351618
doi: 10.1016/j.neuron.2020.03.032
Adir, O. et al. Preparing protein producing synthetic cells using cell free bacterial extracts, liposomes and emulsion transfer. JoVE, e60829 (2020).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
pubmed: 22743772
doi: 10.1038/nmeth.2019
Adir, O., Kurman, Y. & Weiss, L. E. Code for: synthetic cells with self-activating optogenetic proteins communicate with natural cells. Zenodo https://doi.org/10.5281/zenodo.6368147 (2022).