Orthogonal fluorescent chemogenetic reporters for multicolor imaging.
Animals
Benzylidene Compounds
/ chemistry
Biosensing Techniques
COS Cells
Chlorocebus aethiops
Cloning, Molecular
Color
Escherichia coli
/ genetics
Fluorescent Dyes
/ chemistry
Gene Expression
Molecular Biology
/ methods
Oligonucleotides
/ genetics
Optical Imaging
/ methods
Plasmids
/ chemistry
Protein Engineering
Recombinant Proteins
/ chemistry
Saccharomyces cerevisiae
/ genetics
Staining and Labeling
/ methods
Zebrafish
Journal
Nature chemical biology
ISSN: 1552-4469
Titre abrégé: Nat Chem Biol
Pays: United States
ID NLM: 101231976
Informations de publication
Date de publication:
01 2021
01 2021
Historique:
received:
04
04
2020
accepted:
02
07
2020
pubmed:
12
8
2020
medline:
20
2
2021
entrez:
12
8
2020
Statut:
ppublish
Résumé
Spectrally separated fluorophores allow the observation of multiple targets simultaneously inside living cells, leading to a deeper understanding of the molecular interplay that regulates cell function and fate. Chemogenetic systems combining a tag and a synthetic fluorophore provide certain advantages over fluorescent proteins since there is no requirement for chromophore maturation. Here, we present the engineering of a set of spectrally orthogonal fluorogen-activating tags based on the fluorescence-activating and absorption shifting tag (FAST) that are compatible with two-color, live-cell imaging. The resulting tags, greenFAST and redFAST, demonstrate orthogonality not only in their fluorogen recognition capabilities, but also in their one- and two-photon absorption profiles. This pair of orthogonal tags allowed the creation of a two-color cell cycle sensor capable of detecting very short, early cell cycles in zebrafish development and the development of split complementation systems capable of detecting multiple protein-protein interactions by live-cell fluorescence microscopy.
Identifiants
pubmed: 32778846
doi: 10.1038/s41589-020-0611-0
pii: 10.1038/s41589-020-0611-0
pmc: PMC7610487
mid: EMS118352
doi:
Substances chimiques
Benzylidene Compounds
0
Fluorescent Dyes
0
Oligonucleotides
0
Recombinant Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
30-38Subventions
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : European Research Council
ID : 724705
Pays : International
Organisme : European Research Council
ID : 863869
Pays : International
Organisme : Wellcome Trust
ID : 203141
Pays : United Kingdom
Références
Tsien, R. Y. Constructing and exploiting the fluorescent protein paintbox (Nobel Lecture). Angew. Chem. Int. Ed. Engl. 48, 5612–5626 (2009).
pubmed: 19565590
Grimm, J. B. et al. A general method to improve fluorophores for live-cell and single-molecule microscopy. Nat. Methods 12, 244–250 (2015).
pubmed: 25599551
pmcid: 4344395
Los, G. V. et al. HaloTag: a novel protein labeling technology for cell imaging and protein analysis. ACS Chem. Biol. 3, 373–382 (2008).
pubmed: 18533659
Keppler, A. et al. A general method for the covalent labeling of fusion proteins with small molecules in vivo. Nat. Biotechnol. 21, 86–89 (2002).
pubmed: 12469133
Gautier, A. et al. An engineered protein tag for multiprotein labeling in living cells. Chem. Biol. 15, 128–136 (2008).
pubmed: 18291317
Gautier, A. & Tebo, A. G. Fluorogenic protein-based strategies for detection, actuation, and sensing. Bio. Essays 67, 509–510 (2018).
Li, C. et al. Dynamic multicolor protein labeling in living cells. Chem. Sci. 8, 5598–5605 (2017).
pubmed: 28970939
pmcid: 5618792
Plamont, M.-A. et al. Small fluorescence-activating and absorption-shifting tag for tunable protein imaging in vivo. Proc. Natl Acad. Sci. USA 113, 497–502 (2016).
pubmed: 26711992
Tebo, A. G., Pimenta, F. M., Zhang, Y. & Gautier, A. Improved chemical-genetic fluorescent markers for live cell microscopy. Biochemistry 57, 5648–5653 (2018).
pubmed: 30204425
Tebo, A. G. & Gautier, A. A split fluorescent reporter with rapid and reversible complementation. Nat. Commun. 10, 2822 (2019).
pubmed: 31249300
pmcid: 6597557
Glasgow, J. E., Salit, M. L. & Cochran, J. R. In vivo site-specific protein tagging with diverse amines using an engineered sortase variant. J. Am. Chem. Soc. 138, 7496–7499 (2016).
pubmed: 27280683
Thomas, F. et al. De novo-designed α-helical barrels as receptors for small molecules. ACS Synth. Biol. 7, 1808–1816 (2018).
pubmed: 29944338
Obexer, R. et al. Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase. Nat. Chem. 9, 50–56 (2017).
pubmed: 27995916
Martínez, L. et al. Gaining ligand selectivity in thyroid hormone receptors via entropy. Proc. Natl Acad. Sci. USA 106, 20717–20722 (2009).
pubmed: 19926848
Das, R. et al. Dynamically driven ligand selectivity in cyclic nucleotide binding domains. J. Biol. Chem. 284, 23682–23696 (2009).
pubmed: 19403523
pmcid: 2749143
Pessoa, J., Fonseca, F., Furini, S. & Morais-Cabral, J. H. Determinants of ligand selectivity in a cyclic nucleotide-regulated potassium channel. J. Gen. Physiol. 144, 41–54 (2014).
pubmed: 24981229
pmcid: 4076524
Brogi, S., Tafi, A., Désaubry, L. & Nebigil, C. G. Discovery of GPCR ligands for probing signal transduction pathways. Front. Pharmacol. 5, 255 (2014).
pubmed: 25506327
pmcid: 4246677
Engelowski, E. et al. Synthetic cytokine receptors transmit biological signals using artificial ligands. Nat. Commun. 9, 2034 (2018).
pubmed: 29789554
pmcid: 5964073
Grimm, J. B. et al. A general method to fine-tune fluorophores for live-cell and in vivo imaging. Nat. Methods 14, 987–994 (2017).
pubmed: 28869757
pmcid: 5621985
Chen, X. et al. Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs. Nat. Biotechnol. 37, 1287–1293 (2019).
pubmed: 31548726
Philip, A. F., Nome, R. A., Papadantonakis, G. A., Scherer, N. F. & Hoff, W. D. Spectral tuning in photoactive yellow protein by modulation of the shape of the excited state energy surface. Proc. Natl Acad. Sci. USA 107, 5821–5826 (2010).
pubmed: 20220103
Shaner, N. C. et al. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat. Biotechnol. 22, 1567–1572 (2004).
pubmed: 15558047
Pimenta, F. M. et al. Chromophore renewal and fluorogen-binding tags: a match made to last. Sci. Rep. 7, 12316 (2017).
pubmed: 28951577
pmcid: 5615068
Padilla-Parra, S., Audugé, N., Tramier, M. & Coppey-Moisan, M. Time-domain fluorescence lifetime imaging microscopy: a quantitative method to follow transient protein–protein interactions in living cells. Cold Spring Harb. Protoc. 2015, 508–521 (2015).
Dertinger, T., Colyer, R., Iyer, G., Weiss, S. & Enderlein, J. Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI). Proc. Natl Acad. Sci. USA 106, 22287–22292 (2009).
pubmed: 20018714
Dedecker, P., Mo, G. C. H., Dertinger, T. & Zhang, J. Widely accessible method for superresolution fluorescence imaging of living systems. Proc. Natl Acad. Sci. USA 109, 10909–10914 (2012).
pubmed: 22711840
Moeyaert, B. & Dedecker, P. PcSOFI as a smart label-based superresolution microscopy technique. Methods Mol. Biol. 1148, 261–276 (2014).
pubmed: 24718807
Zhang, X. et al. Development of a reversibly switchable fluorescent protein for super-resolution optical fluctuation imaging (SOFI). ACS Nano 9, 2659–2667 (2015).
pubmed: 25695314
Moeyaert, B., Vandenberg, W. & Dedecker, P. SOFIevaluator: a strategy for the quantitative quality assessment of SOFI data. Biomed. Opt. Express 11, 636 (2020).
pubmed: 32133218
pmcid: 7041449
Vandenberg, W., Leutenegger, M., Duwé, S. & Dedecker, P. An extended quantitative model for super-resolution optical fluctuation imaging (SOFI). Opt. Express 27, 25749–25766 (2019).
pubmed: 31510441
Sakaue-Sawano, A. et al. Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell 132, 487–498 (2008).
pubmed: 18267078
Sugiyama, M. et al. Illuminating cell-cycle progression in the developing zebrafish embryo. Proc. Natl Acad. Sci. USA 106, 20812–20817 (2009).
pubmed: 19923430
Sakaue-Sawano, A. et al. Genetically encoded tools for optical dissection of the mammalian cell cycle. Mol. Cell 68, 626–640.e5 (2017).
pubmed: 29107535
Kimmel, C. B. & Law, R. D. Cell lineage of zebrafish blastomeres. I. Cleavage pattern and cytoplasmic bridges between cells. Developmental Biol. 108, 78–85 (1985).
Keller, P. J., Schmidt, A. D., Wittbrodt, J. & Stelzer, E. H. K. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 322, 1065–1069 (2008).
pubmed: 18845710
Olivier, N. et al. Cell lineage reconstruction of early zebrafish embryos using label-free nonlinear microscopy. Science 329, 967–971 (2010).
pubmed: 20724640
Mendieta-Serrano, M. A., Schnabel, D., Lomelí, H. & Salas-Vidal, E. Cell proliferation patterns in early zebrafish development. Anat. Rec. 296, 759–773 (2013).
Langley, A. R., Smith, J. C., Stemple, D. L. & Harvey, S. A. New insights into the maternal to zygotic transition. Development 141, 3834–3841 (2014).
pubmed: 25294937
Erdmann, R. S. et al. Labeling strategies matter for super-resolution microscopy: a comparison between HaloTags and SNAP-tags. Cell Chem. Biol. 26, 584–592.e6 (2019).
pubmed: 30745239
pmcid: 6474801
Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).
Gietz, R. D. & Schiestl, R. H. High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat. Protoc. 2, 31–34 (2007).
pubmed: 17401334
Duwé, S., Vandenberg, W. & Dedecker, P. Live-cell monochromatic dual-label sub-diffraction microscopy by mt-pcSOFI. Chem. Commun. 53, 7242–7245 (2017).
Pardon, E. et al. A general protocol for the generation of Nanobodies for structural biology. Nat. Protoc. 9, 674–693 (2014).
pubmed: 24577359
pmcid: 4297639
Dedecker, P., Duwé, S., Neely, R. K. & Zhang, J. Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy. J. Biomed. Opt. 17, 126008 (2012).
pubmed: 23208219
pmcid: 3512108