Cited by 48Advanced Fluorescence Microscopy TechniquesBiochemical and Structural CharacterizationBiotin and Related Studies

The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.

A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity

Open access
Bottone, Sara, Joliot, Octave, Cakil, Zeyneb Vildan, El Hajji, Lina, Rakotoarison, Louise-Marie, Boncompain, Gaelle, Perez, Franck, Gautier, Arnaud·2023·Nature Methods

Published version of a preprint

Abstract

Molecular tools enabling the control and observation of the proximity of proteins are essential for studying the functional role of physical distance between two proteins. Here we present CATCHFIRE (chemically assisted tethering of chimera by fluorogenic-induced recognition), a chemically induced proximity technology with intrinsic fluorescence imaging and sensing capabilities. CATCHFIRE relies on genetic fusion to small dimerizing domains that interact upon addition of fluorogenic inducers of proximity that fluoresce upon formation of the ternary assembly, allowing real-time monitoring of the chemically induced proximity. CATCHFIRE is rapid and fully reversible and allows the control and tracking of protein localization, protein trafficking, organelle transport and cellular processes, opening new avenues for studying or controlling biological processes with high spatiotemporal resolution. Its fluorogenic nature allows the design of a new class of biosensors for the study of processes such as signal transduction and apoptosis.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41592-023-01988-8

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 32

  1. Spencer, D. M., Wandless, T. J., Schreiber, S. L. & Crabtree, G. R. Controlling signal transduction with synthetic ligands. Science 262, 1019–1024 (1993). · DOI
  2. Putyrski, M. & Schultz, C. Protein translocation as a tool: the current rapamycin story. FEBS Lett. 586, 2097–2105 (2012). · DOI
  3. Ho, S. N., Biggar, S. R., Spencer, D. M., Schreiber, S. L. & Crabtree, G. R. Dimeric ligands define a role for transcriptional activation domains in reinitiation. Nature 382, 822–826 (1996). · DOI
  4. Zhao, W. et al. A chemically induced proximity system engineered from the plant auxin signaling pathway. Chem. Sci. 9, 5822–5827 (2018). · DOI
  5. Miyamoto, T. et al. Rapid and orthogonal logic gating with a gibberellin-induced dimerization system. Nat. Chem. Biol. 8, 465–470 (2012). · DOI
  6. Liang, F.-S., Ho, W. Q. & Crabtree, G. R. Engineering the ABA plant stress pathway for regulation of induced proximity. Sci. Signal 4, rs2 (2011). · DOI
  7. Ziegler, M. J. et al. Mandipropamid as a chemical inducer of proximity for in vivo applications. Nat. Chem. Biol. 18, 64–69 (2022). · DOI
  8. Gutnick, A., Banghart, M. R., West, E. R. & Schwarz, T. L. The light-sensitive dimerizer zapalog reveals distinct modes of immobilization for axonal mitochondria. Nat. Cell Biol. 21, 768–777 (2019). · DOI
  9. Piston, D. W. & Kremers, G.-J. Fluorescent protein FRET: the good, the bad and the ugly. Trends Biochem. Sci. 32, 407–414 (2007). · DOI
  10. Magliery, T. J. et al. Detecting protein–protein interactions with a green fluorescent protein fragment reassembly trap: scope and mechanism. J. Am. Chem. Soc. 127, 146–157 (2005). · DOI
  11. Tebo, A. G. & Gautier, A. A split fluorescent reporter with rapid and reversible complementation. Nat. Commun. 10, 2822–2828 (2019). · DOI
  12. Benaissa, H. et al. Engineering of a fluorescent chemogenetic reporter with tunable color for advanced live-cell imaging. Nat. Commun. 12, 6989 (2021). · DOI
  13. 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). · DOI
  14. van Unen, J. et al. Plasma membrane restricted RhoGEF activity is sufficient for RhoA-mediated actin polymerization. Sci. Rep. 5, 14693–16 (2015). · DOI
  15. Busch, A., Kiel, T. & Hübner, S. Quantification of nuclear protein transport using induced heterodimerization. Traffic 10, 1221–1227 (2009). · DOI
  16. Boncompain, G. et al. Synchronization of secretory protein traffic in populations of cells. Nat. Methods 9, 493–498 (2012). · DOI
  17. Kapitein, L. C. et al. Mixed microtubules steer dynein-driven cargo transport into dendrites. Curr. Biol. 20, 290–299 (2010). · DOI · Paper page
  18. Cabukusta, B. & Neefjes, J. Mechanisms of lysosomal positioning and movement. Traffic 19, 761–769 (2018). · DOI
  19. Kluss, J. H. et al. Lysosomal positioning regulates Rab10 phosphorylation at LRRK2+ lysosomes. Proc. Natl Acad. Sci. USA 119, e2205492119 (2022). · DOI
  20. Franker, M. A. et al. Three-step model for polarized sorting of KIF17 into dendrites. Curr. Biol. 26, 1705–1712 (2016). · DOI
  21. Napetschnig, J. & Wu, H. Molecular basis of NF-κB signaling. Annu. Rev. Biophys. 42, 443–468 (2013). · DOI
  22. Robinson, M. S., Sahlender, D. A. & Foster, S. D. Rapid inactivation of proteins by rapamycin-induced rerouting to mitochondria. Dev. Cell 18, 324–331 (2010). · DOI
  23. Li, C. et al. A far-red emitting fluorescent chemogenetic reporter for in vivo molecular imaging. Angew. Chem. Int. Ed. 59, 17917–17923 (2020). · DOI
  24. Tebo, A. G. et al. Orthogonal fluorescent chemogenetic reporters for multicolor imaging. Nat. Chem. Biol. 17, 30–38 (2021). · DOI
  25. Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Meth. 6, 343–345 (2009). · DOI
  26. Li, C. et al. Dynamic multicolor protein labeling in living cells. Chem. Sci. 8, 5598–5605 (2017). · DOI
  27. Miyamoto, T. et al. Rapid manipulation of mitochondrial morphology in a living cell with iCMM. Cell Rep. Methods 1, 100052 (2021). · DOI
  28. Wu, H. D. et al. Rational design and implementation of a chemically inducible heterotrimerization system. Nat. Methods 17, 928–936 (2020). · DOI
  29. Chen, L. F., Fischle, W., Verdin, E. & Greene, W. C. Duration of nuclear NF-κB action regulated by reversible acetylation. Science 293, 1653–1657 (2001). · DOI
  30. Vargas, J. N. S. et al. Spatiotemporal control of ULK1 activation by NDP52 and TBK1 during selective autophagy. Mol. Cell 74, 347–362 (2019). · DOI
  31. Narendra, D. P. et al. PINK1 is selectively stabilized on impaired mitochondria to activate Parkin. PLoS Biol. 8, e1000298 (2010). · DOI · Paper page
  32. Jordan, M. & Wurm, F. Transfection of adherent and suspended cells by calcium phosphate. Methods 33, 136–143 (2004). · DOI

Metadata

Authors
Bottone, S., Joliot, O., Cakil, Z. V., El Hajji, L., Rakotoarison, L.-M., Boncompain, G., Perez, F., & Gautier, A.
Affiliations
  • Centre National de la Recherche Scientifique (FR)
  • Université Paris Sciences et Lettres (FR)
Corresponding author
  • Perez, Franck
  • Gautier, Arnaud
Venue
Nature Methods
Published
2023-08-28
Volume
20
Issue
10
Pages
1553-1562
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
OpenAlex
W4386216012
Cited by
48
References
4
Citations by year
2026: 18 · 2025: 17 · 2024: 9 · 2023: 4
FWCI
5.95
Type
journal article
Language
en
Open access
Locations
  • Nature Methods (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by-nc-nd)
Funders
  • Agence Nationale de la Recherche (ANR-19-CE13-0026, ANR-10-IDEX-0001, ANR‐19, ANR-19-CE13-0006, ANR-10-IDEX0001-02., ANR-10-IDEX, ANR-20-CE14-0017, ANR-11-LABX-0038, 11-LBX-0038, ANR10IDEX000102 PSL, ANR-19-CE13-0002, ANR-10, IDEX-0001-02)
  • Fondation pour la Recherche Médicale (ANR-10-IDEX-0001-02 PSL, EQU201903007925)
  • Institut Universitaire de France
  • Sorbonne Université
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Biotin and Related Studies
Keywords
turn-on fluorescence, protein trafficking, organelle transport, protein localization, biosensors, signal transduction, apoptosis
MeSH terms
Fluorescent Dyes, Humans, Microscopy, Fluorescence, Proteins, Biosensing Techniques, Protein Transport, Protein Multimerization

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review