Quantification of organelle contact sites by split-GFP-based contact site sensors (SPLICS) in living cells

Tito Calì, Marisa Brini

Published: 2021-10-21 DOI: 10.1038/s41596-021-00614-1

split-GFP

SPLICS

organelle contact sites

microscopy

automated quantification

AI 解读

Supplementary information

Reporting Summary

Efficient and safe single-cell cloning of human pluripotent stem cells using the CEPT cocktail

Profiling native pulmonary basement membrane stiffness using atomic force microscopy

Genetic circuit design automation with Cello 2.0

Synthesis of siRNA nanoparticles to silence plaque-destabilizing gene in atherosclerotic lesional macrophages

Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2)

A practical guide to scanning light-field microscopy with digital adaptive optics

Effective high-throughput isolation of fully human antibodies targeting infectious pathogens

Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments

MOF-derived nanoporous carbons with diverse tunable nanoarchitectures

Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease

查看全部

Sections

Figures

References

Supplementary information

Berenguer-Escuder, C. et al. Variants in Miro1 cause alterations of ER-mitochondria contact sites in fibroblasts from Parkinson’s disease patients. J. Clin. Med. http://doi.org/10.3390/jcm8122226 (2019).
Cali, T. et al. splitGFP technology reveals dose-dependent ER-mitochondria interface modulation by α-synuclein A53T and A30P mutants. Cells 8, 1072 (2019).
Carreras-Sureda, A. et al. Non-canonical function of IRE1alpha determines mitochondria-associated endoplasmic reticulum composition to control calcium transfer and bioenergetics. Nat. Cell Biol. 21, 755–767 (2019).
Cieri, D. et al. SPLICS: a split green fluorescent protein-based contact site sensor for narrow and wide heterotypic organelle juxtaposition. Cell Death Differ. 25, 1131–1145 (2018).
Doghman-Bouguerra, M. et al. FATE1 antagonizes calcium- and drug-induced apoptosis by uncoupling ER and mitochondria. EMBO Rep. 17, 1264–1280 (2016).
Filadi, R. et al. TOM70 sustains cell bioenergetics by promoting IP3R3-mediated ER to mitochondria Ca2+ transfer. Curr. Biol. 28, 369–382 e366 (2018).
Gomez-Suaga, P. et al. The VAPB-PTPIP51 endoplasmic reticulum-mitochondria tethering proteins are present in neuronal synapses and regulate synaptic activity. Acta Neuropathol. Commun. 7, 35 (2019).
Granatiero, V. et al. Reduced mitochondrial Ca2+ transients stimulate autophagy in human fibroblasts carrying the 13514A>G mutation of the ND5 subunit of NADH dehydrogenase. Cell Death Differ. 23, 231–241 (2016).
Gutierrez, T. et al. The ER chaperone calnexin controls mitochondrial positioning and respiration. Sci. Signal. http://doi.org/10.1126/scisignal.aax6660 (2020).
Hewitt, V. L. et al. Decreasing pdzd8-mediated mitochondrial-ER contacts in neurons improves fitness by increasing mitophagy. Preprint at bioRxiv http://doi.org/10.1101/2020.11.14.382861 (2020).
Vallese, F. et al. An expanded palette of improved SPLICS reporters detects multiple organelle contacts in vitro and in vivo. Nat. Commun. 11, 6069 (2020).
Yeshaw, W. M. et al. Human VPS13A is associated with multiple organelles and influences mitochondrial morphology and lipid droplet motility. eLife 8, http://doi.org/10.7554/eLife.43561 (2019).
Cieri, D. et al. Tau localises within mitochondrial sub-compartments and its caspase cleavage affects ER-mitochondria interactions and cellular Ca2+ handling. Biochim. Biophys. Acta Mol. Basis Dis. 1864, 3247–3256 (2018).
Dematteis, G. et al. Proteomic analysis links alterations of bioenergetics, mitochondria-ER interactions and proteostasis in hippocampal astrocytes from 3xTg-AD mice. Cell Death Dis. 11, 645 (2020).
Naia, L. et al. Neuronal cell-based high-throughput screen for enhancers of mitochondrial function reveals luteolin as a modulator of mitochondria-endoplasmic reticulum coupling. BMC Biol. http://doi.org/10.1186/s12915-021-00979-5 (2021).
Ciscato, F. et al. Hexokinase 2 displacement from mitochondria-associated membranes prompts Ca2+-dependent death of cancer cells. EMBO Rep. 21, e49117 (2020).
Lopez-Crisosto, C. et al. Endoplasmic reticulum–mitochondria coupling increases during doxycycline-induced mitochondrial stress in HeLa cells. Cell Death Dis. 12, 657 (2021).
Cabantous, S., Terwilliger, T. C. & Waldo, G. S. Protein tagging and detection with engineered self-assembling fragments of green fluorescent protein. Nat. Biotechnol. 23, 102–107 (2005).
Pedelacq, J. D., Cabantous, S., Tran, T., Terwilliger, T. C. & Waldo, G. S. Engineering and characterization of a superfolder green fluorescent protein. Nat. Biotechnol. 24, 79–88 (2006).
Cabantous, S. & Waldo, G. S. In vivo and in vitro protein solubility assays using split GFP. Nat. Methods 3, 845–854 (2006).
Ryan, M. D., King, A. M. & Thomas, G. P. Cleavage of foot-and-mouth disease virus polyprotein is mediated by residues located within a 19 amino acid sequence. J. Gen. Virol. 72, 2727–2732 (1991).
Csordas, G. et al. Structural and functional features and significance of the physical linkage between ER and mitochondria. J. Cell Biol. 174, 915–921 (2006).
Giacomello, M. et al. Ca2+ hot spots on the mitochondrial surface are generated by Ca2+ mobilization from stores, but not by activation of store-operated Ca2+ channels. Mol. Cell 38, 280–290 (2010).
Gonzalo, S., Greentree, W. K. & Linder, M. E. SNAP-25 is targeted to the plasma membrane through a novel membrane-binding domain. J. Biol. Chem. 274, 21313–21318 (1999).
Macpherson, L. J. et al. Dynamic labelling of neural connections in multiple colours by trans-synaptic fluorescence complementation. Nat. Commun. 6, 10024 (2015).
Silva, B. S. C. et al. Maintaining social contacts: the physiological relevance of organelle interactions. Biochim. Biophys. Acta Mol. Cell Res. 1867, 118800 (2020).
Filadi, R. et al. Mitofusin 2 ablation increases endoplasmic reticulum-mitochondria coupling. Proc. Natl Acad. Sci. USA 112, E2174–E2181 (2015).
Rizzuto, R., Brini, M., Murgia, M. & Pozzan, T. Microdomains with high Ca2+ close to IP3-sensitive channels that are sensed by neighboring mitochondria. Science 262, 744–747 (1993).
Brunstein, M., Wicker, K., Herault, K., Heintzmann, R. & Oheim, M. Full-field dual-color 100-nm super-resolution imaging reveals organization and dynamics of mitochondrial and ER networks. Opt. Express 21, 26162–26173 (2013).
Bottanelli, F. et al. Two-colour live-cell nanoscale imaging of intracellular targets. Nat. Commun. 7, 10778 (2016).
Alford, S. C., Abdelfattah, A. S., Ding, Y. & Campbell, R. E. A fluorogenic red fluorescent protein heterodimer. Chem. Biol. 19, 353–360 (2012).
Alford, S. C., Ding, Y., Simmen, T. & Campbell, R. E. Dimerization-dependent green and yellow fluorescent proteins. ACS Synth. Biol. 1, 569–575 (2012).
Tchekanda, E., Sivanesan, D. & Michnick, S. W. An infrared reporter to detect spatiotemporal dynamics of protein-protein interactions. Nat. Methods 11, 641–644 (2014).
Csordas, G. et al. Imaging interorganelle contacts and local calcium dynamics at the ER-mitochondrial interface. Mol. Cell 39, 121–132 (2010).
Kakimoto, Y. et al. Visualizing multiple inter-organelle contact sites using the organelle-targeted split-GFP system. Sci. Rep. 8, 6175 (2018).
Copeland, D. E. & Dalton, A. J. An association between mitochondria and the endoplasmic reticulum in cells of the pseudobranch gland of a teleost. J. Biophys. Biochem. Cytol. 5, 393–396 (1959).
Bernhard, W. & Rouiller, C. Close topographical relationship between mitochondria and ergastoplasm of liver cells in a definite phase of cellular activity. J. Biophys. Biochem. Cytol. 2, 73–78 (1956).
Wieckowski, M. R., Giorgi, C., Lebiedzinska, M., Duszynski, J. & Pinton, P. Isolation of mitochondria-associated membranes and mitochondria from animal tissues and cells. Nat. Protoc. 4, 1582–1590 (2009).
Cho, I. T. et al. Ascorbate peroxidase proximity labeling coupled with biochemical fractionation identifies promoters of endoplasmic reticulum-mitochondrial contacts. J. Biol. Chem. 292, 16382–16392 (2017).
Hung, V. et al. Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation. eLife http://doi.org/10.7554/eLife.24463 (2017).
Soderberg, O. et al. Direct observation of individual endogenous protein complexes in situ by proximity ligation. Nat. Methods 3, 995–1000 (2006).
Ravikumar, B., Duden, R. & Rubinsztein, D. C. Aggregate-prone proteins with polyglutamine and polyalanine expansions are degraded by autophagy. Hum. Mol. Genet. 11, 1107–1117 (2002).
Shi, F. et al. Optogenetic control of endoplasmic reticulum-mitochondria tethering. ACS Synth. Biol. 7, 2–9 (2018).
Yang, Z., Zhao, X., Xu, J., Shang, W. & Tong, C. A novel fluorescent reporter detects plastic remodeling of mitochondria-ER contact sites. J. Cell Sci. http://doi.org/10.1242/jcs.208686 (2018).
Harmon, M., Larkman, P., Hardingham, G., Jackson, M. & Skehel, P. A bi-fluorescence complementation system to detect associations between the endoplasmic reticulum and mitochondria. Sci. Rep. 7, 17467 (2017).
Shai, N. et al. Systematic mapping of contact sites reveals tethers and a function for the peroxisome-mitochondria contact. Nat. Commun. 9, 1761 (2018).
Cali, T. & Brini, M. Quantification of organelle contact sites by split-GFP-based contact site sensors (SPLICS) in living cells. Zenodo http://doi.org/10.5281/zenodo.5031309 (2021).
Ottolini, D., Cali, T. & Brini, M. Methods to measure intracellular Ca2+ fluxes with organelle-targeted aequorin-based probes. Methods Enzymol. 543, 21–45 (2014).
Ottolini, D., Cali, T. & Brini, M. Measurements of Ca2+ concentration with recombinant targeted luminescent probes. Methods Mol. Biol. 937, 273–291 (2013).
Graham, F. L. & van der Eb, A. J. A new technique for the assay of infectivity of human adenovirus 5 DNA. Virology 52, 456–467 (1973).

Quantification of organelle contact sites by split-GFP-based contact site sensors (SPLICS) in living cells

Supplementary information

Reporting Summary

推荐阅读