Molecular recording of calcium signals via calcium-dependent proximity labeling

Bagur, R. & Hajnóczky, G. Intracellular Ca2+ sensing: its role in calcium homeostasis and signaling. Mol. Cell 66, 780–788 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Berridge, M. J. Calcium microdomains: organization and function. Cell Calcium 40, 405–412 (2006).

Article  CAS  PubMed  Google Scholar 

Augustine, G. J., Santamaria, F. & Tanaka, K. Local calcium signaling in neurons. Neuron 40, 331–346 (2003).

Article  CAS  PubMed  Google Scholar 

Greer, P. L. & Greenberg, M. E. From synapse to nucleus: calcium-dependent gene transcription in the control of synapse development and function. Neuron 59, 846–860 (2008).

Article  CAS  PubMed  Google Scholar 

Simms, B. A. & Zamponi, G. W. Neuronal voltage-gated calcium channels: structure, function, and dysfunction. Neuron 82, 24–45 (2014).

Article  CAS  PubMed  Google Scholar 

Lin, M. Z. & Schnitzer, M. J. Genetically encoded indicators of neuronal activity. Nat. Neurosci. 19, 1142–1153 (2016).

Article  PubMed  PubMed Central  Google Scholar 

Qin, W., Cho, K. F., Cavanagh, P. E. & Ting, A. Y. Deciphering molecular interactions by proximity labeling. Nat. Methods 18, 133–143 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Branon, T. C. et al. Efficient proximity labeling in living cells and organisms with TurboID. Nat. Biotechnol. 36, 880–887 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Roux, K. J., Kim, D. I., Raida, M. & Burke, B. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. J. Cell Biol. 196, 801–810 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Han, S., Li, J. & Ting, A. Y. Proximity labeling: spatially resolved proteomic mapping for neurobiology. Curr. Opin. Neurobiol. 50, 17–23 (2018).

Article  CAS  PubMed  Google Scholar 

Uezu, A. & Soderling, S. Identifying synaptic proteins by in vivo bioid from mouse brain. Methods Mol. Biol. 2008, 107–119 (2019).

Article  CAS  PubMed  Google Scholar 

Uezu, A. et al. Identification of an elaborate complex mediating postsynaptic inhibition. Science 353, 1123–1129 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen, T.-W. et al. Ultrasensitive fluorescent proteins for imaging neuronal activity. Nature 499, 295–300 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schopp, I. M. et al. Split-BioID a conditional proteomics approach to monitor the composition of spatiotemporally defined protein complexes. Nat. Commun. 8, 15690 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Munter, S. D. et al. Split-BioID: a proximity biotinylation assay for dimerization-dependent protein interactions. FEBS Lett. 591, 415–424 (2017).

Article  PubMed  Google Scholar 

Cho, K. F. et al. Split-TurboID enables contact-dependent proximity labeling in cells. Proc. Natl Acad. Sci. USA 117, 12143–12154 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kwak, C. et al. Contact-ID, a tool for profiling organelle contact sites, reveals regulatory proteins of mitochondrial-associated membrane formation. Proc. Natl Acad. Sci. USA 117, 12109–12120 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Choy, E. et al. Endomembrane trafficking of Ras the CAAX motif targets proteins to the ER and Golgi. Cell 98, 69–80 (1999).

Article  CAS  PubMed  Google Scholar 

Davidson, A. E., Gratsch, T. E., Morell, M. H., O’Shea, K. S. & Krull, C. E. Use of the Sleeping Beauty transposon system for stable gene expression in mouse embryonic stem cells. Cold Spring Harb. Protoc. 10.1101/pdb.prot5270 (2009).

Kowarz, E., Löscher, D. & Marschalek, R. Optimized Sleeping Beauty transposons rapidly generate stable transgenic cell lines. Biotechnol. J. 10, 647–653 (2015).

Article  CAS  PubMed  Google Scholar 

Helassa, N., Nugues, C., Rajamanoharan, D., Burgoyne, R. D. & Haynes, L. P. A centrosome-localized calcium signal is essential for mammalian cell mitosis. FASEB J. 33, 14602–14610 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Whitaker, M. Calcium microdomains and cell cycle control. Cell Calcium 40, 585–592 (2006).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Groigno, L. & Whitaker, M. An anaphase calcium signal controls chromosome disjunction in early sea urchin embryos. Cell 92, 193–204 (1998).

Article  CAS  PubMed  Google Scholar 

Lagos-Cabré, R., Ivanova, A. & Taylor, C. W. Ca2+ release by IP3 receptors is required to orient the mitotic spindle. Cell Rep. 33, 108483 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Fazal, F. M. et al. Atlas of subcellular RNA localization revealed by APEX-seq. Cell 178, 473–490.e26 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Padrón, A., Iwasaki, S. & Ingolia, N. T. Proximity RNA labeling by APEX-Seq reveals the organization of translation initiation complexes and repressive RNA granules. Mol. Cell 75, 875–887.e5 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Qin, W., Myers, S. A., Carey, D. K., Carr, S. A. & Ting, A. Y. Spatiotemporally-resolved mapping of RNA binding proteins via functional proximity labeling reveals a mitochondrial mRNA anchor promoting stress recovery. Nat. Commun. 12, 4980 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhong, X., Liu, L., Zhao, A., Pfeifer, G. P. & Xu, X. The abnormal spindle-like, microcephaly-associated (ASPM) gene encodes a centrosomal protein. Cell Cycle Georget. Tex. 4, 1227–1229 (2005).

Article  CAS  Google Scholar 

Hart, M. J., Callow, M. G., Souza, B. & Polakis, P. IQGAP1, a calmodulin-binding protein with a rasGAP-related domain, is a potential effector for cdc42Hs. EMBO J. 15, 2997–3005 (1996).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mammucari, C., Gherardi, G. & Rizzuto, R. Structure, activity regulation, and role of the mitochondrial calcium uniporter in health and disease. Front. Oncol. 7, 139 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Zhang, X. et al. The mouse FKBP23 binds to BiP in ER and the binding of C‐terminal domain is interrelated with Ca2+ concentration. FEBS Lett. 559, 57–60 (2004).

Article  CAS  PubMed  Google Scholar 

Oeffinger, M., Fatica, A., Rout, M. P. & Tollervey, D. Yeast Rrp14p is required for ribosomal subunit synthesis and for correct positioning of the mitotic spindle during mitosis. Nucleic Acids Res. 35, 1354–1366 (2007).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zheng, Q. et al. Calcium transients on the ER surface trigger liquid-liquid phase separation of FIP200 to specify autophagosome initiation sites. Cell 185, 4082–4098.e22 (2022).

Article  CAS  PubMed  Google Scholar 

Chen, F., Tillberg, P. W. & Boyden, E. S. Expansion microscopy. Science 347, 543–548 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tillberg, P. W. et al. Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies. Nat. Biotechnol. 34, 987–992 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gao, R. et al. Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution. Science 363, eaau8302 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bootman, M. D. & Bultynck, G. Fundamentals of cellular calcium signaling: a primer. Cold Spring Harb. Perspect. Biol. 12, a038802 (2020).

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