Fluorescent and Bioluminescent Calcium Indicators with Tuneable Colors and Affinities

We introduce a family of bright, rhodamine-based calcium indicators with tuneable affinities and colors. The indicators can be specifically localized to different cellular compartments and are compatible with both fluorescence and bioluminescence readouts through conjugation to HaloTag fusion proteins. Importantly, their increase in fluorescence upon localization enables no-wash live-cell imaging, which greatly facilitates their use in biological assays. Applications as fluorescent indicators in rat hippocampal neurons include the detection of single action potentials and of calcium fluxes in the endoplasmic reticulum (ER). Applications as bioluminescent indicators include the recording of the pharmacological modulation of nuclear calcium in high-throughput-compatible assays. The versatility and remarkable ease of use of these indicators make them powerful tools for bioimaging and bioassays. Graphical abstract

[1]  J. Ries,et al.  Systematic Tuning of Rhodamine Spirocyclization for Super-Resolution Microscopy , 2021, bioRxiv.

[2]  J. Reinstein,et al.  Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag , 2021, bioRxiv.

[3]  E. Schreiter,et al.  The HaloTag as a general scaffold for far-red tunable chemigenetic indicators , 2021, Nature Chemical Biology.

[4]  E. Schreiter,et al.  Far-red fluorescent genetically encoded calcium ion indicators , 2020, bioRxiv.

[5]  K. Johnsson,et al.  Environmentally Sensitive Color‐Shifting Fluorophores for Bioimaging , 2020, Angewandte Chemie.

[6]  Luke D. Lavis,et al.  Isomeric tuning yields bright and targetable red Ca2+ indicators. , 2019, Journal of the American Chemical Society.

[7]  B. Koch,et al.  A general strategy to develop cell permeable and fluorogenic probes for multicolour nanoscopy , 2019, bioRxiv.

[8]  Takeharu Nagai,et al.  Genetically Encoded Fluorescence/Bioluminescence Bimodal Indicators for Ca2+ Imaging. , 2019, ACS sensors.

[9]  Michael Z. Lin,et al.  An orange calcium-modulated bioluminescent indicator for non-invasive activity imaging , 2019, Nature Chemical Biology.

[10]  Stephan Uphoff,et al.  Choosing the right label for single-molecule tracking in live bacteria: side-by-side comparison of photoactivatable fluorescent protein and Halo tag dyes , 2018, bioRxiv.

[11]  Robert E Campbell,et al.  A Bioluminescent Ca2+ Indicator Based on a Topological Variant of GCaMP6s , 2018, Chembiochem : a European journal of chemical biology.

[12]  Luke D Lavis,et al.  Synthetic and genetically encoded fluorescent neural activity indicators , 2018, Current Opinion in Neurobiology.

[13]  Takeharu Nagai,et al.  Bioluminescent Low-Affinity Ca2+ Indicator for ER with Multicolor Calcium Imaging in Single Living Cells. , 2018, ACS chemical biology.

[14]  L. Reymond,et al.  Luciferases with Tunable Emission Wavelengths. , 2017, Angewandte Chemie.

[15]  L. Lavis Chemistry Is Dead. Long Live Chemistry! , 2017, Biochemistry.

[16]  Donna Webb,et al.  Coupling optogenetic stimulation with NanoLuc-based luminescence (BRET) Ca++ sensing , 2016, Nature Communications.

[17]  D. Herten,et al.  Protein-specific localization of a rhodamine-based calcium-sensor in living cells. , 2016, Organic & biomolecular chemistry.

[18]  Ian Parker,et al.  A comparison of fluorescent Ca²⁺ indicators for imaging local Ca²⁺ signals in cultured cells. , 2015, Cell calcium.

[19]  E. Schreiter,et al.  A Low Affinity GCaMP3 Variant (GCaMPer) for Imaging the Endoplasmic Reticulum Calcium Store , 2015, PloS one.

[20]  Y. Kudo,et al.  High Cell Density Upregulates Calcium Oscillation by Increasing Calcium Store Content via Basal Mitogen-Activated Protein Kinase Activity , 2015, PloS one.

[21]  Mayeul Collot,et al.  New red-fluorescent calcium indicators for optogenetics, photoactivation and multi-color imaging. , 2014, Biochimica et biophysica acta.

[22]  S. Hell,et al.  Fluorogenic probes for live-cell imaging of the cytoskeleton , 2014, Nature Methods.

[23]  Amy E. Palmer,et al.  Fluorescent Sensors for Measuring Metal Ions in Living Systems , 2014, Chemical reviews.

[24]  Vivek Jayaraman,et al.  A Neuron-Based Screening Platform for Optimizing Genetically-Encoded Calcium Indicators , 2013, PloS one.

[25]  Stefan R. Pulver,et al.  Ultra-sensitive fluorescent proteins for imaging neuronal activity , 2013, Nature.

[26]  R. Blum,et al.  Direct imaging of ER calcium with targeted-esterase induced dye loading (TED). , 2013, Journal of visualized experiments : JoVE.

[27]  Suliana Manley,et al.  A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins. , 2013, Nature chemistry.

[28]  A. Cardona,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[29]  Kai Johnsson,et al.  Localizable and highly sensitive calcium indicator based on a BODIPY fluorophore. , 2010, Analytical chemistry.

[30]  K. Johnsson,et al.  Indo-1 derivatives for local calcium sensing. , 2009, ACS chemical biology.

[31]  Wei Zheng,et al.  Chemical calcium indicators. , 2008, Methods.

[32]  Amy E Palmer,et al.  Measuring calcium dynamics in living cells with genetically encodable calcium indicators. , 2008, Methods.

[33]  Marjeta Urh,et al.  HaloTag: a novel protein labeling technology for cell imaging and protein analysis. , 2008, ACS chemical biology.

[34]  Dylan W Domaille,et al.  Synthetic fluorescent sensors for studying the cell biology of metals. , 2008, Nature chemical biology.

[35]  D. Clapham,et al.  Calcium Signaling , 2007, Cell.

[36]  Terrence J Sejnowski,et al.  Calcium Green FlAsH as a genetically targeted small-molecule calcium indicator. , 2007, Nature chemical biology.

[37]  S. Kaech,et al.  Culturing hippocampal neurons , 2006, Nature Protocols.

[38]  Thomas D. Y. Chung,et al.  A Simple Statistical Parameter for Use in Evaluation and Validation of High Throughput Screening Assays , 1999, Journal of biomolecular screening.

[39]  R. Tsien,et al.  A new generation of Ca2+ indicators with greatly improved fluorescence properties. , 1985, The Journal of biological chemistry.

[40]  R. Tsien A non-disruptive technique for loading calcium buffers and indicators into cells , 1981, Nature.

[41]  M. Bootman Calcium Signaling , 2012, Advances in Experimental Medicine and Biology.

[42]  Alexei Verkhratsky,et al.  Physiology and pathophysiology of the calcium store in the endoplasmic reticulum of neurons. , 2005, Physiological reviews.

[43]  Andreas Beck,et al.  Calcium release from intracellular stores in rodent astrocytes and neurons in situ. , 2004, Cell calcium.

[44]  H. Vogel,et al.  A general method for the covalent labeling of fusion proteins with small molecules in vivo , 2003, Nature Biotechnology.

[45]  Juan C. Scaiano,et al.  Modern Molecular Photochemistry of Organic Molecules , 1978 .